scholarly journals Proteomic Analysis of Stationary Phase in the Marine Bacterium “Candidatus Pelagibacter ubique”

2008 ◽  
Vol 74 (13) ◽  
pp. 4091-4100 ◽  
Author(s):  
Sarah M. Sowell ◽  
Angela D. Norbeck ◽  
Mary S. Lipton ◽  
Carrie D. Nicora ◽  
Stephen J. Callister ◽  
...  
Keyword(s):  
Stationary Phase ◽  
Thioredoxin Reductase ◽  
Capillary Liquid Chromatography ◽  
Nutrient Concentrations ◽  
Ambient Conditions ◽  
Term Survival ◽  
Protein Encoding ◽  
Quantitative Examination ◽  
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 reveals no evidence of global regulatory mechanisms for adaptation to stationary phase. High-resolution capillary liquid chromatography coupled online to an LTQ mass spectrometer was used to build an accurate mass and time (AMT) tag library that enabled quantitative examination of proteomic differences between exponential- and stationary-phase “Ca. Pelagibacter ubique” cells cultivated in a seawater medium. The AMT tag library represented 65% of the predicted protein-encoding genes. “Ca. Pelagibacter ubique” appears to respond adaptively to stationary phase by increasing the abundance of a suite of proteins that contribute to homeostasis rather than undergoing a major remodeling of its proteome. Stationary-phase abundances increased significantly for OsmC and thioredoxin reductase, which may mitigate oxidative damage in “Ca. Pelagibacter,” as well as for molecular chaperones, enzymes involved in methionine and cysteine biosynthesis, proteins involved in ρ-dependent transcription termination, and the signal transduction enzyme CheY-FisH. We speculate that this limited response may enable “Ca. Pelagibacter ubique” to cope with ambient conditions that deprive it of nutrients for short periods and, furthermore, that the ability to resume growth overrides the need for a more comprehensive global stationary-phase response to create a capacity for long-term survival.

scholarly journals Anaerobic Survival of Pseudomonas aeruginosa by Pyruvate Fermentation Requires an Usp-Type Stress Protein

2006 ◽  
Vol 188 (2) ◽  
pp. 659-668 ◽  
Author(s):  
Kerstin Schreiber ◽  
Nelli Boes ◽  
Martin Eschbach ◽  
Lothar Jaensch ◽  
Juergen Wehland ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Stationary Phase ◽  
Gene Fusion ◽  
Laser Scanning Microscopy ◽  
Green Fluorescent Protein Gene ◽  
Confocal Laser ◽  
Term Survival ◽  
Long Term Survival ◽  
Pyruvate Fermentation

ABSTRACT Recently, we identified a pyruvate fermentation pathway in Pseudomonas aeruginosa sustaining anaerobic survival in the absence of alternative anaerobic respiratory and fermentative energy generation systems (M. Eschbach, K. Schreiber, K. Trunk, J. Buer, D. Jahn, and M. Schobert, J. Bacteriol. 186:4596-4604, 2004). Anaerobic long-term survival of P. aeruginosa might be essential for survival in deeper layers of a biofilm and the persistent infection of anaerobic mucus plaques in the cystic fibrosis lung. Proteome analysis of P. aeruginosa cells during a 7-day period of pyruvate fermentation revealed the induced synthesis of three enzymes involved in arginine fermentation, ArcA, ArcB, and ArcC, and the outer membrane protein OprL. Moreover, formation of two proteins of unknown function, PA3309 and PA4352, increased by factors of 72- and 22-fold, respectively. Both belong to the group of universal stress proteins (Usp). Long-term survival of a PA3309 knockout mutant by pyruvate fermentation was found drastically reduced. The oxygen-sensing regulator Anr controls expression of the P PA3309-lacZ reporter gene fusion after a shift to anaerobic conditions and further pyruvate fermentation. PA3309 expression was also found induced during the anaerobic and aerobic stationary phases. This aerobic stationary-phase induction is independent of the regulatory proteins Anr, RpoS, RelA, GacA, RhlR, and LasR, indicating a currently unknown mechanism of stationary-phase-dependent gene activation. PA3309 promoter activity was detected in the deeper layers of a P. aeruginosa biofilm using a P PA3309-gfp (green fluorescent protein gene) fusion and confocal laser-scanning microscopy. This is the first description of an Anr-dependent, anaerobically induced, and functional Usp-like protein in bacteria.

scholarly journals A metabolic strategy to enhance long-term survival by Phx1 through stationary phase-specific pyruvate decarboxylases in fission yeast

Aging ◽  
2014 ◽  
Vol 6 (7) ◽  
pp. 587-601 ◽  
Author(s):  
Ji-Yoon Kim ◽  
Eun-Jung Kim ◽  
Luis Lopez-Maury ◽  
Jürg Bähler ◽  
Jung-Hye Roe
Keyword(s):  
Stationary Phase ◽  
Fission Yeast ◽  
Term Survival ◽  
Long Term Survival

scholarly journals Staphylococcus aureus ClpC Is Required for Stress Resistance, Aconitase Activity, Growth Recovery, and Death

2005 ◽  
Vol 187 (13) ◽  
pp. 4488-4496 ◽  
Author(s):  
Indranil Chatterjee ◽  
Petra Becker ◽  
Matthias Grundmeier ◽  
Markus Bischoff ◽  
Greg A. Somerville ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Stationary Phase ◽  
Critical Role ◽  
Tca Cycle ◽  
Term Survival ◽  
Phase Recovery ◽  
Growth And Survival ◽  
Aconitase Activity

ABSTRACT The ability of Staphylococcus aureus to adapt to various conditions of stress is the result of a complex regulatory response. Previously, it has been demonstrated that Clp homologues are important for a variety of stress conditions, and our laboratory has shown that a clpC homologue was highly expressed in the S. aureus strain DSM20231 during biofilm formation relative to expression in planktonic cells. Persistence and long-term survival are a hallmark of biofilm-associated staphylococcal infections, as cure frequently fails even in the presence of bactericidal antimicrobials. To determine the role of clpC in this context, we performed metabolic, gene expression, and long-term growth and survival analyses of DSM20231 as well as an isogenic clpC allelic-replacement mutant, a sigB mutant, and a clpC sigB double mutant. As expected, the clpC mutant showed increased sensitivity to oxidative and heat stresses. Unanticipated, however, was the reduced expression of the tricarboxylic acid (TCA) cycle gene citB (encoding aconitase), resulting in the loss of aconitase activity and preventing the catabolization of acetate during the stationary phase. clpC inactivation abolished post-stationary-phase recovery but also resulted in significantly enhanced stationary-phase survival compared to that of the wild-type strain. These data demonstrate the critical role of the ClpC ATPase in regulating the TCA cycle and implicate ClpC as being important for recovery from the stationary phase and also for entering the death phase. Understanding the stationary- and post-stationary-phase recovery in S. aureus may have important clinical implications, as little is known about the mechanisms of long-term persistence of chronic S. aureus infections associated with formation of biofilms.

scholarly journals Culture Volume and Vessel Affect Long-Term Survival, Mutation Frequency, and Oxidative Stress of Escherichia coli

2013 ◽  
Vol 80 (5) ◽  
pp. 1732-1738 ◽  
Author(s):  
Karin E. Kram ◽  
Steven E. Finkel
Keyword(s):  
Oxidative Stress ◽  
Escherichia Coli ◽  
Stationary Phase ◽  
Mutation Frequency ◽  
Physiological Responses ◽  
Culture Vessel ◽  
Term Survival ◽  
Long Term Survival ◽  
Content Type

ABSTRACTBacteria such asEscherichia coliare frequently studied during exponential- and stationary-phase growth. However, many strains can survive in long-term stationary phase (LTSP), without the addition of nutrients, from days to several years. During LTSP, cells experience a variety of stressors, including reactive oxidative species, nutrient depletion, and metabolic toxin buildup, that lead to physiological responses and changes in genetic stability. In this study, we monitored survival during LTSP, as well as reporters of genetic and physiological change, to determine how the physical environment affectsE. coliduring long-term batch culture. We demonstrate differences in yield during LTSP in cells incubated in LB medium in test tubes versus Erlenmeyer flasks, as well as growth in different volumes of medium. We determined that these differences are only partially due to differences in oxygen levels by incubating the cells in different volumes of media under anaerobic conditions. Since we hypothesized that differences in long-term survival are the result of changes in physiological outputs during the late log and early stationary phases, we monitored alkalization, mutation frequency, oxidative stress response, and glycation. Although initial cell yields are essentially equivalent under each condition tested, physiological responses vary greatly in response to culture environment. Incubation in lower-volume cultures leads to higheroxyRexpression but lower mutation frequency and glycation levels, whereas incubation in high-volume cultures has the opposite effect. We show here that even under commonly used experimental conditions that are frequently treated as equivalent, the stresses experienced by cells can differ greatly, suggesting that culture vessel and incubation conditions should be carefully considered in the planning or analysis of experiments.

Recovery from long-term stationary phase and stress survival in Escherichia coli require the l-isoaspartyl protein carboxyl methyltransferase at alkaline pH

Microbiology ◽  
2005 ◽  
Vol 151 (7) ◽  
pp. 2151-2158 ◽  
Author(s):  
Wade M. Hicks ◽  
Matthew V. Kotlajich ◽  
Jonathan E. Visick
Keyword(s):  
Escherichia Coli ◽  
Stationary Phase ◽  
Alkaline Ph ◽  
Term Survival ◽  
Long Term Survival ◽  
E Coli ◽  
Carboxyl Methyltransferase ◽  
Protein Carboxyl Methyltransferase ◽  
Stress Survival

The l-isoaspartyl protein carboxyl methyltransferase (pcm) can stimulate repair of isoaspartyl residues arising spontaneously in proteins to normal l-aspartyl residues. PCM is needed in Escherichia coli for maximal long-term survival when exposed to oxidative stress, osmotic stress, repeated heat stress or methanol. The effect of pH on a pcm mutant during long-term stationary phase was examined. PCM was not required for long-term survival of E. coli subjected to pH stress alone; however, PCM-deficient cells showed impaired resistance to paraquat and methanol only at elevated pH. The mutant also showed stress-survival phenotypes in minimal medium buffered to pH 9·0. Accumulation of isoaspartyl residues was accelerated at pH 8·0 or 9·0 in vivo, though PCM-deficient cells did not show higher levels of damage. However, the pcm mutant displayed an extended lag phase in recovering from stationary phase at pH 9·0. Protein repair by PCM thus plays a key role in long-term stress survival only at alkaline pH in E. coli, and it may function primarily to repair damage in cells that are recovering from nutrient limitation and in those cells that are able to divide during long-term stationary phase.

scholarly journals Nanocalorimetry Reveals the Growth Dynamics ofEscherichia coliCells Undergoing Adaptive Evolution during Long-Term Stationary Phase

2019 ◽  
Vol 85 (15) ◽  
Author(s):  
Alberto Robador ◽  
Jan P. Amend ◽  
Steven E. Finkel
Keyword(s):  
Stationary Phase ◽  
Isothermal Calorimetry ◽  
Growth Dynamics ◽  
Energy Conditions ◽  
Exponential Growth Phase ◽  
Natural Environments ◽  
Term Survival ◽  
Prolonged Incubation

ABSTRACTBacterial populations in long-term stationary-phase (LTSP) laboratory cultures can provide insights into physiological and genetic adaptations to low-energy conditions and population dynamics in natural environments. While overall population density remains stable, these communities are very dynamic and are characterized by the rapid emergence and succession of distinct mutants expressing the growth advantage in stationary phase (GASP) phenotype, which can reflect an increased capacity to withstand energy limitations and environmental stress. Here, we characterize the metabolic heat signatures and growth dynamics of GASP mutants within an evolving population using isothermal calorimetry. We agedEscherichia coliin anaerobic batch cultures over 20 days inside an isothermal nanocalorimeter and observed distinct heat events related to the emergence of three mutant populations expressing the GASP phenotype after 1.5, 3, and 7 days. Given the heat produced by each population, the maximum number of GASP mutant cells was calculated, revealing abundances of ∼2.5 × 107, ∼7.5 × 106, and ∼9.9 × 106cells in the populations, respectively. These data indicate that mutants capable of expressing the GASP phenotype can be acquired during the exponential growth phase and subsequently expressed in LTSP culture.IMPORTANCEThe present study is innovative in that we have identified previously unknown growth dynamics related to the temporal expression of the growth advantage in stationary phase (GASP) phenotype that allow mutants in long-term stationary-phase cultures to capitalize on the decrease of energy over prolonged incubation periods. By remaining in an active, but growth-limited, metabolic state similar to that observed in GASP cells grownin vitro, natural microbial communities might be able to prevail over much longer time scales. We believe this report to be a remarkable methodological and conceptual breakthrough in the study of the long-term survival and evolution of bacteria.

Proteomics analysis of a long-term survival strain of Escherichia coli K-12 exhibiting a growth advantage in stationary-phase (GASP) phenotype

PROTEOMICS ◽  
2016 ◽  
Vol 16 (6) ◽  
pp. 963-972 ◽  
Author(s):  
Assunta Gagliardi ◽  
Egidio Lamboglia ◽  
Laura Bianchi ◽  
Claudia Landi ◽  
Alessandro Armini ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Stationary Phase ◽  
Proteomics Analysis ◽  
Term Survival ◽  
Long Term Survival ◽  
K 12

scholarly journals Dynamics of Metabolic Activities and Gene Expression in the Roseobacter Clade Bacterium Phaeobacter sp. Strain MED193 during Growth with Thiosulfate

2014 ◽  
Vol 80 (22) ◽  
pp. 6933-6942 ◽  
Author(s):  
Saraladevi Muthusamy ◽  
Federico Baltar ◽  
José M. González ◽  
Jarone Pinhassi
Keyword(s):  
Gene Expression ◽  
Stationary Phase ◽  
Sulfur Oxidation ◽  
Active Growth ◽  
Additional Energy ◽  
Term Survival ◽  
Content Type ◽  
Important Pathway ◽  
Metabolic Activities

ABSTRACTMetagenomic analyses of surface seawater reveal that genes for sulfur oxidation are widespread in bacterioplankton communities. However, little is known about the metabolic processes used to exploit the energy potentially gained from inorganic sulfur oxidation in oxic seawater. We therefore studied thesoxgene system containingRoseobacterclade isolatePhaeobactersp. strain MED193 in acetate minimal medium with and without thiosulfate. The addition of thiosulfate enhanced the bacterial growth yields up to 40% in this strain. Concomitantly,soxBandsoxYgene expression increased about 8-fold with thiosulfate and remained 11-fold higher than that in controls through stationary phase. At stationary phase, thiosulfate stimulated protein synthesis and anaplerotic CO2fixation rates up to 5- and 35-fold, respectively. Several genes involved in anaplerotic CO2fixation (i.e., pyruvate carboxylase, propionyl coenzyme A [CoA], and crotonyl-CoA carboxylase) were highly expressed during active growth, coinciding with high CO2fixation rates. The high expression of key genes in the ethylmalonyl-CoA pathway suggests that this is an important pathway for the utilization of two-carbon compounds inPhaeobactersp. MED193. Overall, our findings imply thatRoseobacterclade bacteria carryingsoxgenes can use their lithotrophic potential to gain additional energy from sulfur oxidation for both increasing their growth capacity and improving their long-term survival.

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