ChlOR, a GMC family oxidoreductase that evolved independently from the actinomycete, confers resistance to amphenicol antibiotics

Abstract

Overuse of the amphenicol antibiotics chloramphenicol (CHL) and thiamphenicol (TAP) poses a great threat to ecosystem safety and human health. The strain, Nocardioides sp. LMS‐CY, Nocardioides sp. QY071 and Nocardioides sp. L‐11A, classified as a gram‐positive actinomycete, harbours a complete CHL metabolic pathway. However, the metabolic genes (clusters) involved in the entire pathway in gram‐positive actinomycetes are still limited. Here, chlOR_LMS, chlOR_QY071 and chlOR_L‐11A completely from the actinomycete Nocardioides spp. were found to act on the C₁‐OH of the CHL/TAP side chain, directly converting CHL/TAP to 4‐nitrobenzaldehyde (PNBD)/4‐methylsulfonyl benzaldehyde (PMBD) and transforming PNBD/PMBD into 4‐nitrobenzyl alcohol (PNBM)/4‐methylsulfonyl phenyl methanol (PMBM). Furthermore, oxidoreductases can transform PNBM into 4‐nitrobenzoate (PNBA). The oxidoreductases ChlOR_LMS, ChlOR_QY071 and ChlOR_L‐11A were all classified as cellobiose dehydrogenases from the glucose methanol choline (GMC) family. Based on the Swiss‐Prot database, ChlOR_QY071 exhibited a lower identity (27.12%–35.10% similarity) with the reported oxidoreductases. Enzymatic and molecular docking analyses showed that ChlOR_QY071 and ChlOR_L‐11A from the two similar genomes were remarkably more effective in metabolizing CHL than ChlOR_LMS. Overall, the detailed resistance mechanism of CHL/TAP by actinomycete strains isolated from soil and livestock manure will provide insights into the occurrence of CHL/TAP resistance genes in the environment, resistance risk and bioremediation of CHL/TAP‐contaminated environments.