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Comparative analysis of global transcriptional profile of Escherichia coli and Schizosaccharomyces pombe in respiratory and fermentative growth: Inferring the evolution of analog circuits of post-transcriptional regulation

ABSTRACT: 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.

ORGANISM(S): Escherichia coli Schizosaccharomyces pombe

PROVIDER: GSE138088 | GEO | 2020/09/25

REPOSITORIES: GEO

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Project description:Background: The biotechnology industry has extensively exploited Escherichia coli for producing recombinant proteins, biofuels etc. However, high growth rate aerobic E. coli cultivations are accompanied by acetate excretion i.e. overflow metabolism which is harmful as it inhibits growth, diverts valuable carbon from biomass formation and is detrimental for target product synthesis. Although overflow metabolism has been studied for decades, its regulation mechanisms still remain unclear. Results: In the current work, growth rate dependent acetate overflow metabolism of E. coli was continuously monitored using advanced continuous cultivation methods (A-stat and D-stat). The first step in acetate overflow switch (at μ = 0.27 ± 0.02 1/h) is the repression of acetyl-CoA synthethase (Acs) activity triggered by carbon catabolite repression resulting in decreased assimilation of acetate produced by phosphotransacetylase (Pta), and disruption of the PTA-ACS node. This was indicated by acetate synthesis pathways PTA-ACKA and POXB component expression down-regulation before the overflow switch at μ = 0.27 ± 0.02 1/h with concurrent 5-fold stronger repression of acetate-consuming Acs. This in turn suggests insufficient Acs activity for consuming all the acetate produced by Pta, leading to disruption of the acetate cycling process in PTA-ACS node where constant acetyl phosphate or acetate regeneration is essential for E. coli chemotaxis, proteolysis, pathogenesis etc. regulation. In addition, two-substrate A-stat and D-stat experiments showed that acetate consumption capability of E. coli decreased drastically, just as Acs expression, before the start of overflow metabolism. The second step in overflow switch is the sharp decline in cAMP production at μ = 0.45 1/h leading to total Acs inhibition and fast accumulation of acetate. Conclusion: This study is an example of how a systems biology approach allowed to propose a new regulation mechanism for overflow metabolism in E. coli shown by proteomic, transcriptomic and metabolomic levels coupled to two-phase acetate accumulation: acetate overflow metabolism in E. coli is triggered by Acs down-regulation resulting in decreased assimilation of acetic acid produced by Pta, and disruption of the PTA-ACS node.

Project description:Background: The biotechnology industry has extensively exploited Escherichia coli for producing recombinant proteins, biofuels etc. However, high growth rate aerobic E. coli cultivations are accompanied by acetate excretion i.e. overflow metabolism which is harmful as it inhibits growth, diverts valuable carbon from biomass formation and is detrimental for target product synthesis. Although overflow metabolism has been studied for decades, its regulation mechanisms still remain unclear. Results: In the current work, growth rate dependent acetate overflow metabolism of E. coli was continuously monitored using advanced continuous cultivation methods (A-stat and D-stat). The first step in acetate overflow switch (at μ = 0.27 ± 0.02 1/h) is the repression of acetyl-CoA synthethase (Acs) activity triggered by carbon catabolite repression resulting in decreased assimilation of acetate produced by phosphotransacetylase (Pta), and disruption of the PTA-ACS node. This was indicated by acetate synthesis pathways PTA-ACKA and POXB component expression down-regulation before the overflow switch at μ = 0.27 ± 0.02 1/h with concurrent 5-fold stronger repression of acetate-consuming Acs. This in turn suggests insufficient Acs activity for consuming all the acetate produced by Pta, leading to disruption of the acetate cycling process in PTA-ACS node where constant acetyl phosphate or acetate regeneration is essential for E. coli chemotaxis, proteolysis, pathogenesis etc. regulation. In addition, two-substrate A-stat and D-stat experiments showed that acetate consumption capability of E. coli decreased drastically, just as Acs expression, before the start of overflow metabolism. The second step in overflow switch is the sharp decline in cAMP production at μ = 0.45 1/h leading to total Acs inhibition and fast accumulation of acetate. Accumulation of acetate was also coupled to excretion of products such as orotate and N-carbomoyl-L-aspartate making it a novel carbon spilling mechanism in E. coli. Conclusion: This study is an example of how a systems biology approach allowed to propose a new regulation mechanism for overflow metabolism in E. coli shown by proteomic, transcriptomic and metabolomic levels coupled to two-phase acetate accumulation: acetate overflow metabolism in E. coli is triggered by Acs down-regulation resulting in decreased assimilation of acetic acid produced by Pta, and disruption of the PTA-ACS node. Reference samples at specific growth rate (μ) 0.11 1/h were compared to the ones acquired at μ 0.21, 0.26, 0.31, 0.36, 0.40 and 0.48 1/h

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Comparative analysis of global transcriptional profile of Escherichia coli and Schizosaccharomyces pombe in respiratory and fermentative growth: Inferring the evolution of analog circuits of post-transcriptional regulation

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