Regulation of plasmid-encoded isoprene metabolism in Rhodococcus, a representative of an important link in the global isoprene cycle.
Emissions of biogenic volatile organic compounds (VOCs) 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 VOCs, 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, Rhodococcus sp. AD45, and, using mutagenesis shows that a plasmid-encoded soluble di-iron centre isoprene monooxygenase (IsoMO) is essential for isoprene metabolism. Using RNA sequencing (RNAseq) 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 IsoMO, 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 IsoMO-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.
University of East Anglia, Norwich Research Park, Norwich, UK.
Andrew T
AT
Crombie
University of East Anglia, Norwich Research Park, Norwich, UK.
Myriam El
ME
Khawand
DuPont Industrial Biosciences, 925 Page Mill Road, Palo Alto, CA, 94304, USA.
Virgil A
VA
Rhodius
DuPont Pioneer, 7200 NW 62nd Avenue, Johnston, IA, 50131, USA.
Kevin A
KA
Fengler
DuPont Industrial Biosciences, 925 Page Mill Road, Palo Alto, CA, 94304, USA.
Michael C
MC
Miller
DuPont Industrial Biosciences, 925 Page Mill Road, Palo Alto, CA, 94304, USA.
Gregg M
GM
Whited
University of Essex, Wivenhoe Park, Colchester, UK.
Terry J
TJ
McGenity
University of East Anglia, Norwich Research Park, Norwich, UK.
J Colin
JC
Murrell
D001483:Base Sequence; D002070:Butadienes / Q000378:metabolism*; D057486:Carbon Cycle / Q000502:physiology*; D002980:Climate; D017753:Ecosystem; D020869:Gene Expression Profiling; D016680:Genome, Bacterial; D045782:Hemiterpenes / Q000378:metabolism*; D008969:Molecular Sequence Data; D010420:Pentanes / Q000378:metabolism*; D010944:Plants / Q000378:metabolism; D010957:Plasmids / Q000235:genetics; D012329:RNA, Bacterial / Q000235:genetics; D012240:Rhodococcus / Q000235:genetics / Q000378:metabolism*; D017423:Sequence Analysis, RNA; D055549:Volatile Organic Compounds / Q000378:metabolism*
D002070:Butadienes; D045782:Hemiterpenes; D010420:Pentanes; D012329:RNA, Bacterial; D055549:Volatile Organic Compounds; C005059:isoprene