Transcriptomic analysis of the highly efficient oil-degrading bacterium Acinetobacter venetianus RAG-1 reveals genes important in dodecane uptake and utilization

Abstract

The hydrocarbonoclastic bacterium Acinetobacter venetianus RAG-1 has attracted substantial attention due to its powerful oil-degrading capabilities and its potential to play an important ecological role in the cleanup of alkanes. In this study, we compare the transcriptome of the strain RAG-1 grown in dodecane, the corresponding alkanol (dodecanol), and sodium acetate for the characterization of genes involved in dodecane uptake and utilization. Comparison of the transcriptional responses of RAG-1 grown on dodecane led to the identification of 1074 genes that were differentially expressed relative to sodium acetate. Of these, 622 genes were upregulated when grown in dodecane. The highly upregulated genes were involved in alkane catabolism, along with stress response. Our data suggest AlkMb to be primarily involved in dodecane oxidation. Transcriptional response of RAG-1 grown on dodecane relative to dodecanol also led to the identification of permease, outer membrane protein and thin fimbriae coding genes potentially involved in dodecane uptake. This study provides the first model for key genes involved in alkane uptake and metabolism in A. venetianus RAG-1.

Keywords: Acinetobacter venetianus RAG-1 ATCC 31012; alkane hydroxylase; alkane monooxygenase; alkane uptake; dodecane; transcriptomic.

Figure 1.

(a) Genetic organization of genes involved in alkane metabolism. Genes depicted—ygiY: acyl carrier protein UDP-M acetyl glucosamine O acyl trasferase, alkRa: regulator for alkMa, alkMa: alkane monooxygenase, gshR: glutathionine reductase, Hyp1: hypothetical protein-coding gene 1, alkG: rubredoxin, alkT: rubredoxin reductase, estB: esterase, oxyR: LysR-type transcriptional regulator, mdmC: O methyl transferase, alkRb: regulator for alkMb, alkMb: alkane monooxygenase, Hyp2: hypothetical protein-coding gene 2, aphC: alkyl hydroperoxide reductase protein, alkJ: alcohol dehydrogenase, acoR: transcriptional activator of acetoin/glycerol metabolism, alkH: aldehyde dehydrogenase and Hyp3: hypothetical protein-coding gene 3. Volcano plots reporting FDR (−log₁₀FDR) on y-axis as a function of log2 fold change on x-axis for (b) sodium acetate vs. dodecane (c) sodium acetate vs. dodecanol and (d) dodecane vs. dodecanol. Genes involved in alkane catabolism are highlighted with the color scheme in Fig. 1a.

Figure 2.

Schematic representation of the transcriptional response to dodecane and dodecanol relative to sodium acetate in A. venetianus RAG-1. Yellow represents genes upregulated when grown in dodecane relative to dodecanol and sodium acetate, green represents genes upregulated when grown in dodecane and dodecanol relative to sodium acetate and blue represents genes upregulated when grown in dodecanol relative to dodecane and sodium acetate. The proteins depicted are alkane hydroxylase (AlkM), rubredoxin (AlkG), rubredoxin reductase (AlkT), aldehyde dehydrogenase (AlkH), alcohol dehydrogenase (AlkJ), acyl coenzyme A synthetase (AlkK) and an outer membrane protein putatively involved in alkane transport (AlkL). Sizes are not to scale. Red asterisks refer to the prediction of protein localization not being experimentally confirmed (prediction is based on sequence data).