Integrated transcriptomic and proteomic analysis of nicotine metabolism in Paenarthrobacter nicotinovorans ATCC 49919

The global tobacco industry produces significant amounts of nicotine-containing wastes, being regarded as a major environmental threat. The appropriate treatment of nicotine-contaminated waste is required for the removal of the toxic alkaloid before safe disposal. In this context, nicotine-degrading microorganisms and their enzymatic apparatus are of major interest for decontaminating and repurposing nicotine waste. Here, by combining long-read direct RNA sequencing data and nanoLC-MS/MS based proteomics data, we focused on the multiomic characterisation of the bacterial nicotine catabolic process from Paenarthrobacter nicotinovorans ATCC 49919. The nicotine-related expression of 25 annotated nic -genes and proteins was confirmed, eight of these genes ( JMY29_20530 , JMY29_20550 , perm , coxF , coxE , JMY29_20640 , JMY29_20655 , modB ) being reported here first as having nicotine-related expression. Insights regarding the active mechanisms involved in integrating the nicotine catabolic pathway with the general metabolism of the bacterial cell and the defence systems employed against the oxidative stress generated during nicotine degradation are also presented. This study provides the first multiomic investigation of P. nicotinovorans ATCC 49919 and, moreover, the first multiomic assessment of a bacterial nicotine catabolic pathway. • Direct RNA-seq of a bacterial transcriptome was performed on a MinION/Flongle device. • Bacterial transcriptomic and proteomic data was integrated. • The first multiomic study of a nicotine-degrading bacterium.