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Title: Proteomic Analysis of Stationary Phase in the Marine Bacterium 'Candidatus Pelagibacter ubique'

Abstract

Candidatus Pelagibacter ubique, an abundant marine alphaproteobacterium, subsists in nature at low ambient nutrient concentrations and may often be exposed to nutrient limitation, but its genome revealed no evidence of global regulatory adaptations to stationary phase. We used high-resolution capillary liquid chromatography (LC) coupled online to an LTQ mass spectrometer to build an Accurate Mass and Time (AMT) tag library, and employed the AMT tag approach to quantitatively examine proteome differences between exponentially growing and stationary phase Cand. P. ubique cells cultivated in a seawater medium. The AMT tag library represented 72% of the predicted protein coding genes. Stationary phase protein abundance increased for OsmC, which mitigates oxidative damage, and for molecular chaperones, enzymes involved in methionine and cysteine biosynthesis, proteins involved in rho-dependent transcription termination, and the signal transduction enzymes CheY-FisH and ChvG. Our findings indicate that Cand. P. ubique responds adaptively to stationary phase by increasing the abundance of a suite of proteins that contribute to homeostasis, but does not undergo major proteome remodeling. We speculate that this limited response may enable Cand. P. ubique to cope with ambient conditions in which nutrients are often insufficient for short periods, and the ability to resume growth overrides the capacitymore » for long term survival afforded by more comprehensive global stationary phase responses.« less

Authors:
; ; ; ; ; ; ;
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
937380
Report Number(s):
PNNL-SA-59403
Journal ID: ISSN 0099-2240; AEMIDF; KP1501021; TRN: US200819%%103
DOE Contract Number:  
AC05-76RL01830
Resource Type:
Journal Article
Journal Name:
Applied and Environmental Microbiology, 74(13):4091-4100
Additional Journal Information:
Journal Volume: 74; Journal Issue: 13; Journal ID: ISSN 0099-2240
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; ABUNDANCE; BIOSYNTHESIS; CAPACITY; CHROMATOGRAPHY; CYSTEINE; ENZYMES; GENES; HOMEOSTASIS; MASS SPECTROMETERS; METHIONINE; NUTRIENTS; PROTEINS; SEAWATER; TRANSCRIPTION

Citation Formats

Sowell, Sarah M, Norbeck, Angela D, Lipton, Mary S, Nicora, Carrie D, Callister, Stephen J, Smith, Richard D, Barofsky, Douglas F, and Giovannoni, Stephen J. Proteomic Analysis of Stationary Phase in the Marine Bacterium 'Candidatus Pelagibacter ubique'. United States: N. p., 2008. Web. doi:10.1128/AEM.00599-08.
Sowell, Sarah M, Norbeck, Angela D, Lipton, Mary S, Nicora, Carrie D, Callister, Stephen J, Smith, Richard D, Barofsky, Douglas F, & Giovannoni, Stephen J. Proteomic Analysis of Stationary Phase in the Marine Bacterium 'Candidatus Pelagibacter ubique'. United States. https://doi.org/10.1128/AEM.00599-08
Sowell, Sarah M, Norbeck, Angela D, Lipton, Mary S, Nicora, Carrie D, Callister, Stephen J, Smith, Richard D, Barofsky, Douglas F, and Giovannoni, Stephen J. 2008. "Proteomic Analysis of Stationary Phase in the Marine Bacterium 'Candidatus Pelagibacter ubique'". United States. https://doi.org/10.1128/AEM.00599-08.
@article{osti_937380,
title = {Proteomic Analysis of Stationary Phase in the Marine Bacterium 'Candidatus Pelagibacter ubique'},
author = {Sowell, Sarah M and Norbeck, Angela D and Lipton, Mary S and Nicora, Carrie D and Callister, Stephen J and Smith, Richard D and Barofsky, Douglas F and Giovannoni, Stephen J},
abstractNote = {Candidatus Pelagibacter ubique, an abundant marine alphaproteobacterium, subsists in nature at low ambient nutrient concentrations and may often be exposed to nutrient limitation, but its genome revealed no evidence of global regulatory adaptations to stationary phase. We used high-resolution capillary liquid chromatography (LC) coupled online to an LTQ mass spectrometer to build an Accurate Mass and Time (AMT) tag library, and employed the AMT tag approach to quantitatively examine proteome differences between exponentially growing and stationary phase Cand. P. ubique cells cultivated in a seawater medium. The AMT tag library represented 72% of the predicted protein coding genes. Stationary phase protein abundance increased for OsmC, which mitigates oxidative damage, and for molecular chaperones, enzymes involved in methionine and cysteine biosynthesis, proteins involved in rho-dependent transcription termination, and the signal transduction enzymes CheY-FisH and ChvG. Our findings indicate that Cand. P. ubique responds adaptively to stationary phase by increasing the abundance of a suite of proteins that contribute to homeostasis, but does not undergo major proteome remodeling. We speculate that this limited response may enable Cand. P. ubique to cope with ambient conditions in which nutrients are often insufficient for short periods, and the ability to resume growth overrides the capacity for long term survival afforded by more comprehensive global stationary phase responses.},
doi = {10.1128/AEM.00599-08},
url = {https://www.osti.gov/biblio/937380}, journal = {Applied and Environmental Microbiology, 74(13):4091-4100},
issn = {0099-2240},
number = 13,
volume = 74,
place = {United States},
year = {Thu May 01 00:00:00 EDT 2008},
month = {Thu May 01 00:00:00 EDT 2008}
}