scholarly journals High-throughput transcriptome sequencing and comparative analysis of Escherichia coli and Schizosaccharomyces pombe in respiratory and fermentative growth

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0248513
Author(s):  
Joivier Vichi ◽  
Emmanuel Salazar ◽  
Verónica Jiménez Jacinto ◽  
Leticia Olvera Rodriguez ◽  
Ricardo Grande ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Membrane Proteins ◽  
Schizosaccharomyces Pombe ◽  
Aerobic Glycolysis ◽  
Carbon Sources ◽  
Differentially Expressed ◽  
Growth Media ◽  
Galactose Metabolism ◽  
Regulatory Processes ◽  
Fermentative Growth

In spite of increased complexity in eukaryotes compared to prokaryotes, several basic metabolic and regulatory processes are conserved. Here we explored analogies in the eubacteria Escherichia coli and the unicellular fission yeast Schizosaccharomyces pombe transcriptomes under two carbon sources: 2% glucose; or a mix of 2% glycerol and 0.2% sodium acetate using the same growth media and growth phase. Overall, twelve RNA-seq libraries were constructed. A total of 593 and 860 genes were detected as differentially expressed for E. coli and S. pombe, respectively, with a log2 of the Fold Change ≥ 1 and False Discovery Rate ≤ 0.05. In aerobic glycolysis, most of the expressed genes were associated with cell proliferation in both organisms, including amino acid metabolism and glycolysis. In contrast in glycerol/acetate condition, genes related to flagellar assembly and membrane proteins were differentially expressed such as the general transcription factors fliA, flhD, flhC, and flagellum assembly genes were detected in E. coli, whereas in S. pombe genes for hexose transporters, integral membrane proteins, galactose metabolism, and ncRNAs related to cellular stress were overexpressed. In general, our study shows that a conserved "foraging behavior" response is observed in these eukaryotic and eubacterial organisms in gluconeogenic carbon sources.

scholarly journals Label-free quantitative proteomic analysis of the inhibition effect of Lactobacillus rhamnosus GG on Escherichia coli biofilm formation in co-culture

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Huiyi Song ◽  
Ni Lou ◽  
Jianjun Liu ◽  
Hong Xiang ◽  
Dong Shang
Keyword(s):  
Escherichia Coli ◽  
Proteomic Analysis ◽  
Biofilm Formation ◽  
Lactobacillus Rhamnosus ◽  
Differentially Expressed ◽  
Differentially Expressed Proteins ◽  
Label Free ◽  
Quantitative Proteomic Analysis ◽  
E Coli ◽  
Protein Ubiquitination

Abstract Background Escherichia coli (E. coli) is the principal pathogen that causes biofilm formation. Biofilms are associated with infectious diseases and antibiotic resistance. This study employed proteomic analysis to identify differentially expressed proteins after coculture of E. coli with Lactobacillus rhamnosus GG (LGG) microcapsules. Methods To explore the relevant protein abundance changes after E. coli and LGG coculture, label-free quantitative proteomic analysis and qRT-PCR were applied to E. coli and LGG microcapsule groups before and after coculture, respectively. Results The proteomic analysis characterised a total of 1655 proteins in E. coli K12MG1655 and 1431 proteins in the LGG. After coculture treatment, there were 262 differentially expressed proteins in E. coli and 291 in LGG. Gene ontology analysis showed that the differentially expressed proteins were mainly related to cellular metabolism, the stress response, transcription and the cell membrane. A protein interaction network and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis indicated that the differentiated proteins were mainly involved in the protein ubiquitination pathway and mitochondrial dysfunction. Conclusions These findings indicated that LGG microcapsules may inhibit E. coli biofilm formation by disrupting metabolic processes, particularly in relation to energy metabolism and stimulus responses, both of which are critical for the growth of LGG. Together, these findings increase our understanding of the interactions between bacteria under coculture conditions.

scholarly journals MexAB-OprM Efflux Pump Interaction with the Peptidoglycan of Escherichia coli and Pseudomonas aeruginosa

2021 ◽  
Vol 22 (10) ◽  
pp. 5328
Author(s):  
Miao Ma ◽  
Margaux Lustig ◽  
Michèle Salem ◽  
Dominique Mengin-Lecreulx ◽  
Gilles Phan ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Pseudomonas Aeruginosa ◽  
Cell Division ◽  
Membrane Proteins ◽  
Outer Membrane ◽  
Efflux Pump ◽  
Gram Negative Bacteria ◽  
Gram Negative ◽  
Active Efflux

One of the major families of membrane proteins found in prokaryote genome corresponds to the transporters. Among them, the resistance-nodulation-cell division (RND) transporters are highly studied, as being responsible for one of the most problematic mechanisms used by bacteria to resist to antibiotics, i.e., the active efflux of drugs. In Gram-negative bacteria, these proteins are inserted in the inner membrane and form a tripartite assembly with an outer membrane factor and a periplasmic linker in order to cross the two membranes to expulse molecules outside of the cell. A lot of information has been collected to understand the functional mechanism of these pumps, especially with AcrAB-TolC from Escherichia coli, but one missing piece from all the suggested models is the role of peptidoglycan in the assembly. Here, by pull-down experiments with purified peptidoglycans, we precise the MexAB-OprM interaction with the peptidoglycan from Escherichia coli and Pseudomonas aeruginosa, highlighting a role of the peptidoglycan in stabilizing the MexA-OprM complex and also differences between the two Gram-negative bacteria peptidoglycans.

scholarly journals Conditional Essentiality of the csrA Gene in Escherichia coli

2008 ◽  
Vol 191 (5) ◽  
pp. 1722-1724 ◽  
Author(s):  
Johan Timmermans ◽  
Laurence Van Melderen
Keyword(s):  
Escherichia Coli ◽  
Growth Inhibition ◽  
Deletion Mutant ◽  
Glycogen Synthesis ◽  
Synthetic Medium ◽  
Carbon Sources ◽  
Krebs Cycle ◽  
Physiological Processes

ABSTRACT CsrA is a global posttranscriptional regulator of numerous physiological processes, such as glycogenesis and glycolysis. Here, we show that the csrA gene of Escherichia coli is essential for growth on LB and on synthetic medium containing glycolytic carbon sources. However, csrA is not necessary for growth on synthetic medium containing pyruvate, showing that the Krebs cycle is functional in the csrA::cat deletion mutant. Deletion of the glgCAP operon in the csrA::cat mutant restored the ability to grow on LB and on synthetic medium containing glycolytic carbon sources, showing that growth inhibition is due to an excess of glycogen synthesis.

scholarly journals Pilot-Scale Production of Fatty Acid Ethyl Esters by an Engineered Escherichia coli Strain Harboring the p(Microdiesel) Plasmid

2010 ◽  
Vol 76 (13) ◽  
pp. 4560-4565 ◽  
Author(s):  
Yasser Elbahloul ◽  
Alexander Steinbüchel
Keyword(s):  
Escherichia Coli ◽  
Fatty Acid ◽  
Carbon Sources ◽  
Dry Mass ◽  
Pilot Scale ◽  
Coli Strain ◽  
Fatty Acid Ethyl Esters ◽  
Ethyl Esters ◽  
Scale Production ◽  
A Cell

ABSTRACT Fatty acid ethyl esters (FAEEs) were produced in this study by the use of an engineered Escherichia coli p(Microdiesel) strain. Four fed-batch pilot scale cultivations were carried out by first using glycerol as sole carbon source for biomass production before glucose and oleic acid were added as carbon sources. Cultivations yielded a cell density of up to 61 ± 3.1 g of cell dry mass (CDM) per liter and a maximal FAEE content of 25.4% ± 1.1% (wt/wt) of CDM.

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