skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

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

Authors:
; ; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1400075
Report Number(s):
LLNL-JRNL-729344
Journal ID: ISSN 1471-2164
DOE Contract Number:  
AC52-07NA27344
Resource Type:
Journal Article
Journal Name:
BMC Genomics
Additional Journal Information:
Journal Volume: 18; Journal Issue: 1; Journal ID: ISSN 1471-2164
Publisher:
Springer
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Grady, Sarah L., Malfatti, Stephanie A., Gunasekera, Thusitha S., Dalley, Brian K., Lyman, Matt G., Striebich, Richard C., Mayhew, Michael B., Zhou, Carol L., Ruiz, Oscar N., and Dugan, Larry C. A comprehensive multi-omics approach uncovers adaptations for growth and survival of Pseudomonas aeruginosa on n-alkanes. United States: N. p., 2017. Web. doi:10.1186/s12864-017-3708-4.
Grady, Sarah L., Malfatti, Stephanie A., Gunasekera, Thusitha S., Dalley, Brian K., Lyman, Matt G., Striebich, Richard C., Mayhew, Michael B., Zhou, Carol L., Ruiz, Oscar N., & Dugan, Larry C. A comprehensive multi-omics approach uncovers adaptations for growth and survival of Pseudomonas aeruginosa on n-alkanes. United States. doi:10.1186/s12864-017-3708-4.
Grady, Sarah L., Malfatti, Stephanie A., Gunasekera, Thusitha S., Dalley, Brian K., Lyman, Matt G., Striebich, Richard C., Mayhew, Michael B., Zhou, Carol L., Ruiz, Oscar N., and Dugan, Larry C. Fri . "A comprehensive multi-omics approach uncovers adaptations for growth and survival of Pseudomonas aeruginosa on n-alkanes". United States. doi:10.1186/s12864-017-3708-4. https://www.osti.gov/servlets/purl/1400075.
@article{osti_1400075,
title = {A comprehensive multi-omics approach uncovers adaptations for growth and survival of Pseudomonas aeruginosa on n-alkanes},
author = {Grady, Sarah L. and Malfatti, Stephanie A. and Gunasekera, Thusitha S. and Dalley, Brian K. and Lyman, Matt G. and Striebich, Richard C. and Mayhew, Michael B. and Zhou, Carol L. and Ruiz, Oscar N. and Dugan, Larry C.},
abstractNote = {},
doi = {10.1186/s12864-017-3708-4},
journal = {BMC Genomics},
issn = {1471-2164},
number = 1,
volume = 18,
place = {United States},
year = {2017},
month = {4}
}

Works referenced in this record:

Detection of Host-Derived Sphingosine by Pseudomonas aeruginosa Is Important for Survival in the Murine Lung
journal, January 2014


Molecular mechanism for sphingosine-induced Pseudomonas ceramidase expression through the transcriptional regulator SphR
journal, December 2016

  • Okino, Nozomu; Ito, Makoto
  • Scientific Reports, Vol. 6, Issue 1
  • DOI: 10.1038/srep38797

Transcriptional Profiling Suggests that Multiple Metabolic Adaptations are Required for Effective Proliferation of Pseudomonas aeruginosa in Jet Fuel
journal, November 2013

  • Gunasekera, Thusitha S.; Striebich, Richard C.; Mueller, Susan S.
  • Environmental Science & Technology, Vol. 47, Issue 23
  • DOI: 10.1021/es403163k

Global quantification of mammalian gene expression control
journal, May 2011

  • Schwanhäusser, Björn; Busse, Dorothea; Li, Na
  • Nature, Vol. 473, Issue 7347
  • DOI: 10.1038/nature10098

Biodegradation and surfactant-mediated biodegradation of diesel fuel by 218 microbial consortia are not correlated to cell surface hydrophobicity
journal, May 2009

  • Owsianiak, Mikołaj; Szulc, Alicja; Chrzanowski, Łukasz
  • Applied Microbiology and Biotechnology, Vol. 84, Issue 3
  • DOI: 10.1007/s00253-009-2040-6

The hierarchy quorum sensing network in Pseudomonas aeruginosa
journal, September 2014


Enhanced annotations and features for comparing thousands of Pseudomonas genomes in the Pseudomonas genome database
journal, November 2015

  • Winsor, Geoffrey L.; Griffiths, Emma J.; Lo, Raymond
  • Nucleic Acids Research, Vol. 44, Issue D1
  • DOI: 10.1093/nar/gkv1227

Roles of Pseudomonas aeruginosa las and rhl quorum-sensing systems in control of elastase and rhamnolipid biosynthesis genes.
journal, September 1997


Draft Genome Sequence of Pseudomonas aeruginosa ATCC 33988, a Bacterium Highly Adapted to Fuel-Polluted Environments
journal, November 2014


Microarray Analysis of Pseudomonas aeruginosa Quorum-Sensing Regulons: Effects of Growth Phase and Environment
journal, April 2003


Correlation between Protein and mRNA Abundance in Yeast
journal, March 1999

  • Gygi, Steven P.; Rochon, Yvan; Franza, B. Robert
  • Molecular and Cellular Biology, Vol. 19, Issue 3
  • DOI: 10.1128/MCB.19.3.1720

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
journal, January 2009


Examination of post-transcriptional regulations in prokaryotes by integrative biology
journal, November 2009

  • Picard, Flora; Dressaire, Clémentine; Girbal, Laurence
  • Comptes Rendus Biologies, Vol. 332, Issue 11
  • DOI: 10.1016/j.crvi.2009.09.005

Protein Sequence Annotation Tool (PSAT): a centralized web-based meta-server for high-throughput sequence annotations
journal, January 2016


Large-scale analysis of the yeast proteome by multidimensional protein identification technology
journal, March 2001

  • Washburn, Michael P.; Wolters, Dirk; Yates, John R.
  • Nature Biotechnology, Vol. 19, Issue 3
  • DOI: 10.1038/85686

Alkane biodegradation in Pseudomonas aeruginosa strains isolated from a polluted zone: identification of alkB and alkB-related genes
journal, July 2002


Degradation of alkanes by bacteria
journal, October 2009


Integrating multiple 'omics' analysis for microbial biology: application and methodologies
journal, November 2009


Adherence of bacteria to hydrocarbons: A simple method for measuring cell-surface hydrophobicity
journal, September 1980


Integrative Analysis of Transcriptomic and Proteomic Data: Challenges, Solutions and Applications
journal, January 2007


The OprB porin plays a central role in carbohydrate uptake in Pseudomonas aeruginosa.
journal, June 1995


Evidence for Direct Control of Virulence and Defense Gene Circuits by the Pseudomonas aeruginosa Quorum Sensing Regulator, MvfR
journal, September 2016

  • Maura, Damien; Hazan, Ronen; Kitao, Tomoe
  • Scientific Reports, Vol. 6, Issue 1
  • DOI: 10.1038/srep34083

Role of low-concentration monorhamnolipid in cell surface hydrophobicity of Pseudomonas aeruginosa: adsorption or lipopolysaccharide content variation
journal, July 2014

  • Liu, Yang; Ma, Xiaoling; Zeng, Guangming
  • Applied Microbiology and Biotechnology, Vol. 98, Issue 24
  • DOI: 10.1007/s00253-014-5957-3

Pseudomonas Evades Immune Recognition of Flagellin in Both Mammals and Plants
journal, August 2011


The Glycerol-Dependent Metabolic Persistence of Pseudomonas putida KT2440 Reflects the Regulatory Logic of the GlpR Repressor
journal, March 2015

  • Nikel, Pablo I.; Romero-Campero, Francisco J.; Zeidman, Joshua A.
  • mBio, Vol. 6, Issue 2
  • DOI: 10.1128/mBio.00340-15

Defining the transcriptome and proteome in three functionally different human cell lines
journal, January 2010

  • Lundberg, Emma; Fagerberg, Linn; Klevebring, Daniel
  • Molecular Systems Biology, Vol. 6, Issue 1
  • DOI: 10.1038/msb.2010.106

Biosurfactant-mediated biodegradation of straight and methyl-branched alkanes by Pseudomonas aeruginosa ATCC 55925
journal, January 2011

  • Rocha, Carlos A.; Pedregosa, Ana M.; Laborda, Fernando
  • AMB Express, Vol. 1, Issue 1
  • DOI: 10.1186/2191-0855-1-9

Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen
journal, August 2000

  • Stover, C. K.; Pham, X. Q.; Erwin, A. L.
  • Nature, Vol. 406, Issue 6799, p. 959-964
  • DOI: 10.1038/35023079

Multiple N-acyl-L-homoserine lactone signal molecules regulate production of virulence determinants and secondary metabolites in Pseudomonas aeruginosa.
journal, September 1995

  • Winson, M. K.; Camara, M.; Latifi, A.
  • Proceedings of the National Academy of Sciences, Vol. 92, Issue 20
  • DOI: 10.1073/pnas.92.20.9427

Methods for the integration of multi-omics data: mathematical aspects
journal, January 2016


Relationships among colony morphotypes, cell-surface properties and bacterial adhesion to substrata in Rhodococcus
journal, July 2003

  • Iwabuchi, Noriyuki; Sunairi, Michio; Anzai, Hirosi
  • Colloids and Surfaces B: Biointerfaces, Vol. 30, Issue 1-2
  • DOI: 10.1016/S0927-7765(03)00036-5

Strain-dependent diversity in the Pseudomonas aeruginosa quorum-sensing regulon
journal, September 2012

  • Chugani, S.; Kim, B. S.; Phattarasukol, S.
  • Proceedings of the National Academy of Sciences, Vol. 109, Issue 41
  • DOI: 10.1073/pnas.1214128109

The AprX protein of Pseudomonas aeruginosa : a new substrate for the Apr type I secretion system
journal, January 2001


Biodegradation of diesel/biodiesel blends by a consortium of hydrocarbon degraders: Effect of the type of blend and the addition of biosurfactants
journal, February 2009


Epigenetic Control of Virulence Gene Expression in Pseudomonas aeruginosa by a LysR-Type Transcription Regulator
journal, December 2009


Characterization of the F-76 diesel and Jet-A aviation fuel hydrocarbon degradation profiles of Pseudomonas aeruginosa and Marinobacter hydrocarbonoclasticus
journal, September 2014

  • Striebich, Richard C.; Smart, Caitlin E.; Gunasekera, Thusitha S.
  • International Biodeterioration & Biodegradation, Vol. 93
  • DOI: 10.1016/j.ibiod.2014.04.024

New insights into small RNA-dependent translational regulation in prokaryotes
journal, February 2013

  • Desnoyers, Guillaume; Bouchard, Marie-Pier; Massé, Eric
  • Trends in Genetics, Vol. 29, Issue 2
  • DOI: 10.1016/j.tig.2012.10.004

Selective ribosome profiling as a tool for studying the interaction of chaperones and targeting factors with nascent polypeptide chains and ribosomes
journal, October 2013

  • Becker, Annemarie H.; Oh, Eugene; Weissman, Jonathan S.
  • Nature Protocols, Vol. 8, Issue 11
  • DOI: 10.1038/nprot.2013.133

The RAST Server: Rapid Annotations using Subsystems Technology
journal, January 2008

  • Aziz, Ramy K.; Bartels, Daniela; Best, Aaron A.
  • BMC Genomics, Vol. 9, Issue 1, Article No. 75
  • DOI: 10.1186/1471-2164-9-75

Differential Expression of the Components of the Two Alkane Hydroxylases from Pseudomonas aeruginosa
journal, May 2003


    Works referencing / citing this record:

    A comprehensive multi-omics approach uncovers adaptations for growth and survival of Pseudomonas aeruginosa on n-alkanes [Supplementary Data]
    collection, April 2017

    • Grady, Sarah; Malfatti, Stephanie; Gunasekera, Thusitha
    • Figshare-Supplementary information for journal article at DOI: 10.1186/s12864-017-3708-4, 10 files
    • DOI: 10.6084/m9.figshare.c.3767636

    Additional file 9: Figure S3. of A comprehensive multi-omics approach uncovers adaptations for growth and survival of Pseudomonas aeruginosa on n-alkanes
    figure, April 2017

    • Grady, Sarah; Malfatti, Stephanie; Dalley, Brian
    • figshare-Supplementary information for journal article at DOI: 10.1186/s12864-017-3708-4, 1 PPTX file (46.56 kB)
    • DOI: 10.6084/m9.figshare.c.3767636_d10

    Additional file 2: Tables S5-S8. of A comprehensive multi-omics approach uncovers adaptations for growth and survival of Pseudomonas aeruginosa on n-alkanes
    dataset, April 2017

    • Grady, Sarah; Malfatti, Stephanie; Gunasekera, Thusitha
    • figshare-Supplementary information for journal article at DOI: 10.1186/s12864-017-3708-4, 1 XLSX file (141.54 kB)
    • DOI: 10.6084/m9.figshare.c.3767636_d3

    Additional file 5: Tables S17-S20. of A comprehensive multi-omics approach uncovers adaptations for growth and survival of Pseudomonas aeruginosa on n-alkanes
    dataset, April 2017

    • Grady, Sarah; Malfatti, Stephanie; Gunasekera, Thusitha
    • figshare-Supplementary information for journal article at DOI: 10.1186/s12864-017-3708-4, 1 XLSX file (373.62 kB)
    • DOI: 10.6084/m9.figshare.c.3767636_d6

    Additional file 6: Tables S21-S24. of A comprehensive multi-omics approach uncovers adaptations for growth and survival of Pseudomonas aeruginosa on n-alkanes
    dataset, April 2017

    • Grady, Sarah; Malfatti, Stephanie; Gunasekera, Thusitha
    • figshare-Supplementary information for journal article at DOI: 10.1186/s12864-017-3708-4, 1 XLSX file (85.8 kB)
    • DOI: 10.6084/m9.figshare.c.3767636_d7

    Additional file 7: Figure S1. of A comprehensive multi-omics approach uncovers adaptations for growth and survival of Pseudomonas aeruginosa on n-alkanes
    figure, April 2017

    • Grady, Sarah; Malfatti, Stephanie; Gunasekera, Thusitha
    • figshare-Supplementary information for journal article at DOI: 10.1186/s12864-017-3708-4, 1 PPTX file (81.82 kB)
    • DOI: 10.6084/m9.figshare.c.3767636_d8

    Additional file 8: Figure S2. of A comprehensive multi-omics approach uncovers adaptations for growth and survival of Pseudomonas aeruginosa on n-alkanes
    figure, April 2017

    • Grady, Sarah; Malfatti, Stephanie; Gunasekera, Thusitha
    • Figshare-Supplementary information for journal article at DOI: 10.1186/s12864-017-3708-4, 1 pptx file (76.63 kB)
    • DOI: 10.6084/m9.figshare.c.3767636_d9

    Implications of microbial adaptation for the assessment of environmental persistence of chemicals
    journal, June 2019

    • Poursat, Baptiste A. J.; van Spanning, Rob J. M.; de Voogt, Pim
    • Critical Reviews in Environmental Science and Technology, Vol. 49, Issue 23
    • DOI: 10.1080/10643389.2019.1607687