Transcriptomic analysis of the highly efficient oil-degrading bacterium Acinetobacter venetianus RAG-1 reveals genes important in dodecane uptake and utilization.
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.
Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8099, USA.
Ankita
A
Kothari
Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8099, USA.
Marimikel
M
Charrier
Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8099, USA.|Graduate Institute of Biomedical Informatics, Taipei Medical University, Taipei 110, Taiwan Biosciences.
Yu-Wei
YW
Wu
Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550-5507, USA.
Stephanie
S
Malfatti
Computing Applications and Research Department, Lawrence Livermore National Laboratory, Livermore, CA 94550-9234, USA.
Carol E
CE
Zhou
Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8099, USA.
Steven W
SW
Singer
Graduate Institute of Biomedical Informatics, Taipei Medical University, Taipei 110, Taiwan Biosciences.|Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550-5507, USA.
Larry
L
Dugan
Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8099, USA amukhopadhyay@lbl.gov.
Aindrila
A
Mukhopadhyay
D000085:Acetates / Q000378:metabolism; D000150:Acinetobacter / Q000235:genetics* / Q000378:metabolism*; D000473:Alkanes / Q000378:metabolism*; D001673:Biodegradation, Environmental; D001692:Biological Transport / Q000235:genetics*; D004269:DNA, Bacterial / Q000235:genetics; D007851:Dodecanol / Q000378:metabolism*; D010861:Fimbriae, Bacterial / Q000235:genetics*; D020869:Gene Expression Profiling; D026901:Membrane Transport Proteins / Q000235:genetics*; D059392:Petroleum Pollution; D017422:Sequence Analysis, DNA
D000085:Acetates; D000473:Alkanes; D004269:DNA, Bacterial; D026901:Membrane Transport Proteins; C007548:n-dodecane; D007851:Dodecanol
Acinetobacter venetianus RAG-1 ATCC 31012; alkane hydroxylase; alkane monooxygenase; alkane uptake; dodecane; transcriptomic
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