Regulation of plasmid‐encoded isoprene metabolism in <scp><i>R</i></scp><i>hodococcus</i>, a representative of an important link in the global isoprene cycle

<jats:title>Summary</jats:title><jats:p>Emissions of biogenic volatile organic compounds (<jats:styled-content style="fixed-case">VOCs</jats:styled-content>) form an important part of the global carbon cycle, comprising a significant proportion of net ecosystem productivity. They impact atmospheric chemistry and contribute directly and indirectly to greenhouse gases. Isoprene, emitted largely from plants, comprises one third of total <jats:styled-content style="fixed-case">VOCs</jats:styled-content>, yet in contrast to methane, which is released in similar quantities, we know little of its biodegradation. Here, we report the genome of an isoprene degrading isolate, <jats:styled-content style="fixed-case"><jats:italic>R</jats:italic></jats:styled-content><jats:italic>hodococcus</jats:italic> sp. <jats:styled-content style="fixed-case">AD</jats:styled-content>45, and, using mutagenesis shows that a plasmid‐encoded soluble di‐iron centre isoprene monooxygenase (<jats:styled-content style="fixed-case">IsoMO</jats:styled-content>) is essential for isoprene metabolism. Using <jats:styled-content style="fixed-case">RNA</jats:styled-content> sequencing (<jats:styled-content style="fixed-case">RNAseq</jats:styled-content>) to analyse cells exposed to isoprene or epoxyisoprene in a substrate‐switch time‐course experiment, we show that transcripts from 22 contiguous genes, including those encoding <jats:styled-content style="fixed-case">IsoMO</jats:styled-content>, were highly upregulated, becoming among the most abundant in the cell and comprising over 25% of the entire transcriptome. Analysis of gene transcription in the wild type and an <jats:styled-content style="fixed-case">IsoMO</jats:styled-content>‐disrupted mutant strain showed that epoxyisoprene, or a subsequent product of isoprene metabolism, rather than isoprene itself, was the inducing molecule. We provide a foundation of molecular data for future research on the environmental biological consumption of this important, climate‐active compound.</jats:p>