title: Transcriptional response of Desulfatibacillum alkenivorans AK-01 to growth on alkanes: insights from RT-qPCR and microarray analyses.
abstract: 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 (C13 to C18) 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.
authors.affiliation: Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA.
authors.forename: Anjumala
authors.initials: A
authors.lastname: Herath
authors.affiliation: Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA.
authors.forename: Boris
authors.initials: B
authors.lastname: Wawrik
authors.affiliation: Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA Institute of Environmental Genomics, Stephenson Research Center, 101 David L. Boren Blvd, Norman, OK 73019, USA.
authors.forename: Yujia
authors.initials: Y
authors.lastname: Qin
authors.affiliation: Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA Institute of Environmental Genomics, Stephenson Research Center, 101 David L. Boren Blvd, Norman, OK 73019, USA Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94270, USA State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
authors.forename: Jizhong
authors.initials: J
authors.lastname: Zhou
authors.affiliation: Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA acallaghan@ou.edu.
authors.forename: Amy V
authors.initials: AV
authors.lastname: Callaghan
mesh_terms: D000473:Alkanes / Q000378:metabolism*; D001673:Biodegradation, Environmental; D020564:Deltaproteobacteria / Q000145:classification / Q000201:enzymology* / Q000235:genetics* / Q000378:metabolism; D004785:Environmental Pollutants / Q000378:metabolism*; D005227:Fatty Acids / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D019308:Palmitic Acid / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction; D014158:Transcription, Genetic; D015854:Up-Regulation
chemical_list: D000473:Alkanes; D004785:Environmental Pollutants; D005227:Fatty Acids; D019308:Palmitic Acid; C007932:n-hexadecane
keywords: alkane; alkylsuccinate synthase; anaerobic; microarray; transcription