Genome-wide mutational diversity inEscherichia colipopulation evolving in prolonged stationary-phase

AbstractProlonged stationary-phase is an approximation of natural environments presenting a range of stresses. Survival in prolonged stationary-phase requires alternative metabolic pathways for survival. This study describes the repertoire of mutations accumulating in starvingE. colipopulations in lysogeny broth. A wide range of mutations accumulate over the course of one month in stationary-phase. SNPs constitute 64% of all mutations. A majority of these mutations are non-synonymous and are located at conserved loci. There is an increase in genetic diversity in the evolving populations over time. Computer simulations of evolution in stationary phase suggest that the maximum frequency obtained by mutations in our experimental populations can not be explained by neutral drift. Moreover there is frequent genetic parallelism across populations suggesting that these mutations are under positive selection. Finally functional analysis of mutations suggests that regulatory mutations are frequent targets of selection.

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Genomewide Mutational Diversity in Escherichia coli Population Evolving in Prolonged Stationary Phase

mSphere ◽

10.1128/msphere.00059-17 ◽

2017 ◽

Vol 2 (3) ◽

Cited By ~ 13

Author(s):

Savita Chib ◽

Farhan Ali ◽

Aswin Sai Narain Seshasayee

Keyword(s):

Escherichia Coli ◽

Genetic Diversity ◽

Stationary Phase ◽

Phenotypic Diversity ◽

Model System ◽

Content Type ◽

Neutral Drift ◽

E Coli ◽

Evolution By Natural Selection ◽

Over Time

ABSTRACT Prolonged stationary phase in bacteria, contrary to its name, is highly dynamic, with extreme nutrient limitation as a predominant stress. Stationary-phase cultures adapt by rapidly selecting a mutation(s) that confers a growth advantage in stationary phase (GASP). The phenotypic diversity of starving E. coli populations has been studied in detail; however, only a few mutations that accumulate in prolonged stationary phase have been described. This study documented the spectrum of mutations appearing in Escherichia coli during 28 days of prolonged starvation. The genetic diversity of the population increases over time in stationary phase to an extent that cannot be explained by random, neutral drift. This suggests that prolonged stationary phase offers a great model system to study adaptive evolution by natural selection. Prolonged stationary phase is an approximation of natural environments presenting a range of stresses. Survival in prolonged stationary phase requires alternative metabolic pathways for survival. This study describes the repertoire of mutations accumulating in starving Escherichia coli populations in lysogeny broth. A wide range of mutations accumulates over the course of 1 month in stationary phase. Single nucleotide polymorphisms (SNPs) constitute 64% of all mutations. A majority of these mutations are nonsynonymous and are located at conserved loci. There is an increase in genetic diversity in the evolving populations over time. Computer simulations of evolution in stationary phase suggest that the maximum frequency of mutations observed in our experimental populations cannot be explained by neutral drift. Moreover, there is frequent genetic parallelism across populations, suggesting that these mutations are under positive selection. Finally, functional analysis of mutations suggests that regulatory mutations are frequent targets of selection. IMPORTANCE Prolonged stationary phase in bacteria, contrary to its name, is highly dynamic, with extreme nutrient limitation as a predominant stress. Stationary-phase cultures adapt by rapidly selecting a mutation(s) that confers a growth advantage in stationary phase (GASP). The phenotypic diversity of starving E. coli populations has been studied in detail; however, only a few mutations that accumulate in prolonged stationary phase have been described. This study documented the spectrum of mutations appearing in Escherichia coli during 28 days of prolonged starvation. The genetic diversity of the population increases over time in stationary phase to an extent that cannot be explained by random, neutral drift. This suggests that prolonged stationary phase offers a great model system to study adaptive evolution by natural selection.

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How drain flies manage to almost never get washed away

Scientific Reports ◽

10.1038/s41598-020-73583-2 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Nathan B. Speirs ◽

Gauri A. Mahadik ◽

Sigurdur T. Thoroddsen

Keyword(s):

Fluid Dynamics ◽

Behavioral Response ◽

Natural Environments ◽

Hierarchical Roughness ◽

Wide Range ◽

Over Time

Abstract Drain flies, Pshycoda spp. (Order Diptera, Family Psychodidae), commonly reside in our homes, annoying us in our bathrooms, kitchens, and laundry rooms. They like to stay near drains where they lay their eggs and feed on microorganisms and liquid carbohydrates found in the slime that builds up over time. Though they generally behave very sedately, they react quite quickly when threatened with water. A squirt from the sink induces them to fly away, seemingly unaffected, and flushing the toilet with flies inside does not necessarily whisk them down. We find that drain flies’ remarkable ability to evade such potentially lethal threats does not stem primarily from an evolved behavioral response, but rather from a unique hair covering with a hierarchical roughness. This covering, that has never been previously explored, imparts superhydrophobicity against large droplets and pools and antiwetting properties against micron-sized droplets and condensation. We examine how this hair covering equips them to take advantage of the relevant fluid dynamics and flee water threats in domestic and natural environments including: millimetric-sized droplets, mist, waves, and pools of water. Our findings elucidate drain flies’ astounding ability to cope with a wide range of water threats and almost never get washed down the drain.

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Transcriptome signature of E. coli under a prolonged starvation environment

10.1101/2020.05.11.085241 ◽

2020 ◽

Author(s):

Sotaro Takano ◽

Hiromi Takahashi ◽

Yoshie Yama ◽

Ryo Miyazaki ◽

Saburo Tsuru

Keyword(s):

Stationary Phase ◽

Molecular Mechanisms ◽

Expression Profiles ◽

Physiological State ◽

Exponential Growth Phase ◽

Transcriptional Responses ◽

E Coli ◽

Viable Cells ◽

Genome Wide

ABSTRACTBackground“Non-growing” is a dominant life form of microorganisms in nature, where available nutrients and resources are extremely limited. However, the knowledge of the manner in which microorganisms resist nutrient deficiency is still rudimentary compared to those of the growing cells. In laboratory culture, Escherichia coli can survive for several years under starvation, denoted as long-term stationary phase (LSP), where a small fraction of the cells survive by recycling resources released from the starved nonviable cells and constitute a model system for understanding survival mechanisms under long-term starvation. Although the physiology by which viable cells in LSP adapt to long-term starvation is of great interest, their genome-wide response has not yet been fully understood.ResultsTo understand the physiological state of viable cells in the LSP environment, we analyzed the transcriptional profiles of cells exposed to the supernatant of LSP culture. We found that high expression of transporter genes and low expression of biosynthesis genes are the primary responses of the cells in the LSP supernatant compared to growing cells, which display similar responses to cells entering the stationary phase from the exponential growth phase. We also revealed some specific transcriptional responses in the LSP supernatant, such as higher expression of stress-response genes and lower expression of translation-related genes, compared to other non-growing conditions. This suggests that cells in LSP are highly efficient in terms of cellular survival and maintenance functions under starvation conditions. We also found population-density-dependent gene expression profiles in LSP, which are also informative to understand the survival mechanism of bacterial population.ConclusionOur current comprehensive analysis of the transcriptome of E. coli cells provides an overview of the genome-wide response to the long-term starvation environment. We detected both common and distinctive responses in the primary transcriptional changes between the short- and long-term stationary phase cultures, which could provide clues to understand the possible molecular mechanisms underlying survivability in the starved environment.

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Roles of NhaA, NhaB, and NhaD Na+/H+ Antiporters in Survival of Vibrio cholerae in a Saline Environment

Journal of Bacteriology ◽

10.1128/jb.185.4.1236-1244.2003 ◽

2003 ◽

Vol 185 (4) ◽

pp. 1236-1244 ◽

Cited By ~ 53

Author(s):

Katia Herz ◽

Sophie Vimont ◽

Etana Padan ◽

Patrick Berche

Keyword(s):

Stationary Phase ◽

Vibrio Cholerae ◽

Ph Regulation ◽

Molecular System ◽

Specific Inhibitor ◽

Ion Pump ◽

Quinone Oxidoreductase ◽

Saline Environment ◽

E Coli ◽

Wide Range

ABSTRACT Vibrio cholerae, the causative agent of cholera, is a normal inhabitant of aquatic environments, where it survives in a wide range of conditions of pH and salinity. In this work, we investigated the role of three Na+/H+ antiporters on the survival of V. cholerae in a saline environment. We have previously cloned the Vc-nhaA gene encoding the V. cholerae homolog of Escherichia coli. Here we identified two additional antiporter genes, designated Vc-nhaB and Vc-nhaD, encoding two putative proteins of 530 and 477 residues, respectively, highly homologous to the respective antiporters of Vibrio species and E. coli. We showed that both Vc-NhaA and Vc-NhaB confer Na+ resistance and that Vc-NhaA displays an antiport activity in E. coli, which is similar in magnitude, kinetic parameters, and pH regulation to that of E. coli NhaA. To determine the roles of the Na+/H+ antiporters in V. cholerae, we constructed nhaA, nhaB, and nhaD mutants (single, double, and triple mutants). In contrast to E. coli, the inactivation of the three putative antiporter genes (Vc-nhaABD) in V. cholerae did not alter the bacterial exponential growth in the presence of high Na+ concentrations and had only a slight effect in the stationary phase. In contrast, a pronounced and similar Li+-sensitive phenotype was found with all mutants lacking Vc-nhaA during the exponential phase of growth and also with the triple mutant in the stationary phase of growth. By using 2-n-nonyl-4-hydroxyquinoline N-oxide, a specific inhibitor of the electron-transport-linked Na+ pump NADH-quinone oxidoreductase (NQR), we determined that in the absence of NQR activity, the Vc-NhaA Na+/H+ antiporter activity becomes essential for the resistance of V. cholerae to Na+ at alkaline pH. Since the ion pump NQR is Na+ specific, we suggest that its activity masks the Na+/H+ but not the Li+/H+ antiporter activities. Our results indicate that the Na+ resistance of the human pathogen V. cholerae requires a complex molecular system involving multiple antiporters and the NQR pump.

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Molecular determinants of surface colonisation in diarrhoeagenic Escherichia coli (DEC): from bacterial adhesion to biofilm formation

FEMS Microbiology Reviews ◽

10.1093/femsre/fuaa008 ◽

2020 ◽

Vol 44 (3) ◽

pp. 314-350 ◽

Cited By ~ 2

Author(s):

Valentin Ageorges ◽

Ricardo Monteiro ◽

Sabine Leroy ◽

Catherine M Burgess ◽

Mariagrazia Pizza ◽

...

Keyword(s):

Escherichia Coli ◽

Human Infection ◽

Point Of View ◽

Surface Proteins ◽

Extracellular Dna ◽

Extracellular Polysaccharides ◽

Natural Environments ◽

E Coli ◽

Wide Range ◽

Molecular Determinants

ABSTRACT Escherichia coli is primarily known as a commensal colonising the gastrointestinal tract of infants very early in life but some strains being responsible for diarrhoea, which can be especially severe in young children. Intestinal pathogenic E. coli include six pathotypes of diarrhoeagenic E. coli (DEC), namely, the (i) enterotoxigenic E. coli, (ii) enteroaggregative E. coli, (iii) enteropathogenic E. coli, (iv) enterohemorragic E. coli, (v) enteroinvasive E. coli and (vi) diffusely adherent E. coli. Prior to human infection, DEC can be found in natural environments, animal reservoirs, food processing environments and contaminated food matrices. From an ecophysiological point of view, DEC thus deal with very different biotopes and biocoenoses all along the food chain. In this context, this review focuses on the wide range of surface molecular determinants acting as surface colonisation factors (SCFs) in DEC. In the first instance, SCFs can be broadly discriminated into (i) extracellular polysaccharides, (ii) extracellular DNA and (iii) surface proteins. Surface proteins constitute the most diverse group of SCFs broadly discriminated into (i) monomeric SCFs, such as autotransporter (AT) adhesins, inverted ATs, heat-resistant agglutinins or some moonlighting proteins, (ii) oligomeric SCFs, namely, the trimeric ATs and (iii) supramolecular SCFs, including flagella and numerous pili, e.g. the injectisome, type 4 pili, curli chaperone-usher pili or conjugative pili. This review also details the gene regulatory network of these numerous SCFs at the various stages as it occurs from pre-transcriptional to post-translocational levels, which remains to be fully elucidated in many cases.

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Differential Bacteriophage Mortality on Exposure to Copper

Applied and Environmental Microbiology ◽

10.1128/aem.05661-11 ◽

2011 ◽

Vol 77 (19) ◽

pp. 6878-6883 ◽

Cited By ~ 17

Author(s):

Jinyu Li ◽

John J. Dennehy

Keyword(s):

Microbial Growth ◽

Copper Toxicity ◽

Final Concentration ◽

Lysogeny Broth ◽

Bacterial Host ◽

Double Stranded Rna ◽

Wide Range ◽

Effect Of Copper ◽

Over Time ◽

Significant Mortality

ABSTRACTMany studies report that copper can be used to control microbial growth, including that of viruses. We determined the rates of copper-mediated inactivation for a wide range of bacteriophages. We used two methods to test the effect of copper on bacteriophage survival. One method involved placing small volumes of bacteriophage lysate on copper and stainless steel coupons. Following exposure, metal coupons were rinsed with lysogeny broth, and the resulting fluid was serially diluted and plated on agar with the corresponding bacterial host. The second method involved adding copper sulfate (CuSO4) to bacteriophage lysates to a final concentration of 5 mM. Aliquots were removed from the mixture, serially diluted, and plated with the appropriate bacterial host. Significant mortality was observed among the double-stranded RNA (dsRNA) bacteriophages Φ6 and Φ8, the single-stranded RNA (ssRNA) bacteriophage PP7, the ssDNA bacteriophage ΦX174, and the dsDNA bacteriophage PM2. However, the dsDNA bacteriophages PRD1, T4, and λ were relatively unaffected by copper. Interestingly, lipid-containing bacteriophages were most susceptible to copper toxicity. In addition, in the first experimental method, the pattern of bacteriophage Φ6 survival over time showed a plateau in mortality after lysates dried out. This finding suggests that copper's effect on bacteriophage is mediated by the presence of water.

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Functional principal component based time-series genome-wide association in sorghum

10.1101/2020.02.16.951467 ◽

2020 ◽

Cited By ~ 1

Author(s):

Chenyong Miao ◽

Yuhang Xu ◽

Sanzhen Liu ◽

Patrick S. Schnable ◽

James C. Schnable

Keyword(s):

Time Series ◽

Principal Component ◽

Functional Principal Component Analysis ◽

Genome Wide Association ◽

Phenotypic Change ◽

Genome Wide Association Studies ◽

Functional Principal Component ◽

Genome Wide ◽

Wide Range ◽

Over Time

ABSTRACTThe phenotypes of plants develop over time and change in response to the environment. New engineering and computer vision technologies track phenotypic change over time. Identifying genetic loci regulating differences in the pattern of phenotypic change remains challenging. In this study we used functional principal component analysis (FPCA) to achieve this aim. Time-series phenotype data was collected from a sorghum diversity panel using a number of technologies including RGB and hyperspectral imaging. Imaging lasted for thirty-seven days centered on reproductive transition. A new higher density SNP set was generated for the same population. Several genes known to controlling trait variation in sorghum have been cloned and characterized. These genes were not confidently identified in genome-wide association analyses at single time points. However, FPCA successfully identified the same known and characterized genes. FPCA analyses partitioned the role these genes play in controlling phenotype. Partitioning was consistent with the known molecular function of the individual cloned genes. FPCA-based genome-wide association studies can enable robust time-series mapping analyses in a wide range of contexts. Time-series analysis can increase the accuracy and power of quantitative genetic analyses.

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The E. coli molecular phenotype under different growth conditions

10.1101/082032 ◽

2016 ◽

Author(s):

Mehmet U. Caglar ◽

John R. Houser ◽

Craig S. Barnhart ◽

Daniel R. Boutz ◽

Sean M. Carroll ◽

...

Keyword(s):

Stationary Phase ◽

Carbon Sources ◽

Growth Conditions ◽

Central Carbon Metabolism ◽

Growth Media ◽

Data Set ◽

E Coli ◽

Wide Range ◽

Time Courses

AbstractModern systems biology requires extensive, carefully curated measurements of cellular components in response to different environmental conditions. While high-throughput methods have made transcriptomics and proteomics datasets widely accessible and relatively economical to generate, systematic measurements of both mRNA and protein abundances under a wide range of different conditions are still relatively rare. Here we present a detailed, genome-wide transcriptomics and proteomics dataset of E. coli grown under 34 different conditions. Additionally, we provide measurements of doubling times and in-vivo metabolic fluxes through the central carbon metabolism. We manipulate concentrations of sodium and magnesium in the growth media, and we consider four different carbon sources glucose, gluconate, lactate, and glycerol. Moreover, samples are taken both in exponential and stationary phase, and we include two extensive time-courses, with multiple samples taken between 3 hours and 2 weeks. We find that exponential-phase samples systematically differ from stationary-phase samples, in particular at the level of mRNA. Regulatory responses to different carbon sources or salt stresses are more moderate, but we find numerous differentially expressed genes for growth on gluconate and under salt and magnesium stress. Our data set provides a rich resource for future computational modeling of E. coli gene regulation, transcription, and translation.

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A Review of the Taxonomy, Genetics and Biology of the Genus Escherichia and the Type Species Escherichia coli

Canadian Journal of Microbiology ◽

10.1139/cjm-2020-0508 ◽

2021 ◽

Author(s):

Daniel Yu ◽

Graham Banting ◽

Norman Neumann

Keyword(s):

Escherichia Coli ◽

Genetic Diversity ◽

Natural Waters ◽

Distinct Species ◽

Taxonomic Classification ◽

Natural Environments ◽

Microbial World ◽

E Coli ◽

Wide Range

Historically, bacteriologists have relied heavily on biochemical and structural phenotypes for bacterial taxonomic classification. However, advances in comparative genomics has led to greater insights into the remarkable genetic diversity within the microbial world, and even within well-accepted species such as Escherichia coli. The extraordinary genetic diversity in E. coli recapitulates the evolutionary radiation of this species in exploiting a wide range of niches (i.e., ecotypes), including the gastrointestinal system of diverse vertebrate hosts as well as non-host natural environments (soil, natural waters, wastewater), which drives the adaptation, natural selection and evolution of intragenotypic conspecific specialism as a strategy for survival. Over the last several years, a growing body of evidence suggests that many E. coli strains appear to be very host (or niche)-specific. While biochemical and phylogenetic evidence support the classification of E. coli as a distinct species, the vast genomic (diverse pan-genome and intragenotypic variability), phenotypic (e.g., metabolic pathways), and ecotypic (host-/niche-specificity) diversity, comparable to the diversity observed in known species complexes, suggests that E. coli is better represented as a complex. Herein we review the taxonomic classification of the genus Escherichia and discuss how phenotype, genotype and ecotype recapitulate our understanding of the biology of this remarkable bacterium.

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Small Molecule Permeation Across Membrane Channels: Chemical Modification to Quantify Transport Across OmpF

10.26434/chemrxiv.7040354.v1 ◽

2018 ◽

Author(s):

Jiajun Wang ◽

Jayesh Arun Bafna ◽

Satya Prathyusha Bhamidimarri ◽

Mathias Winterhalter

Keyword(s):

Dwell Time ◽

Covalent Binding ◽

Channel Structure ◽

Ion Current ◽

E Coli ◽

Current Fluctuation ◽

Wide Range ◽

Outer Membrane Channel ◽

Biological Channels ◽

Constriction Region

Biological channels facilitate the exchange of small molecules across membranes, but surprisingly there is a lack of general tools for the identification and quantification of transport (i.e., translocation and binding). Analyzing the ion current fluctuation of a typical channel with its constriction region in the middle does not allow a direct conclusion on successful transport. For this, we created an additional barrier acting as a molecular counter at the exit of the channel. To identify permeation, we mainly read the molecule residence time in the channel lumen as the indicator whether the molecule reached the exit of the channel. As an example, here we use the well-studied porin, OmpF, an outer membrane channel from E. coli. Inspection of the channel structure suggests that aspartic acid at position 181 is located below the constriction region (CR) and we subsequently mutated this residue to cysteine, where else cysteine free and functionalized it by covalent binding with 2-sulfonatoethyl methanethiosulfonate (MTSES) or the larger glutathione (GLT) blockers. Using the dwell time as the signal for transport, we found that both mono-arginine and tri-arginine permeation process is prolonged by 20% and 50% respectively through OmpFE181CMTSES, while the larger sized blocker modification OmpFE181CGLT drastically decreased the permeation of mono-arginine by 9-fold and even blocked the pathway of the tri-arginine. In case of the hepta-arginine as substrate, both chemical modifications led to an identical ‘blocked’ pattern observed by the dwell time of ion current fluctuation of the OmpFwt. As an instance for antibiotic permeation, we analyzed norfloxacin, a fluoroquinolone antimicrobial agent. The modulation of the interaction dwell time suggests possible successful permeation of norfloxacin across OmpFwt. This approach may discriminate blockages from translocation events for a wide range of substrates. A potential application could be screening for scaffolds to improve the permeability of antibiotics.

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