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

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.

Download Full-text

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

Journal of Biological Chemistry ◽

10.1074/jbc.ra120.014107 ◽

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.

Download Full-text

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

10.1101/2020.03.30.016519 ◽

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.

Download Full-text

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

Applied and Environmental Microbiology ◽

10.1128/aem.69.3.1759-1774.2003 ◽

2003 ◽

Vol 69 (3) ◽

pp. 1759-1774 ◽

Cited By ~ 78

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.

Download Full-text

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

Biochemical Society Transactions ◽

10.1042/bst20180502 ◽

2018 ◽

Vol 46 (6) ◽

pp. 1721-1728 ◽

Cited By ~ 6

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.

Download Full-text

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

Journal of Bacteriology ◽

10.1128/jb.00172-20 ◽

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.

Download Full-text

Determinants of RNA recognition by the FinO domain of the Escherichia coli ProQ protein

Nucleic Acids Research ◽

10.1093/nar/gkaa497 ◽

2020 ◽

Cited By ~ 2

Author(s):

Ewa M Stein ◽

Joanna Kwiatkowska ◽

Maciej M Basczok ◽

Chandra M Gravel ◽

Katherine E Berry ◽

...

Keyword(s):

Gene Expression ◽

Escherichia Coli ◽

Small Rnas ◽

Rna Binding ◽

Rna Binding Proteins ◽

Regulation Of Gene Expression ◽

Rna Recognition ◽

Rna Molecules ◽

E Coli ◽

Rna Ligands

Abstract The regulation of gene expression by small RNAs in Escherichia coli depends on RNA binding proteins Hfq and ProQ, which bind mostly distinct RNA pools. To understand how ProQ discriminates between RNA substrates, we compared its binding to six different RNA molecules. Full-length ProQ bound all six RNAs similarly, while the isolated N-terminal FinO domain (NTD) of ProQ specifically recognized RNAs with Rho-independent terminators. Analysis of malM 3′-UTR mutants showed that tight RNA binding by the ProQ NTD required a terminator hairpin of at least 2 bp preceding an 3′ oligoU tail of at least four uridine residues. Substitution of an A-rich sequence on the 5′ side of the terminator to uridines strengthened the binding of several ProQ-specific RNAs to the Hfq protein, but not to the ProQ NTD. Substitution of the motif in the malM-3′ and cspE-3′ RNAs also conferred the ability to bind Hfq in E. coli cells, as measured using a three-hybrid assay. In summary, these data suggest that the ProQ NTD specifically recognizes 3′ intrinsic terminators of RNA substrates, and that the discrimination between RNA ligands by E. coli ProQ and Hfq depends both on positive determinants for binding to ProQ and negative determinants against binding to Hfq.

Download Full-text

The Interplay of RNA Binding Proteins, Oxidative Stress and Mitochondrial Dysfunction in ALS

Antioxidants ◽

10.3390/antiox10040552 ◽

2021 ◽

Vol 10 (4) ◽

pp. 552

Author(s):

Jasmine Harley ◽

Benjamin E. Clarke ◽

Rickie Patani

Keyword(s):

Oxidative Stress ◽

Gene Expression ◽

Mitochondrial Dysfunction ◽

Binding Proteins ◽

Rna Binding ◽

Rna Binding Proteins ◽

Binding Protein ◽

Rna Binding Protein ◽

Therapeutic Strategies ◽

Lateral Sclerosis

RNA binding proteins fulfil a wide number of roles in gene expression. Multiple mechanisms of RNA binding protein dysregulation have been implicated in the pathomechanisms of several neurodegenerative diseases including amyotrophic lateral sclerosis (ALS). Oxidative stress and mitochondrial dysfunction also play important roles in these diseases. In this review, we highlight the mechanistic interplay between RNA binding protein dysregulation, oxidative stress and mitochondrial dysfunction in ALS. We also discuss different potential therapeutic strategies targeting these pathways.

Download Full-text

RNA–Binding Protein HuD as a Versatile Factor in Neuronal and Non–Neuronal Systems

Biology ◽

10.3390/biology10050361 ◽

2021 ◽

Vol 10 (5) ◽

pp. 361

Author(s):

Myeongwoo Jung ◽

Eun-Kyung Lee

Keyword(s):

Gene Expression ◽

Neural Plasticity ◽

Molecular Mechanisms ◽

Neuronal Development ◽

Rna Binding ◽

Binding Protein ◽

Rna Binding Protein ◽

Novel Treatments ◽

Target Mrnas ◽

Neuronal Systems

HuD (also known as ELAVL4) is an RNA–binding protein belonging to the human antigen (Hu) family that regulates stability, translation, splicing, and adenylation of target mRNAs. Unlike ubiquitously distributed HuR, HuD is only expressed in certain types of tissues, mainly in neuronal systems. Numerous studies have shown that HuD plays essential roles in neuronal development, differentiation, neurogenesis, dendritic maturation, neural plasticity, and synaptic transmission by regulating the metabolism of target mRNAs. However, growing evidence suggests that HuD also functions as a pivotal regulator of gene expression in non–neuronal systems and its malfunction is implicated in disease pathogenesis. Comprehensive knowledge of HuD expression, abundance, molecular targets, and regulatory mechanisms will broaden our understanding of its role as a versatile regulator of gene expression, thus enabling novel treatments for diseases with aberrant HuD expression. This review focuses on recent advances investigating the emerging role of HuD, its molecular mechanisms of target gene regulation, and its disease relevance in both neuronal and non–neuronal systems.

Download Full-text