Genome mining-guided activation of two silenced tandem genes in Raoultella ornithinolytica XF201 for complete biodegradation of phthalate acid esters

Phthalates (PAEs) are ubiquitous in soils and food products and thus pose a high risk to human health. Herein, genome mining revealed a great diversity of bacteria with PAEs-degrading potential. Mining of the genome of Raoultella ornithinolytica XF201, a novel strain isolated from Dongxiang wild rice rhizosphere, revealed the presence of two si-lenced tandem genes pcdGH (encoding protocatechuate 3,4-dioxygenase, 3,4-PCD), key aromatic ring-cleaving genes in PAEs biodegradation. Ribosome engineering was successfully utilized to activate the expression of pcdGH genes to produce 3,4-PCD in the mutant XF201-G2U5. The mutant XF201-G2U5 showed high 3,4-PCD activity and could remove 94.5 % of di-n butyl phthalate (DBP) in 72 h. The degradation kinetics obeyed the first-order kinetic model. Strain XF201-G2U5 could also degrade the other PAEs and the main intermediate metabolites, ultimately lead-ing to tricarboxylic acid cycle. Therefore, this strategy facilitates novel bacterial resources discovery for bioremedia-tion of PAEs and other emerging contaminants.

Automated summary

Genome mining identified bacteria with potential to degrade phthalates (PAEs), which are widely present in soils and food products and pose a high risk to human health. Ribosome engineering was used to activate the expression of key genes involved in PAEs biodegradation, resulting in a mutant strain XF201-G2U5 that showed high activity in degrading di-n butyl phthalate (DBP) and other PAEs. This strategy enables the discovery of novel bacterial resources for the bioremediation of PAEs and other emerging contaminants.