Transcriptional response of Desulfatibacillum alkenivorans AK-01 to growth on alkanes: insights from RT-qPCR and microarray analyses

Microbial transformation of n-alkanes in anaerobic ecosystems plays a pivotal role in biogeochemical carbon cycling and bioremediation, but the requisite genetic machinery is not well elucidated. Desulfatibacillum alkenivorans AK-01 utilizes n-alkanes (C-13 to C-18) and contains two genomic loci encoding alkylsuccinate synthase (ASS) gene clusters. ASS catalyzes alkane addition to fumarate to form methylalkylsuccinic acids. We hypothesized that the genes in the two clusters would be differentially expressed depending on the alkane substrate utilized for growth. RT-qPCR was used to investigate ass-gene expression across AK-01's known substrate range, and microarray-based transcriptomic analysis served to investigate whole-cell responses to growth on n-hexadecane versus hexadecanoate. RT-qPCR revealed induction of ass gene cluster 1 during growth on all tested alkane substrates, and the transcriptional start sites in cluster 1 were determined via 5'RACE. Induction of ass gene cluster 2 was not observed under the tested conditions. Transcriptomic analysis indicated that the upregulation of genes potentially involved in methylalkylsuccinate metabolism, including methylmalonyl-CoA mutase and a putative carboxyl transferase. These findings provide new directions for studying the transcriptional regulation of genes involved in alkane addition to fumarate, fumarate recycling and the processing of methylalkylsuccinates with regard to isolates, enrichment cultures and ecological datasets.