High-throughput transcriptome sequencing and comparative analysis of Escherichia coli and Schizosaccharomyces pombe in respiratory and fermentative growth.
Joivier VichiEmmanuel SalazarVerónica Jiménez JacintoLeticia Olvera RodriguezRicardo GrandeEdgar Dantán-GonzálezEnrique MorettArmando Hernández-MendozaPublished in: PloS one (2021)
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.
Keyphrases
- escherichia coli
- single cell
- rna seq
- genome wide
- transcription factor
- high throughput
- genome wide identification
- bioinformatics analysis
- cell proliferation
- genome wide analysis
- dna methylation
- magnetic resonance imaging
- drinking water
- gene expression
- type diabetes
- magnetic resonance
- klebsiella pneumoniae
- blood glucose
- blood pressure
- wastewater treatment
- metabolic syndrome
- dna binding
- weight loss
- contrast enhanced
- glycemic control
- heat stress