Dataset Information

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

ABSTRACT: 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.

SUBMITTER: Vichi J

PROVIDER: S-EPMC7968713 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

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

Vichi Joivier J Salazar Emmanuel E Jacinto Verónica Jiménez VJ Rodriguez Leticia Olvera LO Grande Ricardo R Dantán-González Edgar E Morett Enrique E Hernández-Mendoza Armando A

PloS one 20210317 3

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 ...[more]

PMID: 33730068

Similar Datasets

Project description:Next Generation sequencing techniques have ushered in a new era in life sciences, especially genomic research. Currently, massive RNA sequencing (RNA-seq) has increased knowledge about the "RNA universe" from the global characterization of transcriptomes, differential gene expression studies and the continued discovery of non-coding regulatory transcripts such as non-coding RNAs (ncRNAs). Post-transcriptional gene regulation is a mechanism for controlling gene expression that is present in both prokaryote and eukaryote organisms and regulates multiple biological processes. Examples of ncRNAs that regulate the levels of transcripts of genes related to central carbon metabolism have been described in bacteria and higher eukaryotes. In order to describe whether analogies exist in regulatory circuits mediated by ncRNAs in two cell patterns, a comparative analysis of the transcriptome of Escherichia coli and Schizosaccharomyces pombe in similar growth conditions was carried out using two carbon source, 2 % glucose and a mix of 2% glycerol and 0.2 % sodium acetate. Twelve RNA-seq libraries were performed. The RNA-seq data contained a number unambiguously mapped readings on the genome of each organism ranged from 1-1.3 million. A total of 739 and 743 genes were detected as differentially expressed for E. coli and S, pombe respectively with a module of log FC > 1 and FDR > 0.05. In aerobic glicolisis GO asciated to cell proliferetionweres detected in both organisms. Among the genes differentially expressed in glycerol/acetate general transcription factors such as fliA, 11 literature validated sRNAs, and assembly flagellum maquinary gene were detected in E. coli, whereas in fission yeast, hexose transporters, switches integral membrane proteins and ncRNAs related to cellular stress are highlighted. In general, our study shows that a conserved "foraging behaviour" response is observed in eukaryotic and procaryotic organism when there is no present glycolityc carbon source.

Project description:Over the last decades, predictive microbiology has made significant advances in the mathematical description of microbial spoiler and pathogen dynamics in or on food products. Recently, the focus of predictive microbiology has shifted from a (semi-)empirical population-level approach towards mechanistic models including information about the intracellular metabolism in order to increase model accuracy and genericness. However, incorporation of this subpopulation-level information increases model complexity and, consequently, the required run time to simulate microbial cell and population dynamics. In this paper, results of metabolic flux balance analyses (FBA) with a genome-scale model are used to calibrate a low-complexity linear model describing the microbial growth and metabolite secretion rates of Escherichia coli as a function of the nutrient and oxygen uptake rate. Hence, the required information about the cellular metabolism (i.e., biomass growth and secretion of cell products) is selected and included in the linear model without incorporating the complete intracellular reaction network. However, the applied FBAs are only representative for microbial dynamics under specific extracellular conditions, viz., a neutral medium without weak acids at a temperature of 37℃. Deviations from these reference conditions lead to metabolic shifts and adjustments of the cellular nutrient uptake or maintenance requirements. This metabolic dependency on extracellular conditions has been taken into account in our low-complex metabolic model. In this way, a novel approach is developed to take the synergistic effects of temperature, pH, and undissociated acids on the cell metabolism into account. Consequently, the developed model is deployable as a tool to describe, predict and control E. coli dynamics in and on food products under various combinations of environmental conditions. To emphasize this point,three specific scenarios are elaborated: (i) aerobic respiration without production of weak acid extracellular metabolites, (ii) anaerobic fermentation with secretion of mixed acid fermentation products into the food environment, and (iii) respiro-fermentative metabolic regimes in between the behaviors at aerobic and anaerobic conditions.

Dataset Information

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

Publications

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

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets