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

Abstract

AbstractOveruse 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, chlORLMS, chlORQY071 and chlORL‐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 ChlORLMS, ChlORQY071 and ChlORL‐11A were all classified as cellobiose dehydrogenases from the glucose methanol choline (GMC) family. Based on the Swiss‐Prot database, ChlORQY071 exhibited a lower identity (27.12%–35.10% similarity) with the reported oxidoreductases. Enzymatic and molecular docking analyses showed that ChlORQY071 and ChlORL‐11A from the two similar genomes were remarkably more effective in metabolizing CHL than ChlORLMS. 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.