Long-term continuous adaptation of Escherichia coli to high succinate stress and transcriptome analysis of the tolerant strain

Microarray technology was used to study the cellular events that take place at the transcription level during short-term (physiological) and long-term (genetic) adaptation of the faecal indicator bacterium Escherichia coli K-12 to slow growth under limited nutrient supply. Short-term and long-term adaptation were assessed by comparing the mRNA levels isolated after 40 or 500 h of glucose-limited continuous culture at a dilution rate of 0.3 h−1 with those from batch culture with glucose excess. A large number of genes encoding periplasmic binding proteins were upregulated, indicating that the cells are prepared for high-affinity uptake of all types of carbon sources during glucose-limited growth in continuous culture. All the genes belonging to the maltose (mal/lamB) and galactose (mgl/gal) operons were upregulated. A similar transcription pattern was observed for long-term cultures except that the expression factors were lower than in the short-term adaptation. The patterns of upregulation were confirmed by real-time RT-PCR. A switch from a fully operational citric acid cycle to the PEP-glyoxylate cycle was clearly observed in cells grown in glucose-limited continuous culture when compared to batch-grown cells and this was confirmed by transcriptome analysis. This transcriptome analysis confirms and extends the observations from previous proteome and catabolome studies in the authors' laboratory.

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Faculty Opinions recommendation of Transcriptome analysis of all two-component regulatory system mutants of Escherichia coli K-12.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1010694.163059 ◽

2002 ◽

Author(s):

Stephen Busby

Keyword(s):

Escherichia Coli ◽

Transcriptome Analysis ◽

Regulatory System ◽

Two Component ◽

K 12

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Faculty Opinions recommendation of Genome evolution and adaptation in a long-term experiment with Escherichia coli.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1166598.749168 ◽

2009 ◽

Author(s):

Douglas Bartlett

Keyword(s):

Escherichia Coli ◽

Genome Evolution ◽

Term Experiment ◽

Long Term Experiment

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Long-Term Experimental Evolution in Escherichia coli. VI. Environmental Constraints on Adaptation and Divergence

Genetics ◽

10.1093/genetics/146.2.471 ◽

1997 ◽

Vol 146 (2) ◽

pp. 471-479 ◽

Cited By ~ 2

Author(s):

Michael Travisano

Keyword(s):

Escherichia Coli ◽

Genetic Variation ◽

Experimental Evolution ◽

Population Genetic ◽

Environmental Constraints ◽

Asymmetric Pattern ◽

Nutrient Environment ◽

Mean Fitness ◽

Population Genetic Variation

The effect of environment on adaptation and divergence was examined in two sets of populations of Escherichia coli selected for 1000 generations in either maltose- or glucose-limited media. Twelve replicate populations selected in maltose-limited medium improved in fitness in the selected environment, by an average of 22.5%. Statistically significant among-population genetic variation for fitness was observed during the course of the propagation, but this variation was small relative to the fitness improvement. Mean fitness in a novel nutrient environment, glucose-limited medium, improved to the same extent as in the selected environment, with no statistically significant among-population genetic variation. In contrast, 12 replicate populations previously selected for 1000 generations in glucose-limited medium showed no improvement, as a group, in fitness in maltose-limited medium and substantial genetic variation. This asymmetric pattern of correlated responses suggests that small changes in the environment can have profound effects on adaptation and divergence.

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Biofilm Lithography enables high-resolution cell patterning via optogenetic adhesin expression

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1720676115 ◽

2018 ◽

Vol 115 (14) ◽

pp. 3698-3703 ◽

Cited By ~ 25

Author(s):

Xiaofan Jin ◽

Ingmar H. Riedel-Kruse

Keyword(s):

Escherichia Coli ◽

Cell Patterning ◽

Biophysical Model ◽

Microbial Consortia ◽

Bacterial Biofilms ◽

Surface Pretreatment ◽

Resolution Cell ◽

Stimulation Of

Bacterial biofilms represent a promising opportunity for engineering of microbial communities. However, our ability to control spatial structure in biofilms remains limited. Here we engineerEscherichia coliwith a light-activated transcriptional promoter (pDawn) to optically regulate expression of an adhesin gene (Ag43). When illuminated with patterned blue light, long-term viable biofilms with spatial resolution down to 25 μm can be formed on a variety of substrates and inside enclosed culture chambers without the need for surface pretreatment. A biophysical model suggests that the patterning mechanism involves stimulation of transiently surface-adsorbed cells, lending evidence to a previously proposed role of adhesin expression during natural biofilm maturation. Overall, this tool—termed “Biofilm Lithography”—has distinct advantages over existing cell-depositing/patterning methods and provides the ability to grow structured biofilms, with applications toward an improved understanding of natural biofilm communities, as well as the engineering of living biomaterials and bottom–up approaches to microbial consortia design.

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Long-Term Experimental Evolution in Escherichia coli. IV. Targets of Selection and the Specificity of Adaptation

Genetics ◽

10.1093/genetics/143.1.15 ◽

1996 ◽

Vol 143 (1) ◽

pp. 15-26 ◽

Cited By ~ 23

Author(s):

Michael Travisano ◽

Richard E Lenski

Keyword(s):

Escherichia Coli ◽

Experimental Evolution ◽

Common Ancestor ◽

The Novel ◽

Physiological Mechanisms ◽

Outer Membranes ◽

Limiting Nutrient ◽

Novel Environments ◽

Uptake Mechanisms

Abstract This study investigates the physiological manifestation of adaptive evolutionary change in 12 replicate populations of Escherichia coli that were propagated for 2000 generations in a glucose-limited environment. Representative genotypes from each population were assayed for fitness relative to their common ancestor in the experimental glucose environment and in 11 novel single-nutrient environments. After 2000 generations, the 12 derived genotypes had diverged into at least six distinct phenotypic classes. The nutrients were classified into four groups based upon their uptake physiology. All 12 derived genotypes improved in fitness by similar amounts in the glucose environment, and this pattern of parallel fitness gains was also seen in those novel environments where the limiting nutrient shared uptake mechanisms with glucose. Fitness showed little or no consistent improvement, but much greater genetic variation, in novel environments where the limiting nutrient differed from glucose in its uptake mechanisms. This pattern of fitness variation in the novel nutrient environments suggests that the independently derived genotypes adapted to the glucose environment by similar, but not identical, changes in the physiological mechanisms for moving glucose across both the inner and outer membranes.

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Long-term effects of the proline-rich antimicrobial peptide Oncocin112 on the Escherichia coli translation machinery

Journal of Biological Chemistry ◽

10.1074/jbc.ra120.013587 ◽

2020 ◽

Vol 295 (38) ◽

pp. 13314-13325

Author(s):

Yanyu Zhu ◽

James C. Weisshaar ◽

Mainak Mustafi

Keyword(s):

Escherichia Coli ◽

Antimicrobial Peptides ◽

Binding Site ◽

Elongation Factor ◽

Microscopy Study ◽

Single Step ◽

Long Term Effects ◽

Bacterial Membranes

Proline-rich antimicrobial peptides (PrAMPs) are cationic antimicrobial peptides unusual for their ability to penetrate bacterial membranes and kill cells without causing membrane permeabilization. Structural studies show that many such PrAMPs bind deep in the peptide exit channel of the ribosome, near the peptidyl transfer center. Biochemical studies of the particular synthetic PrAMP oncocin112 (Onc112) suggest that on reaching the cytoplasm, the peptide occupies its binding site prior to the transition from initiation to the elongation phase of translation, thus blocking further initiation events. We present a superresolution fluorescence microscopy study of the long-term effects of Onc112 on ribosome, elongation factor-Tu (EF-Tu), and DNA spatial distributions and diffusive properties in intact Escherichia coli cells. The new data corroborate earlier mechanistic inferences from studies in vitro. Comparisons with the diffusive behavior induced by the ribosome-binding antibiotics chloramphenicol and kasugamycin show how the specific location of each agent's ribosomal binding site affects the long-term distribution of ribosomal species between 30S and 50S subunits versus 70S polysomes. Analysis of the single-step displacements from ribosome and EF-Tu diffusive trajectories before and after Onc112 treatment suggests that the act of codon testing of noncognate ternary complexes (TCs) at the ribosomal A-site enhances the dissociation rate of such TCs from their L7/L12 tethers. Testing and rejection of noncognate TCs on a sub-ms timescale is essential to enable incorporation of the rare cognate amino acids into the growing peptide chain at a rate of ∼20 aa/s.

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