scholarly journals New insights into the adaptive transcriptional response to nitrogen starvation in Escherichia coli

2018 ◽  
Vol 46 (6) ◽  
pp. 1721-1728 ◽  
Author(s):  
Amy Switzer ◽  
Daniel R. Brown ◽  
Sivaramesh Wigneshweraraj
Keyword(s):  
Escherichia Coli ◽  
Adaptive Response ◽  
Large Scale ◽  
Nitrogen Starvation ◽  
Transcriptional Response ◽  
Adaptive Responses ◽  
Nitrogenous Compounds ◽  
E Coli ◽  
N Starvation ◽  
Genome Scale

Bacterial adaptive responses to biotic and abiotic stresses often involve large-scale reprogramming of the transcriptome. Since nitrogen is an essential component of the bacterial cell, the transcriptional basis of the adaptive response to nitrogen starvation has been well studied. The adaptive response to N starvation in Escherichia coli is primarily a ‘scavenging response’, which results in the transcription of genes required for the transport and catabolism of nitrogenous compounds. However, recent genome-scale studies have begun to uncover and expand some of the intricate regulatory complexities that underpin the adaptive transcriptional response to nitrogen starvation in E. coli. The purpose of this review is to highlight some of these new developments.

scholarly journals A role for a conserved kinase in the transcriptional control of methionine biosynthesis inEscherichia coliexperiencing sustained nitrogen starvation

2018 ◽  
Author(s):  
Amy Switzer ◽  
Dimitrios Evangelopoulos ◽  
Rita Figueira ◽  
Luiz Pedro S. de Carvalho ◽  
Daniel R. Brown ◽  
...  
Keyword(s):  
Large Scale ◽  
Transcriptional Control ◽  
Nitrogen Starvation ◽  
Transcriptional Response ◽  
Transcription Activator ◽  
Targeted Metabolomics ◽  
Methionine Biosynthesis ◽  
E Coli ◽  
N Starvation ◽  
Molecular Brake

ABSTRACTThe initial adaptive transcriptional response to nitrogen (N) starvation inEscherichia coliinvolves large-scale alterations to the transcriptome mediated by the transcription activator, NtrC. One of the NtrC-activated genes isyeaG, which encodes a conserved bacterial kinase. Although it is known that YeaG is required for optimal survival under sustained N starvation, the molecular basis by which YeaG benefits N starvedE. coliremains elusive. By combining transcriptomics with targeted metabolomics analyses, we demonstrate that the methionine biosynthesis pathway becomes transcriptionally dysregulated inΔyeaGbacteria experiencing sustained N starvation. This results in the aberrant and energetically costly biosynthesis of methionine and associated metabolites under sustained N starvation with detrimental consequences to cell viability. It appears the activity of the master transcriptional repressor of methionine biosynthesis genes, MetJ, is compromised inΔyeaGbacteria under sustained N starvation, resulting in transcriptional derepression of MetJ-regulated genes. The results suggest that YeaG is a novel regulatory factor and functions as a molecular brake in the transcriptional control of both the NtrC-regulon and methionine biosynthesis genes inE. coliexperiencing sustained N starvation.

scholarly journals DNA Microarray Analyses of the Long-Term Adaptive Response of Escherichia coli to Acetate and Propionate

2003 ◽  
Vol 69 (3) ◽  
pp. 1759-1774 ◽  
Author(s):  
T. Polen ◽  
D. Rittmann ◽  
V. F. Wendisch ◽  
H. Sahm
Keyword(s):  
Escherichia Coli ◽  
Dna Microarray ◽  
Adaptive Response ◽  
Carbon Sources ◽  
Short Chain Fatty Acids ◽  
Adaptive Responses ◽  
General Stress Response ◽  
E Coli ◽  
Short Term Exposure

ABSTRACT In its natural environment, Escherichia coli is exposed to short-chain fatty acids, such as acetic acid or propionic acid, which can be utilized as carbon sources but which inhibit growth at higher concentrations. DNA microarray experiments revealed expression changes during exponential growth on complex medium due to the presence of sodium acetate or sodium propionate at a neutral external pH. The adaptive responses to acetate and propionate were similar and involved genes in three categories. First, the RNA levels for chemotaxis and flagellum genes increased. Accordingly, the expression of chromosomal fliC′-′lacZ and flhDC′-′lacZ fusions and swimming motility increased after adaptation to acetate or propionate. Second, the expression of many genes that are involved in the uptake and utilization of carbon sources decreased, indicating some kind of catabolite repression by acetate and propionate. Third, the expression of some genes of the general stress response increased, but the increases were more pronounced after short-term exposure for this response than for the adaptive response. Adaptation to propionate but not to acetate involved increased expression of threonine and isoleucine biosynthetic genes. The gene expression changes after adaptation to acetate or propionate were not caused solely by uncoupling or osmotic effects but represented specific characteristics of the long-term response of E. coli to either compound.

scholarly journals The adaptive response to long-term nitrogen starvation in Escherichia coli requires the breakdown of allantoin

2020 ◽  
Author(s):  
Amy Switzer ◽  
Lynn Burchell ◽  
Josh McQuail ◽  
Sivaramesh Wigneshweraraj
Keyword(s):  
Escherichia Coli ◽  
Cell Function ◽  
Nitrogen Starvation ◽  
Nutrient Starvation ◽  
Continuous Growth ◽  
E Coli ◽  
Transcriptional Changes ◽  
N Starvation ◽  
Over Time

ABSTRACTBacteria initially respond to nutrient starvation by eliciting large-scale transcriptional changes. The accompanying changes in gene expression and metabolism allow the bacterial cells to effectively adapt to the nutrient starved state. How the transcriptome subsequently changes as nutrient starvation ensues is not well understood. We used nitrogen (N) starvation as a model nutrient starvation condition to study the transcriptional changes in Escherichia coli experiencing long-term N starvation. The results reveal that the transcriptome of N starved E. coli undergoes changes that are required to maximise chances of viability and to effectively recover growth when N starvation conditions become alleviated. We further reveal that, over time, N starved E. coli cells rely on the degradation of allantoin for optimal growth recovery when N becomes replenished. This study provides insights into the temporally coordinated adaptive responses that occur in E. coli experiencing sustained N starvation.IMPORTANCEBacteria in their natural environments seldom encounter conditions that support continuous growth. Hence, many bacteria spend the majority of their time in states of little or no growth due to starvation of essential nutrients. To cope with prolonged periods of nutrient starvation, bacteria have evolved several strategies, primarily manifesting themselves through changes in how the information in their genes is accessed. How these coping strategies change over time under nutrient starvation is not well understood and this knowledge is not only important to broaden our understanding of bacterial cell function, but also to potentially find ways to manage harmful bacteria. This study provides insights into how nitrogen starved Escherichia coli bacteria rely on different genes during long term nitrogen starvation.

scholarly journals The RNA-binding protein Hfq assembles into foci-like structures in nitrogen starved Escherichia coli

2020 ◽  
Vol 295 (35) ◽  
pp. 12355-12367
Author(s):  
Josh McQuail ◽  
Amy Switzer ◽  
Lynn Burchell ◽  
Sivaramesh Wigneshweraraj
Keyword(s):  
Gene Expression ◽  
Escherichia Coli ◽  
Adaptive Response ◽  
Rna Binding ◽  
Nitrogen Starvation ◽  
Binding Protein ◽  
Regulatory Protein ◽  
Rna Binding Protein ◽  
E Coli

The initial adaptive responses to nutrient depletion in bacteria often occur at the level of gene expression. Hfq is an RNA-binding protein present in diverse bacterial lineages that contributes to many different aspects of RNA metabolism during gene expression. Using photoactivated localization microscopy and single-molecule tracking, we demonstrate that Hfq forms a distinct and reversible focus-like structure in Escherichia coli specifically experiencing long-term nitrogen starvation. Using the ability of T7 phage to replicate in nitrogen-starved bacteria as a biological probe of E. coli cell function during nitrogen starvation, we demonstrate that Hfq foci have a role in the adaptive response of E. coli to long-term nitrogen starvation. We further show that Hfq foci formation does not depend on gene expression once nitrogen starvation has set in and occurs indepen-dently of the transcription factor N-regulatory protein C, which activates the initial adaptive response to N starvation in E. coli. These results serve as a paradigm to demonstrate that bacterial adaptation to long-term nutrient starvation can be spatiotemporally coordinated and can occur independently of de novo gene expression during starvation.

scholarly journals The Adaptive Response to Long-Term Nitrogen Starvation in Escherichia coli Requires the Breakdown of Allantoin

2020 ◽  
Vol 202 (17) ◽  
Author(s):  
Amy Switzer ◽  
Lynn Burchell ◽  
Josh McQuail ◽  
Sivaramesh Wigneshweraraj
Keyword(s):  
Escherichia Coli ◽  
Nitrogen Starvation ◽  
Nutrient Starvation ◽  
Continuous Growth ◽  
Content Type ◽  
E Coli ◽  
Transcriptional Changes ◽  
N Starvation ◽  
Over Time

ABSTRACT Bacteria initially respond to nutrient starvation by eliciting large-scale transcriptional changes. The accompanying changes in gene expression and metabolism allow the bacterial cells to effectively adapt to the nutrient-starved state. How the transcriptome subsequently changes as nutrient starvation ensues is not well understood. We used nitrogen (N) starvation as a model nutrient starvation condition to study the transcriptional changes in Escherichia coli experiencing long-term N starvation. The results reveal that the transcriptome of N-starved E. coli undergoes changes that are required to maximize chances of viability and to effectively recover growth when N starvation conditions become alleviated. We further reveal that, over time, N-starved E. coli cells rely on the degradation of allantoin for optimal growth recovery when N becomes replenished. This study provides insights into the temporally coordinated adaptive responses that occur in E. coli experiencing sustained N starvation. IMPORTANCE Bacteria in their natural environments seldom encounter conditions that support continuous growth. Hence, many bacteria spend the majority of their time in states of little or no growth due to starvation of essential nutrients. To cope with prolonged periods of nutrient starvation, bacteria have evolved several strategies, primarily manifesting themselves through changes in how the information in their genes is accessed. How these coping strategies change over time under nutrient starvation is not well understood, and this knowledge is important not only to broaden our understanding of bacterial cell function but also to potentially find ways to manage harmful bacteria. This study provides insights into how nitrogen-starved Escherichia coli bacteria rely on different genes during long-term nitrogen starvation.

scholarly journals The assembly of Hfq into foci-like structures in response to long-term nitrogen starvation in Escherichia coli

2020 ◽  
Author(s):  
Josh McQuail ◽  
Amy Switzer ◽  
Lynn Burchell ◽  
Sivaramesh Wigneshweraraj
Keyword(s):  
Gene Expression ◽  
Escherichia Coli ◽  
Adaptive Response ◽  
Rna Binding ◽  
Cell Function ◽  
Rna Binding Protein ◽  
Rna Metabolism ◽  
E Coli ◽  
N Starvation

AbstractThe initial adaptive responses to nutrient depletion in bacteria often occur at the level of RNA metabolism. Hfq is an RNA-binding protein present in diverse bacterial lineages and contributes to many different aspects of RNA metabolism. We demonstrate that Hfq forms a distinct and reversible focus-like structure in E. coli specifically experiencing long-term nitrogen (N) starvation. Using the ability of T7 phage to replicate in N starved bacteria as a biological probe of E. coli cell function during N starvation, we demonstrate that Hfq foci have a role in the adaptive response to long-term N starvation. We further show that Hfq foci formation does not depend on gene expression during N starvation and occurs independently of the N regulatory protein C (NtrC) activated initial adaptive response to N starvation. The results serve as a paradigm to demonstrate that bacterial adaptation to long-term nutrient starvation can be spatiotemporally coordinated and can occur independently of de novo gene expression during starvation.Significance StatementBacteria have evolved complex strategies to cope with conditions of nitrogen (N) adversity. We now reveal a role for a widely studied RNA binding protein, Hfq, in the processes involved in how Escherichia coli copes with N starvation. We demonstrate that Hfq forms a distinct and reversible focus-like structure in long-term N starved E. coli. We provide evidence to suggest that the Hfq foci are important features required for adjusting E. coli cell function during N starvation for optimal adaptation to long-term N starvation. The results have broad implications for our understanding of bacterial adaptive processes in response to stress.

scholarly journals Iron Acquisition of Urinary Tract Infection Escherichia coli Involves Pathogenicity in Caenorhabditis elegans

2021 ◽  
Vol 9 (2) ◽  
pp. 310
Author(s):  
Masayuki Hashimoto ◽  
Yi-Fen Ma ◽  
Sin-Tian Wang ◽  
Chang-Shi Chen ◽  
Ching-Hao Teng
Keyword(s):  
Escherichia Coli ◽  
Urinary Tract ◽  
Caenorhabditis Elegans ◽  
Large Scale ◽  
Iron Acquisition ◽  
Infection Model ◽  
High Throughput Analysis ◽  
E Coli ◽  
C Elegans ◽  
Tract Infections

Uropathogenic Escherichia coli (UPEC) is a major bacterial pathogen that causes urinary tract infections (UTIs). The mouse is an available UTI model for studying the pathogenicity; however, Caenorhabditis elegans represents as an alternative surrogate host with the capacity for high-throughput analysis. Then, we established a simple assay for a UPEC infection model with C. elegans for large-scale screening. A total of 133 clinically isolated E. coli strains, which included UTI-associated and fecal isolates, were applied to demonstrate the simple pathogenicity assay. From the screening, several virulence factors (VFs) involved with iron acquisition (chuA, fyuA, and irp2) were significantly associated with high pathogenicity. We then evaluated whether the VFs in UPEC were involved in the pathogenicity. Mutants of E. coli UTI89 with defective iron acquisition systems were applied to a solid killing assay with C. elegans. As a result, the survival rate of C. elegans fed with the mutants significantly increased compared to when fed with the parent strain. The results demonstrated, the simple assay with C. elegans was useful as a UPEC infectious model. To our knowledge, this is the first report of the involvement of iron acquisition in the pathogenicity of UPEC in a C. elegans model.

scholarly journals Purification and separation of holo- and apo-forms of Saccharopolyspora erythraea acyl-carrier protein released from recombinant Escherichia coli by freezing and thawing

1993 ◽  
Vol 294 (2) ◽  
pp. 521-527 ◽  
Author(s):  
S A Morris ◽  
W P Revill ◽  
J Staunton ◽  
P F Leadlay
Keyword(s):  
Escherichia Coli ◽  
Large Scale ◽  
Acyl Carrier Protein ◽  
Saccharopolyspora Erythraea ◽  
Carrier Protein ◽  
Freezing And Thawing ◽  
Acyl Carrier Proteins ◽  
Expression Plasmid ◽  
E Coli ◽  
Protein Dimer

Saccharopolyspora erythraea acyl-carrier protein, highly expressed from a T7-based expression plasmid in Escherichia coli, can be selectively released from the cells in near-quantitative yield by a single cycle of freezing and thawing in a neutral buffer. Electrospray mass spectrometry was used to confirm that the recombinant S. erythraea acyl-carrier protein over-expressed in E. coli is present predominantly as the holo-form, with variable amounts of apo-acyl-carrier protein, holo-acyl-carrier protein dimer and holo-acyl-carrier protein glutathione adduct. The holo- and apo-acyl-carrier proteins are both readily purified on a large scale from the freeze-thaw extracts and can be separated from one another by octyl-Sepharose chromatography. The holo-acyl-carrier protein obtained in this way was fully active in supporting the synthesis of acyl-acyl-carrier protein by extracts of S. erythraea.

scholarly journals Extraintestinal Escherichia coli Carrying Virulence Genes in Coastal Marine Sediments

2010 ◽  
Vol 76 (17) ◽  
pp. 5659-5668 ◽  
Author(s):  
G. M. Luna ◽  
C. Vignaroli ◽  
C. Rinaldi ◽  
A. Pusceddu ◽  
L. Nicoletti ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Marine Sediments ◽  
Large Scale ◽  
Microbiological Quality ◽  
Genotypic Diversity ◽  
Coastal Sediments ◽  
Fecal Coliforms ◽  
Biochemical Tests ◽  
Term Survival ◽  
E Coli

ABSTRACT Despite the recognized potential of long-term survival or even growth of fecal indicators bacteria (FIB) in marine sediments, this compartment is largely ignored by health protection authorities. We conducted a large-scale study over approximately 50 km of the Marche coasts (Adriatic Sea) at depths ranging from 2 to 5 m. Total and fecal coliforms (FC) were counted by culture-based methods. Escherichia coli was also quantified using fluorescence in situ hybridization targeting specific 16S rRNA sequences, which yielded significantly higher abundances than culture-based methods, suggesting the potential importance of viable but nonculturable E. coli cells. Fecal coliforms displayed high abundances at most sites and showed a prevalence of E. coli. FC isolates (n = 113) were identified by API 20E, additional biochemical tests, and internal transcribed spacer-PCR. E. coli strains, representing 96% of isolates, were then characterized for genomic relatedness and phylogenetic group (A, B1, B2, and D) of origin by randomly amplified polymorphic DNA and multiplex-PCR. The results indicated that E. coli displayed a wide genotypic diversity, also among isolates from the same station, and that 44 of the 109 E. coli isolates belonged to groups B2 and D. Further characterization of B2 and D isolates for the presence of 11 virulence factor genes (pap, sfa/foc, afa, eaeA, ibeA, traT, hlyA, stx 1, stx 2, aer, and fyuA) showed that 90% of B2 and 65% of D isolates were positive for at least one of these. Most of the variance of both E. coli abundance and assemblage composition (>62%) was explained by a combination of physical-chemical and trophic variables. These findings indicate that coastal sediments could represent a potential reservoir for commensal and pathogenic E. coli and that E. coli distribution in marine coastal sediments largely depends upon the physical and trophic status of the sediment. We conclude that future sampling designs aimed at monitoring the microbiological quality of marine coastal areas should not further neglect the analysis of the sediment and that monitoring of these environments can be improved by including molecular methods as a complement of culture-based techniques.

scholarly journals Stationary-Phase Regulation of RpoS Translation in Escherichia coli

2005 ◽  
Vol 187 (21) ◽  
pp. 7204-7213 ◽  
Author(s):  
Matthew Hirsch ◽  
Thomas Elliott
Keyword(s):  
Escherichia Coli ◽  
Stationary Phase ◽  
Osmotic Shock ◽  
Transcriptional Response ◽  
Enteric Bacteria ◽  
Protein Activity ◽  
E Coli ◽  
Phase Regulation ◽  
Shine Dalgarno Sequence ◽  
Necessary And Sufficient

ABSTRACT In enteric bacteria, adaptation to a number of different stresses is mediated by the RpoS protein, one of several sigma factors that collectively allow a tailored transcriptional response to environmental cues. Stress stimuli including low temperature, osmotic shock, nutrient limitation, and growth to stationary phase (SP) all result in a substantial increase in RpoS abundance and activity. The mechanism of regulation depends on the specific signal but may occur at the level of transcription, translation, protein activity, or targeted proteolysis. In both Escherichia coli and Salmonella enterica, SP induction of RpoS in rich medium is >30 fold and includes effects on both transcription and translation. Recently, we found that SP control of rpoS transcription in S. enterica involves repression of the major rpoS promoter during exponential phase by the global transcription factor Fis. Working primarily with E. coli, we now show that 24 nucleotides of the rpoS ribosome-binding site (RBS) are necessary and sufficient for a large part of the increase in rpoS translation as cells grow to SP. Genetic evidence points to an essential role for the leader nucleotides just upstream of the Shine-Dalgarno sequence but is conflicted on the question of whether sequence or structure is important. SP regulation of rpoS is conserved between E. coli and S. enterica. When combined with an fis mutation to block transcriptional effects, replacement of the rpoS RBS sequence by the lacZ RBS eliminates nearly all SP induction of RpoS.

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