scholarly journals Functional Genomics: Expression Analysis ofEscherichia coli Growing on Minimal and Rich Media

1999 ◽  
Vol 181 (20) ◽  
pp. 6425-6440 ◽  
Author(s):  
Han Tao ◽  
Christoph Bausch ◽  
Craig Richmond ◽  
Frederick R. Blattner ◽  
Tyrrell Conway
Keyword(s):  
Minimal Medium ◽  
Building Blocks ◽  
Acetate Metabolism ◽  
Logarithmic Phase ◽  
Cell Physiology ◽  
Glucose Medium ◽  
Rich Medium ◽  
Genomic Expression ◽  
E Coli ◽  
Minimal Glucose Medium

ABSTRACT DNA arrays of the entire set of Escherichia coli genes were used to measure the genomic expression patterns of cells growing in late logarithmic phase on minimal glucose medium and on Luria broth containing glucose. Ratios of the transcript levels for all 4,290E. coli protein-encoding genes (cds) were obtained, and analysis of the expression ratio data indicated that the physiological state of the cells under the two growth conditions could be ascertained. The cells in the rich medium grew faster, and expression of the majority of the translation apparatus genes was significantly elevated under this growth condition, consistent with known patterns of growth rate-dependent regulation and increased rate of protein synthesis in rapidly growing cells. The cells grown on minimal medium showed significantly elevated expression of many genes involved in biosynthesis of building blocks, most notably the amino acid biosynthetic pathways. Nearly half of the known RpoS-dependent genes were expressed at significantly higher levels in minimal medium than in rich medium, and rpoS expression was similarly elevated. The role of RpoS regulation in these logarithmic phase cells was suggested by the functions of the RpoS dependent genes that were induced. The hallmark features of E. coli cells growing on glucose minimal medium appeared to be the formation and excretion of acetate, metabolism of the acetate, and protection of the cells from acid stress. A hypothesis invoking RpoS and UspA (universal stress protein, also significantly elevated in minimal glucose medium) as playing a role in coordinating these various aspects and consequences of glucose and acetate metabolism was generated. This experiment demonstrates that genomic expression assays can be applied in a meaningful way to the study of whole-bacterial-cell physiology for the generation of hypotheses and as a guide for more detailed studies of particular genes of interest.

scholarly journals Genomic and phenotypic evolution of Escherichia coli in a novel citrate-only resource environment

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Zachary D Blount ◽  
Rohan Maddamsetti ◽  
Nkrumah A Grant ◽  
Sumaya T Ahmed ◽  
Tanush Jagdish ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Cell Death ◽  
Transposable Elements ◽  
Ecological Niches ◽  
Phenotypic Evolution ◽  
Glucose Medium ◽  
Aerobic Growth ◽  
E Coli ◽  
Resource Environment ◽  
Minimal Glucose Medium

Evolutionary innovations allow populations to colonize new ecological niches. We previously reported that aerobic growth on citrate (Cit+) evolved in an Escherichia coli population during adaptation to a minimal glucose medium containing citrate (DM25). Cit+ variants can also grow in citrate-only medium (DM0), a novel environment for E. coli. To study adaptation to this niche, we founded two sets of Cit+ populations and evolved them for 2500 generations in DM0 or DM25. The evolved lineages acquired numerous parallel mutations, many mediated by transposable elements. Several also evolved amplifications of regions containing the maeA gene. Unexpectedly, some evolved populations and clones show apparent declines in fitness. We also found evidence of substantial cell death in Cit+ clones. Our results thus demonstrate rapid trait refinement and adaptation to the new citrate niche, while also suggesting a recalcitrant mismatch between E. coli physiology and growth on citrate.

scholarly journals One of Two OsmC Homologs in Bacillus subtilis Is Part of the ςB-Dependent General Stress Regulon

1998 ◽  
Vol 180 (16) ◽  
pp. 4212-4218 ◽  
Author(s):  
Uwe Völker ◽  
Kasper Krogh Andersen ◽  
Haike Antelmann ◽  
Kevin M. Devine ◽  
Michael Hecker
Keyword(s):  
Escherichia Coli ◽  
Bacillus Subtilis ◽  
Stationary Phase ◽  
Expression Pattern ◽  
Sigma Factor ◽  
Minimal Medium ◽  
Alternative Sigma Factor ◽  
Rich Medium ◽  
E Coli ◽  
Complex Expression

ABSTRACT In this report we present the identification and analysis of twoBacillus subtilis genes, yklA andykzA, which are homologous to the partially RpoS-controlledosmC gene from Escherichia coli. TheyklA gene is expressed at higher levels in minimal medium than in rich medium and is driven by a putative vegetative promoter. Expression of ykzA is not medium dependent but increases dramatically when cells are exposed to stress and starvation. This stress-induced increase in ykzA expression is absolutely dependent on the alternative sigma factor ςB, which controls a large stationary-phase and stress regulon. ykzAis therefore another example of a gene common to the RpoS and ςB stress regulons of E. coli andB. subtilis, respectively. The composite complex expression pattern of the two B. subtilis genes is very similar to the expression profile of osmC in E. coli.

scholarly journals Modification by an R determinant for streptomycin of hissd phenotype in a mutant strain of Escherichia coli B

1968 ◽  
Vol 12 (2) ◽  
pp. 109-116 ◽  
Author(s):  
A. M. Molina ◽  
L. Calegari ◽  
G. Conte
Keyword(s):  
Escherichia Coli ◽  
Cell Membrane ◽  
Mutant Strain ◽  
Minimal Medium ◽  
Specific Requirement ◽  
Resistance Level ◽  
E Coli ◽  
Level Characteristic ◽  
Escherichia Coli B

When an R determinant for streptomycin is transferred into a conditionally streptomycin-dependent E. coli B mutant—which requires in minimal medium either histidine or streptomycin—the latter behaves like a histidineless strain. This phenotype modification shows that the repairing action of streptomycin is prevented. The specific requirement of the strain is not now replaced even by streptomycin concentrations up to 10000 µg/ml at which the conditionally streptomycin-dependent mutant could originally grow, and which are well beyond the resistance level characteristic of the R determinant itself. These data seem to suggest that a reduction in permeability of the cell membrane cannot be held responsible for the phenomenon observed.

Effect of ascorbate on oxygen uptake and growth of Escherichia coli B

1988 ◽  
Vol 34 (6) ◽  
pp. 822-824 ◽  
Author(s):  
Holly E. Richter ◽  
Jacek Switala ◽  
Peter C. Loewen
Keyword(s):  
Escherichia Coli ◽  
Oxygen Uptake ◽  
Electron Acceptor ◽  
Minimal Medium ◽  
Anaerobic Growth ◽  
Rich Medium ◽  
Terminal Electron Acceptor ◽  
Subsequent Change ◽  
Escherichia Coli B

The addition of ascorbate to aerobically growing cultures of Escherichia coli B caused only a short pause in growth and no subsequent change in the rate or extent of growth. The effect of ascorbate on oxygen uptake varied from inhibition in minimal medium to stimulation in rich medium. Cyanide-resistant growth and oxygen uptake were stimulated by ascorbate. Both the rate and extent of anaerobic growth were stimulated in proportion to the amount of ascorbate added when fumarate was the terminal electron acceptor. Ascorbate had no effect on any aspect of anaerobic growth in the absence of a terminal electron acceptor or in the presence of nitrate.

scholarly journals The Essential Genome of Burkholderia cenocepacia H111

2017 ◽  
Vol 199 (22) ◽  
Author(s):  
Steven Higgins ◽  
Maria Sanchez-Contreras ◽  
Stefano Gualdi ◽  
Marta Pinto-Carbó ◽  
Aurélien Carlier ◽  
...  
Keyword(s):  
Minimal Medium ◽  
Essential Genes ◽  
Burkholderia Cenocepacia ◽  
Chromosome 1 ◽  
Biological Research ◽  
Chromosome 2 ◽  
Powerful Method ◽  
Rich Medium ◽  
Content Type ◽  
Autonomous Growth

ABSTRACT The study of the minimum set of genes required to sustain life is a fundamental question in biological research. Recent studies on bacterial essential genes suggested that between 350 and 700 genes are essential to support autonomous bacterial cell growth. Essential genes are of interest as potential new antimicrobial drug targets; hence, our aim was to identify the essential genome of the cystic fibrosis (CF) isolate Burkholderia cenocepacia H111. Using a transposon sequencing (Tn-Seq) approach, we identified essential genes required for growth in rich medium under aerobic and microoxic conditions as well as in a defined minimal medium with citrate as a sole carbon source. Our analysis suggests that 398 genes are required for autonomous growth in rich medium, a number that represents only around 5% of the predicted genes of this bacterium. Five hundred twenty-six genes were required to support growth in minimal medium, and 434 genes were essential under microoxic conditions (0.5% O2). A comparison of these data sets identified 339 genes that represent the minimal set of essential genes required for growth under all conditions tested and can be considered the core essential genome of B. cenocepacia H111. The majority of essential genes were found to be located on chromosome 1, and few such genes were located on chromosome 2, where most of them were clustered in one region. This gene cluster is fully conserved in all Burkholderia species but is present on chromosome 1 in members of the closely related genus Ralstonia, suggesting that the transfer of these essential genes to chromosome 2 in a common ancestor contributed toward the separation of the two genera. IMPORTANCE Transposon sequencing (Tn-Seq) is a powerful method used to identify genes that are essential for autonomous growth under various conditions. In this study, we have identified a set of “core essential genes” that are required for growth under multiple conditions, and these genes represent potential antimicrobial targets. We also identified genes specifically required for growth under low-oxygen and nutrient-limited environments. We generated conditional mutants to verify the results of our Tn-Seq analysis and demonstrate that one of the identified genes was not essential per se but was an artifact of the construction of the mutant library. We also present verified examples of genes that were not truly essential but, when inactivated, showed a growth defect. These examples have identified so-far-underestimated shortcomings of this powerful method.

Analysis of the Crushing Effect about Ultrasound on E. coli and B. subtilis

2012 ◽  
Vol 260-261 ◽  
pp. 1017-1021
Author(s):  
Xin Ying Wang ◽  
Yong Tao Liu ◽  
Min Hui ◽  
Ji Fei Xu
Keyword(s):  
Escherichia Coli ◽  
Cell Wall ◽  
Bacillus Subtilis ◽  
Bacterial Cell ◽  
Logarithmic Phase ◽  
Growth Stages ◽  
Bacterial Cells ◽  
E Coli ◽  
Different Growth Stages ◽  
Main Factor

Escherichia coli and Bacillus subtilis as objects of the study, ultrasonic fragmentation acted on the bacterial cells in different growth stages, results showed that, it’s similar to the crushing effect of ultrasound on E. coli and B. subtilis cells of different growth stages, the highest crushing rate in the logarithmic phase, reached to 95.8% and 94.3% respectively, the crushing rate of adjustment phase is lowest, maintained at around 60%, the crushing rate stability cell was centered, which can be achieved 90%. The structure of the bacterial cell wall didn’t the main factor to decide the ultrasonic fragmentation effect, but different growth periods of bacterial cells did the determinant.

scholarly journals Disruption of aldA Influences the Developmental Process in Myxococcus xanthus

2000 ◽  
Vol 182 (2) ◽  
pp. 546-550 ◽  
Author(s):  
Mandy J. Ward ◽  
Helen Lew ◽  
David R. Zusman
Keyword(s):  
Gene Disruption ◽  
Minimal Medium ◽  
Developmental Process ◽  
Myxococcus Xanthus ◽  
Protein Sequences ◽  
Rich Medium ◽  
Wild Type ◽  
Rate Of Growth ◽  
Alanine Dehydrogenase ◽  
Developmental Conditions

ABSTRACT Previously, we identified a gene (aldA) fromMyxococcus xanthus, which we suggested encoded the enzyme alanine dehydrogenase on the basis of similarity to known Ald protein sequences (M. J. Ward, H. Lew, A. Treuner-Lange, and D. R. Zusman, J. Bacteriol. 180:5668–5675, 1998). In this study, we have confirmed that aldA does encode a functional alanine dehydrogenase, since it catalyzes the reversible conversion of alanine to pyruvate and ammonia. Whereas an aldA gene disruption mutation did not significantly influence the rate of growth or spreading on a rich medium, AldA was required for growth on a minimal medium containing l-alanine as the major source of carbon. Under developmental conditions, the aldA mutation caused delayed aggregation in both wild-type (DZ2) and FB (DZF1) strains. Poorly formed aggregates and reduced levels of spores were apparent in the DZ2 aldA mutant, even after prolonged development.

scholarly journals Chemical synthesis of the pentasaccharide repeating unit of the O-specific polysaccharide from Escherichia coli O132 in the form of its 2-aminoethyl glycoside

2019 ◽  
Vol 15 ◽  
pp. 2563-2568
Author(s):  
Debasish Pal ◽  
Balaram Mukhopadhyay
Keyword(s):  
Escherichia Coli ◽  
Chemical Synthesis ◽  
Building Blocks ◽  
Protecting Group ◽  
E Coli ◽  
Specific Polysaccharide

The total chemical synthesis of the pentasaccharide repeating unit of the O-polysaccharide from E. coli O132 is accomplished in the form of its 2-aminoethyl glycoside. The 2-aminoethyl glycoside is particularly important as it allows further glycoconjugate formation utilizing the terminal amine without affecting the stereochemistry of the reducing end. The target was achieved through a [3 + 2] strategy where the required monosaccharide building blocks are prepared from commercially available sugars through rational protecting group manipulation. The NIS-mediated activation of thioglycosides was used extensively for the glycosylation reactions throughout.

scholarly journals The Role of Metabolites in the Link between DNA Replication and Central Carbon Metabolism in Escherichia coli

Genes ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 447
Author(s):  
Klaudyna Krause ◽  
Monika Maciąg-Dorszyńska ◽  
Anna Wosinski ◽  
Lidia Gaffke ◽  
Joanna Morcinek-Orłowska ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Dna Replication ◽  
Protein Interactions ◽  
Carbon Metabolism ◽  
Molecular Mechanisms ◽  
Central Carbon Metabolism ◽  
Replication Initiation ◽  
Cell Physiology ◽  
E Coli ◽  
Central Carbon

A direct link between DNA replication regulation and central carbon metabolism (CCM) has been previously demonstrated in Bacillus subtilis and Escherichia coli, as effects of certain mutations in genes coding for replication proteins could be specifically suppressed by particular mutations in genes encoding CCM enzymes. However, specific molecular mechanism(s) of this link remained unknown. In this report, we demonstrate that various CCM metabolites can suppress the effects of mutations in different replication genes of E. coli on bacterial growth, cell morphology, and nucleoid localization. This provides evidence that the CCM-replication link is mediated by metabolites rather than direct protein-protein interactions. On the other hand, action of metabolites on DNA replication appears indirect rather than based on direct influence on the replication machinery, as rate of DNA synthesis could not be corrected by metabolites in short-term experiments. This corroborates the recent discovery that in B. subtilis, there are multiple links connecting CCM to DNA replication initiation and elongation. Therefore, one may suggest that although different in detail, the molecular mechanisms of CCM-dependent regulation of DNA replication are similar in E. coli and B. subtilis, making this regulation an important and common constituent of the control of cell physiology in bacteria.

Antibacterial activity and in vitro cytotoxicity evaluation of alginate-AgNP fibers

2016 ◽  
Vol 87 (11) ◽  
pp. 1377-1386 ◽  
Author(s):  
Xihui Zhao ◽  
Qun Li ◽  
Xiaowen Li ◽  
Yanzhi Xia ◽  
Bing Wang ◽  
...  
Keyword(s):  
Antibacterial Activity ◽  
Treatment Time ◽  
Biological Activities ◽  
In Vitro Cytotoxicity ◽  
Cell Counting ◽  
Logarithmic Phase ◽  
E Coli ◽  
Alginate Fibers ◽  
And Staphylococcus Aureus

Biopolymer nanocomposites containing metal nanoparticles have attracted much attention due to their excellent properties and broad applications. In this work, alginate fibers embedded with silver nanoparticles (AgNPs) were prepared. The as-obtained alginate-AgNP fibers exhibited antibacterial activity against both Gram microorganisms of model microbes Escherichia coli (Gram-negative) and Staphylococcus aureus (Gram-positive). A growth kinetic study with S. aureus and E. coli displayed the inhibition of bacterial growth at the logarithmic phase. The cytotoxic effect of the fibers in human cervical cancer (HeLa) cells was assessed by cell counting kit-8 (CCK-8) assay and flow cytometry. The as-prepared alginate-AgNP fibers, particularly with high amount and long treatment time, showed high cell-killing efficiency. These findings emphasize that such alginate-AgNP fibers with multifaceted biological activities are a promising material for applications in the textile or biomedical fields.

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