ArticleBMC systems biology2009
Network analysis of the transcriptional pattern of young and old cells of Escherichia coli during lag phase.
Article in BMC systems biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
14 citing papers in PubMed, 33 citations in OpenAlex.
- Regulation of phosphate starvation-specific responses inMicrobiology (Reading, England) · 2023Review
- Nontraditional systems in aging research: an update.Cellular and molecular life sciences : CMLS · 2021Review
- Nucleoid remodeling during environmental adaptation is regulated by HU-dependent DNA bundling.Nature communications · 2020Article
- Microbial lag phase can be indicative of, or independent from, cellular stress.Scientific reports · 2020Article
- Lag Phase Is a Dynamic, Organized, Adaptive, and Evolvable Period That Prepares Bacteria for Cell Division.Journal of bacteriology · 2019Review
- Article
- Non-essential genes form the hubs of genome scale protein function and environmental gene expression networks in Salmonella enterica serovar Typhimurium.BMC microbiology · 2013Article
- The ability of flux balance analysis to predict evolution of central metabolism scales with the initial distance to the optimum.PLoS computational biology · 2013Article
- Lag phase is a distinct growth phase that prepares bacteria for exponential growth and involves transient metal accumulation.Journal of bacteriology · 2012Article
- Article
- Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress.Molecular & cellular proteomics : MCP · 2012Article
- The transcriptional response of Listeria monocytogenes during adaptation to growth on lactate and diacetate includes synergistic changes that increase fermentative acetoin production.Applied and environmental microbiology · 2011Article
- Bacterial aging: from mechanistic basis to evolutionary perspective.Cellular and molecular life sciences : CMLS · 2010Review
- Modeling the lag period and exponential growth of Listeria monocytogenes under conditions of fluctuating temperature and water activity values.Applied and environmental microbiology · 2010Article
Corrections and comments
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Authors and funding
7 authors at 1 institution in 2 countries.
Funding
Abstract
backgroundThe aging process of bacteria in stationary phase is halted if cells are subcultured and enter lag phase and it is then followed by cellular division. Network science has been applied to analyse the transcriptional response, during lag phase, of bacterial cells starved previously in stationary phase for 1 day (young cells) and 16 days (old cells).
resultsA genome scale network was constructed for E. coli K-12 by connecting genes with operons, transcription and sigma factors, metabolic pathways and cell functional categories. Most of the transcriptional changes were detected immediately upon entering lag phase and were maintained throughout this period. The lag period was longer for older cells and the analysis of the transcriptome revealed different intracellular activity in young and old cells. The number of genes differentially expressed was smaller in old cells (186) than in young cells (467). Relatively, few genes (62) were up- or down-regulated in both cultures. Transcription of genes related to osmotolerance, acid resistance, oxidative stress and adaptation to other stresses was down-regulated in both young and old cells. Regarding carbohydrate metabolism, genes related to the citrate cycle were up-regulated in young cells while old cells up-regulated the Entner Doudoroff and gluconate pathways and down-regulated the pentose phosphate pathway. In both old and young cells, anaerobic respiration and fermentation pathways were down-regulated, but only young cells up-regulated aerobic respiration while there was no evidence of aerobic respiration in old cells.Numerous genes related to DNA maintenance and replication, translation, ribosomal biosynthesis and RNA processing as well as biosynthesis of the cell envelope and flagellum and several components of the chemotaxis signal transduction complex were up-regulated only in young cells. The genes for several transport proteins for iron compounds were up-regulated in both young and old cells. Numerous genes encoding transporters for carbohydrates and organic alcohols and acids were down-regulated in old cells only.
conclusionNetwork analysis revealed very different transcriptional activities during the lag period in old and young cells. Rejuvenation seems to take place during exponential growth by replicative dilution of old cellular components.
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