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Title: A comprehensive multi-omics approach uncovers adaptations for growth and survival of Pseudomonas aeruginosa on n-alkanes

Examination of complex biological systems has long been achieved through methodical investigation of the system’s individual components. While informative, this strategy often leads to inappropriate conclusions about the system as a whole. With the advent of high-throughput “omic” technologies, but, researchers can now simultaneously analyze an entire system at the level of molecule (DNA, RNA, protein, metabolite) and process (transcription, translation, enzyme catalysis). This strategy reduces the likelihood of improper conclusions, provides a framework for elucidation of genotype-phenotype relationships, and brings finer resolution to comparative genomic experiments. Here in this paper, we apply a multi-omic approach to analyze the gene expression profiles of two closely related Pseudomonas aeruginosa strains grown in n-alkanes or glycerol. The environmental P. aeruginosa isolate ATCC 33988 consumed medium-length (C 10–C 16) n-alkanes more rapidly than the laboratory strain PAO1, despite high genome sequence identity (average nucleotide identity >99%). Our data shows that ATCC 33988 induces a characteristic set of genes at the transcriptional, translational and post-translational levels during growth on alkanes, many of which differ from those expressed by PAO1. Of particular interest was the lack of expression from the rhl operon of the quorum sensing (QS) system, resulting in no measurable rhamnolipid production bymore » ATCC 33988. Further examination showed that ATCC 33988 lacked the entire lasI/lasR arm of the QS response. Instead of promoting expression of QS genes, ATCC 33988 up-regulates a small subset of its genome, including operons responsible for specific alkaline proteases and sphingosine metabolism. Our work represents the first time results from RNA-seq, microarray, ribosome footprinting, proteomics, and small molecule LC-MS experiments have been integrated to compare gene expression in bacteria. Altogether, these data provide insights as to why strain ATCC 33988 is better adapted for growth and survival on n-alkanes.« less
Authors:
 [1] ;  [1] ;  [2] ;  [3] ;  [1] ;  [2] ;  [4] ;  [5] ;  [6] ;  [1]
  1. Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Biosciences and Biotechnology Division
  2. Univ. of Dayton, OH (United States). Univ. of Dayton Research Inst.
  3. Univ. of Utah School of Medicine, Salt Lake City, UT (United States). Huntsman Cancer Inst.
  4. Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Computational Engineering Division
  5. Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Computing Applications and Research Dept., Global Security Computing and Applications Division
  6. Air Force Research Lab. (AFRL), Wright-Patterson AFB, OH (United States). Fuels and Energy Branch
Publication Date:
Grant/Contract Number:
AC52-07NA27344; FA8650-10-2-2934
Type:
Accepted Manuscript
Journal Name:
BMC Genomics
Additional Journal Information:
Journal Volume: 18; Journal Issue: 1; Journal ID: ISSN 1471-2164
Publisher:
Springer
Research Org:
Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
Sponsoring Org:
USDOE
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Pseudomonas aeruginosa; Multi-omics; Ribosome footprinting; Quorum sensing; Alkane degradation
OSTI Identifier:
1395307