Time-course analysis of the Shewanella amazonensis SB2B proteome in response to sodium chloride shock.

PubWeight™: 0.76‹?›

🔗 View Article (PMC 3216512)

Published in Sci Rep on June 29, 2011

Authors

J Jacob Parnell1, Stephen J Callister, Giovanni Rompato, Carrie D Nicora, Ljiljana Paša-Tolić, Ashley Williamson, Michael E Pfrender

Author Affiliations

1: Center for Integrated BioSystems and Department of Biology, Utah State University, Logan, UT, USA. jacob.parnell@usu.edu

Articles cited by this

An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J Am Soc Mass Spectrom (1994) 45.51

Bacterial manganese reduction and growth with manganese oxide as the sole electron acceptor. Science (1988) 7.27

Cyclic diguanylate is a ubiquitous signaling molecule in bacteria: insights into biochemistry of the GGDEF protein domain. J Bacteriol (2005) 4.66

Towards environmental systems biology of Shewanella. Nat Rev Microbiol (2008) 4.37

Uptake and synthesis of compatible solutes as microbial stress responses to high-osmolality environments. Arch Microbiol (1998) 4.21

An accurate mass tag strategy for quantitative and high-throughput proteome measurements. Proteomics (2002) 4.10

Osmosensing by bacteria: signals and membrane-based sensors. Microbiol Mol Biol Rev (1999) 3.74

A molecular chaperone, ClpA, functions like DnaK and DnaJ. Proc Natl Acad Sci U S A (1994) 3.51

DAnTE: a statistical tool for quantitative analysis of -omics data. Bioinformatics (2008) 3.51

VIPER: an advanced software package to support high-throughput LC-MS peptide identification. Bioinformatics (2007) 3.15

Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags. Proc Natl Acad Sci U S A (2002) 3.15

Decon2LS: An open-source software package for automated processing and visualization of high resolution mass spectrometry data. BMC Bioinformatics (2009) 2.65

Cyclic di-GMP as a bacterial second messenger. Microbiology (2004) 2.54

Ultrasensitive and quantitative analyses from combined separations-mass spectrometry for the characterization of proteomes. Acc Chem Res (2004) 1.88

Differential growth response of colony-forming alpha- and gamma-proteobacteria in dilution culture and nutrient addition experiments from Lake Kinneret (Israel), the eastern Mediterranean Sea, and the Gulf of Eilat. Appl Environ Microbiol (2003) 1.81

Induction of heat shock proteins DnaK, GroEL, and GroES by salt stress in Lactococcus lactis. Appl Environ Microbiol (1997) 1.74

Osmotic regulation of porin expression: a role for DNA supercoiling. Mol Microbiol (1989) 1.57

Reduction kinetics of Fe(III), Co(III), U(VI), Cr(VI), and Tc(VII) in cultures of dissimilatory metal-reducing bacteria. Biotechnol Bioeng (2002) 1.56

Dissimilatory arsenate and sulfate reduction in sediments of two hypersaline, arsenic-rich soda lakes: Mono and Searles Lakes, California. Appl Environ Microbiol (2006) 1.52

Osmotic stress mechanically perturbs chemoreceptors in Escherichia coli. Proc Natl Acad Sci U S A (2006) 1.50

Signalling pathways in two-component phosphorelay systems. Trends Microbiol (1999) 1.47

Comparative genomics of regulation of fatty acid and branched-chain amino acid utilization in proteobacteria. J Bacteriol (2008) 1.45

Role of HAMP domains in chemotaxis signaling by bacterial chemoreceptors. Proc Natl Acad Sci U S A (2008) 1.40

Microbial response to salinity change in Lake Chaka, a hypersaline lake on Tibetan plateau. Environ Microbiol (2007) 1.34

Temperature sensing and cold acclimation. Curr Opin Plant Biol (2001) 1.33

Shewanella--the environmentally versatile genome. Nat Biotechnol (2002) 1.32

Transcriptome analysis of Shewanella oneidensis MR-1 in response to elevated salt conditions. J Bacteriol (2005) 1.31

Adenylyl cyclase G, an osmosensor controlling germination of Dictyostelium spores. J Biol Chem (1996) 1.21

Effect of temperature and salinity stress on growth and lipid composition of Shewanella gelidimarina. Appl Environ Microbiol (2000) 1.20

Role of DNA supercoiling and rpoS sigma factor in the osmotic and growth phase-dependent induction of the gene osmE of Escherichia coli K12. J Mol Biol (1997) 1.19

Shewanella amazonensis sp. nov., a novel metal-reducing facultative anaerobe from Amazonian shelf muds. Int J Syst Bacteriol (1998) 1.13

Microbial diversity in hypersaline wastewater: the example of tanneries. Extremophiles (2006) 1.12

The use of accurate mass tags for high-throughput microbial proteomics. OMICS (2002) 1.10

Variations of the envelope composition of Bacillus subtilis during growth in hyperosmotic medium. Curr Microbiol (1998) 1.06

A computational strategy to analyze label-free temporal bottom-up proteomics data. J Proteome Res (2008) 1.02

The downstream regulatory element of the proU operon of Salmonella typhimurium inhibits open complex formation by RNA polymerase at a distance. J Biol Chem (2000) 0.97

Identification of genes regulated by changing salinity in the deep-sea bacterium Shewanella sp. WP3 using RNA arbitrarily primed PCR. Extremophiles (2005) 0.92

Comparison between NaCl tolerance response and acclimation to cold temperature in Shewanella putrefaciens. Curr Microbiol (2003) 0.89

An empirical strategy for characterizing bacterial proteomes across species in the absence of genomic sequences. PLoS One (2010) 0.87

SbcCD regulation and localization in Escherichia coli. J Bacteriol (2007) 0.85

Amino acid efflux in response to chemotactic and osmotic signals in Bacillus subtilis. J Bacteriol (1995) 0.84

Articles by these authors

The ecoresponsive genome of Daphnia pulex. Science (2011) 6.55

Subunit compositions of the RNA-silencing enzymes Pol IV and Pol V reveal their origins as specialized forms of RNA polymerase II. Mol Cell (2008) 2.43

Transport functions dominate the SAR11 metaproteome at low-nutrient extremes in the Sargasso Sea. ISME J (2008) 2.11

Conservation in a cup of water: estimating biodiversity and population abundance from environmental DNA. Mol Ecol (2012) 1.90

Phenotypic plasticity facilitates recurrent rapid adaptation to introduced predators. Proc Natl Acad Sci U S A (2010) 1.50

Proteogenomic monitoring of Geobacter physiology during stimulated uranium bioremediation. Appl Environ Microbiol (2009) 1.45

Upper limit of the rate and per generation effects of deleterious genomic mutations. Genet Res (2006) 1.41

Normalization of peak intensities in bottom-up MS-based proteomics using singular value decomposition. Bioinformatics (2009) 1.40

Differential label-free quantitative proteomic analysis of Shewanella oneidensis cultured under aerobic and suboxic conditions by accurate mass and time tag approach. Mol Cell Proteomics (2006) 1.36

Proteomic analysis of stationary phase in the marine bacterium "Candidatus Pelagibacter ubique". Appl Environ Microbiol (2008) 1.33

Phosphoproteome profiling of human skin fibroblast cells in response to low- and high-dose irradiation. J Proteome Res (2006) 1.33

In vitro transcription activities of Pol IV, Pol V, and RDR2 reveal coupling of Pol IV and RDR2 for dsRNA synthesis in plant RNA silencing. Mol Cell (2012) 1.30

Large improvements in MS/MS-based peptide identification rates using a hybrid analysis. J Proteome Res (2011) 1.29

The evolutionary origins of beneficial alleles during the repeated adaptation of garter snakes to deadly prey. Proc Natl Acad Sci U S A (2009) 1.24

Linking genes to communities and ecosystems: Daphnia as an ecogenomic model. Proc Biol Sci (2012) 1.20

A proposal to sequence the genome of a garter snake (Thamnophis sirtalis). Stand Genomic Sci (2011) 1.15

Metagenomic and metaproteomic insights into bacterial communities in leaf-cutter ant fungus gardens. ISME J (2012) 1.15

Predator-induced defences in Daphnia pulex: selection and evaluation of internal reference genes for gene expression studies with real-time PCR. BMC Mol Biol (2010) 1.10

Role of the global transcriptional regulator PrrA in Rhodobacter sphaeroides 2.4.1: combined transcriptome and proteome analysis. J Bacteriol (2008) 1.09

Proteogenomic analysis of a thermophilic bacterial consortium adapted to deconstruct switchgrass. PLoS One (2013) 1.08

The first pilot project of the consortium for top-down proteomics: a status report. Proteomics (2014) 1.08

Application of the accurate mass and time tag approach to the proteome analysis of sub-cellular fractions obtained from Rhodobacter sphaeroides 2.4.1. Aerobic and photosynthetic cell cultures. J Proteome Res (2006) 1.07

The future of liquid chromatography-mass spectrometry (LC-MS) in metabolic profiling and metabolomic studies for biomarker discovery. Biomark Med (2007) 1.06

Rapid evolution in response to introduced predators I: rates and patterns of morphological and life-history trait divergence. BMC Evol Biol (2007) 1.05

Analysis of biostimulated microbial communities from two field experiments reveals temporal and spatial differences in proteome profiles. Environ Sci Technol (2010) 1.04

Two-dimensional liquid chromatography system for online top-down mass spectrometry. Proteomics (2010) 1.03

Constraint shapes convergence in tetrodotoxin-resistant sodium channels of snakes. Proc Natl Acad Sci U S A (2012) 1.03

A computational strategy to analyze label-free temporal bottom-up proteomics data. J Proteome Res (2008) 1.02

FT-ICR MS optimization for the analysis of intact proteins. Int J Mass Spectrom (2009) 1.02

Rapid evolution in response to introduced predators II: the contribution of adaptive plasticity. BMC Evol Biol (2007) 1.01

Leucoagaricus gongylophorus produces diverse enzymes for the degradation of recalcitrant plant polymers in leaf-cutter ant fungus gardens. Appl Environ Microbiol (2013) 1.01

Enhanced top-down characterization of histone post-translational modifications. Genome Biol (2012) 1.01

Genomics of environmentally induced phenotypes in 2 extremely plastic arthropods. J Hered (2011) 1.00

Proteome insights into the symbiotic relationship between a captive colony of Nasutitermes corniger and its hindgut microbiome. ISME J (2010) 1.00

Diurnal rhythms result in significant changes in the cellular protein complement in the cyanobacterium Cyanothece 51142. PLoS One (2011) 1.00

Simple sodium dodecyl sulfate-assisted sample preparation method for LC-MS-based proteomics applications. Anal Chem (2012) 0.99

Proteome analysis of Borrelia burgdorferi response to environmental change. PLoS One (2010) 0.99

Comparison of aerobic and photosynthetic Rhodobacter sphaeroides 2.4.1 proteomes. J Microbiol Methods (2006) 0.97

Transcriptional and translational regulatory responses to iron limitation in the globally distributed marine bacterium Candidatus pelagibacter ubique. PLoS One (2010) 0.96

Loss of the response regulator CtrA causes pleiotropic effects on gene expression but does not affect growth phase regulation in Rhodobacter capsulatus. J Bacteriol (2010) 0.96

Biodiversity in microbial communities: system scale patterns and mechanisms. Mol Ecol (2009) 0.96

MultiAlign: a multiple LC-MS analysis tool for targeted omics analysis. BMC Bioinformatics (2013) 0.95

C60 secondary ion Fourier transform ion cyclotron resonance mass spectrometry. Anal Chem (2011) 0.94

High-throughput proteomics. Annu Rev Anal Chem (Palo Alto Calif) (2014) 0.94

A highly sensitive targeted mass spectrometric assay for quantification of AGR2 protein in human urine and serum. J Proteome Res (2013) 0.94

High mass accuracy and high mass resolving power FT-ICR secondary ion mass spectrometry for biological tissue imaging. Anal Bioanal Chem (2013) 0.93

Genetic architecture of a feeding adaptation: garter snake (Thamnophis) resistance to tetrodotoxin bearing prey. Proc Biol Sci (2010) 0.93

The evolution of salinity tolerance in Daphnia: a functional genomics approach. Ecol Lett (2012) 0.93

Proteomic detection of non-annotated protein-coding genes in Pseudomonas fluorescens Pf0-1. PLoS One (2009) 0.91

Haloferax volcanii archaeosortase is required for motility, mating, and C-terminal processing of the S-layer glycoprotein. Mol Microbiol (2013) 0.91

Proteomic and transcriptomic analyses of "Candidatus Pelagibacter ubique" describe the first PII-independent response to nitrogen limitation in a free-living Alphaproteobacterium. MBio (2013) 0.91

Long-gradient separations coupled with selected reaction monitoring for highly sensitive, large scale targeted protein quantification in a single analysis. Anal Chem (2013) 0.90

Suite of activity-based probes for cellulose-degrading enzymes. J Am Chem Soc (2012) 0.89

Quantitative analysis of human salivary gland-derived intact proteome using top-down mass spectrometry. Proteomics (2014) 0.89

The identification of novel potential injury mechanisms and candidate biomarkers in renal allograft rejection by quantitative proteomics. Mol Cell Proteomics (2013) 0.89

Cryptic postzygotic isolation in an eruptive species of bark beetle (Dendroctonus ponderosae). Evolution (2010) 0.89

Development of a biomarker for Geobacter activity and strain composition; proteogenomic analysis of the citrate synthase protein during bioremediation of U(VI). Microb Biotechnol (2011) 0.89

Evaluation of SDS depletion using an affinity spin column and IMS-MS detection. Proteomics (2012) 0.88

Proteomic approaches to bacterial differentiation. J Microbiol Methods (2006) 0.88

Recent advances in crustacean genomics. Integr Comp Biol (2008) 0.88

An SNP-based second-generation genetic map of Daphnia magna and its application to QTL analysis of phenotypic traits. BMC Genomics (2014) 0.88

De novo protein sequencing by combining top-down and bottom-up tandem mass spectra. J Proteome Res (2014) 0.88

Advanced mass calibration and visualization for FT-ICR mass spectrometry imaging. J Am Soc Mass Spectrom (2012) 0.88

Dynamic proteome analysis of Cyanothece sp. ATCC 51142 under constant light. J Proteome Res (2011) 0.87

An empirical strategy for characterizing bacterial proteomes across species in the absence of genomic sequences. PLoS One (2010) 0.87

Functional genomics of acclimation and adaptation in response to thermal stress in Daphnia. BMC Genomics (2014) 0.87

Global proteomic analysis of the chromate response in Arthrobacter sp. strain FB24. J Proteome Res (2009) 0.87

Optimization for peptide sample preparation for urine peptidomics. Clin Proteomics (2014) 0.87

Functional biogeography as evidence of gene transfer in hypersaline microbial communities. PLoS One (2010) 0.86

Stabilizing selection on behavior and morphology masks positive selection on the signal in a salamander pheromone signaling complex. Mol Biol Evol (2004) 0.85

Sensitive targeted quantification of ERK phosphorylation dynamics and stoichiometry in human cells without affinity enrichment. Anal Chem (2014) 0.85

Development of an ecophysiological model for Diplosphaera colotermitum TAV2, a termite hindgut Verrucomicrobium. ISME J (2013) 0.85

The evolutionary time machine: using dormant propagules to forecast how populations can adapt to changing environments. Trends Ecol Evol (2013) 0.85

Fluctuations in species-level protein expression occur during element and nutrient cycling in the subsurface. PLoS One (2013) 0.84

Proteome analyses of strains ATCC 51142 and PCC 7822 of the diazotrophic cyanobacterium Cyanothece sp. under culture conditions resulting in enhanced H₂ production. Appl Environ Microbiol (2012) 0.84

Correspondence between community structure and function during succession in phenol- and phenol-plus-trichloroethene-fed sequencing batch reactors. Appl Environ Microbiol (2004) 0.84

Activity-based protein profiling of secreted cellulolytic enzyme activity dynamics in Trichoderma reesei QM6a, NG14, and RUT-C30. Mol Biosyst (2013) 0.83

An integrated top-down and bottom-up proteomic approach to characterize the antigen-binding fragment of antibodies. Proteomics (2014) 0.83

Genomics in the ecological arena. Biol Lett (2010) 0.82

The fungus gardens of leaf-cutter ants undergo a distinct physiological transition during biomass degradation. Environ Microbiol Rep (2014) 0.82

Amino acid treatment enhances protein recovery from sediment and soils for metaproteomic studies. Proteomics (2013) 0.82

Characterization of Proteoforms with Unknown Post-translational Modifications Using the MIScore. J Proteome Res (2016) 0.81

Proteomic characterization of the Rhodobacter sphaeroides 2.4.1 photosynthetic membrane: identification of new proteins. J Bacteriol (2007) 0.81

SPOCS: software for predicting and visualizing orthology/paralogy relationships among genomes. Bioinformatics (2013) 0.81

Comparison of Chloroflexus aurantiacus strain J-10-fl proteomes of cells grown chemoheterotrophically and photoheterotrophically. Photosynth Res (2012) 0.80

Characterizing microbial community and geochemical dynamics at hydrothermal vents using osmotically driven continuous fluid samplers. Environ Sci Technol (2013) 0.80

Protein and microRNA biomarkers from lavage, urine, and serum in military personnel evaluated for dyspnea. BMC Med Genomics (2014) 0.80

FRET imaging of diatoms expressing a biosilica-localized ribose sensor. PLoS One (2012) 0.80

Trauma-associated human neutrophil alterations revealed by comparative proteomics profiling. Proteomics Clin Appl (2013) 0.80

Angular averaged profiling of the radial electric field in compensated FTICR Cells. J Am Soc Mass Spectrom (2012) 0.80