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Title: Transcriptomic analysis of the highly efficient oil-degrading bacterium Acinetobacter venetianus RAG-1 reveals genes important in dodecane uptake and utilization [Transcriptomic analysis of the marine 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. As a result, this study provides the first model for key genes involved in alkane uptake and metabolism in A. venetianus RAG-1.

Authors:
 [1];  [1];  [2];  [3];  [3];  [1];  [4];  [1]
  1. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  2. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Taipei Medical Univ., Taipei (Taiwan)
  3. Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
  4. Taipei Medical Univ., Taipei (Taiwan); Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
Publication Date:
Research Org.:
Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1351143
Report Number(s):
LLNL-JRNL-685684
Journal ID: ISSN 0378-1097
Grant/Contract Number:
AC52-07NA27344; AC02-05CH11231
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
FEMS Microbiology Letters
Additional Journal Information:
Journal Volume: 363; Journal Issue: 20; Journal ID: ISSN 0378-1097
Publisher:
Federation of European Microbiological Societies
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; alkane hydroxylase; alkane monooxygenase; dodecane; alkane uptake; transcriptomic; Acinetobacter venetianus RAG-1 ATCC 31012

Citation Formats

Kothari, Ankita, Charrier, Marimikel, Wu, Yu -Wei, Malfatti, Stephanie, Zhou, Carol E., Singer, Steven W., Dugan, Larry, and Mukhopadhyay, Aindrila. Transcriptomic analysis of the highly efficient oil-degrading bacterium Acinetobacter venetianus RAG-1 reveals genes important in dodecane uptake and utilization [Transcriptomic analysis of the marine oil-degrading bacterium Acinetobacter venetianus RAG-1 reveals genes important in dodecane uptake and utilization]. United States: N. p., 2016. Web. doi:10.1093/femsle/fnw224.
Kothari, Ankita, Charrier, Marimikel, Wu, Yu -Wei, Malfatti, Stephanie, Zhou, Carol E., Singer, Steven W., Dugan, Larry, & Mukhopadhyay, Aindrila. Transcriptomic analysis of the highly efficient oil-degrading bacterium Acinetobacter venetianus RAG-1 reveals genes important in dodecane uptake and utilization [Transcriptomic analysis of the marine oil-degrading bacterium Acinetobacter venetianus RAG-1 reveals genes important in dodecane uptake and utilization]. United States. doi:10.1093/femsle/fnw224.
Kothari, Ankita, Charrier, Marimikel, Wu, Yu -Wei, Malfatti, Stephanie, Zhou, Carol E., Singer, Steven W., Dugan, Larry, and Mukhopadhyay, Aindrila. 2016. "Transcriptomic analysis of the highly efficient oil-degrading bacterium Acinetobacter venetianus RAG-1 reveals genes important in dodecane uptake and utilization [Transcriptomic analysis of the marine oil-degrading bacterium Acinetobacter venetianus RAG-1 reveals genes important in dodecane uptake and utilization]". United States. doi:10.1093/femsle/fnw224. https://www.osti.gov/servlets/purl/1351143.
@article{osti_1351143,
title = {Transcriptomic analysis of the highly efficient oil-degrading bacterium Acinetobacter venetianus RAG-1 reveals genes important in dodecane uptake and utilization [Transcriptomic analysis of the marine oil-degrading bacterium Acinetobacter venetianus RAG-1 reveals genes important in dodecane uptake and utilization]},
author = {Kothari, Ankita and Charrier, Marimikel and Wu, Yu -Wei and Malfatti, Stephanie and Zhou, Carol E. and Singer, Steven W. and Dugan, Larry and Mukhopadhyay, Aindrila},
abstractNote = {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. As a result, this study provides the first model for key genes involved in alkane uptake and metabolism in A. venetianus RAG-1.},
doi = {10.1093/femsle/fnw224},
journal = {FEMS Microbiology Letters},
number = 20,
volume = 363,
place = {United States},
year = 2016,
month = 9
}

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