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Transcriptome-proteome profiling in Burkholderia thailandensis during the transition from exponential to stationary phase

ABSTRACT: Transcriptome-proteome profiling in Burkholderia thailandensis during the transition from exponential to stationary phase

PROVIDER: PRJNA1173123 | ENA |

REPOSITORIES: ENA

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Transcriptome-proteome profiling in Burkholderia thailandensis during the transition from exponential to stationary phase

Project description:Burkholderia thailandensis is closely related to highly pathogenic Burkholderia species, and it is an excellent surrogate as it rarely causes disease in humans. Understanding the complex molecular mechanisms that characterize the transition of B. thailandensis from exponential to stationary phases is critical to understanding bacterial responses to stress or nutrient limitation. We present here an integrated transcriptomic and proteomic analysis to profile gene and protein expression changes during entry into stationary phase. We identified 928 differentially expressed genes (DEGs) and 832 differentially expressed proteins (DEPs), highlighting significant transcriptional and translational reprogramming. Genes encoding proteins involved in benzoate degradation and O-antigen nucleotide sugar biosynthesis were among the most highly upregulated in stationary phase, whereas processes such as nitrogen metabolism, translation, and flagellar biosynthesis were downregulated. At the proteome level, proteins related to fatty acid degradation and butanoate metabolism accumulated along with proteins involved in synthesis of secondary metabolites. Markedly downregulated proteins included ribosomal proteins and translation factors as well as the house-keeping iron-sulfur biogenesis proteins. A protein-protein interaction (PPI) network analysis identified clusters involved in processes such as fatty acid metabolism and amino acid degradation. Surprisingly, the RpoS sigma factor, which has been shown to accumulate in stationary phase in several bacterial species, was not significantly increased in B. thailandensis during stationary phase. These findings offer comprehensive insights into B. thailandensis adaptive strategies and provide a foundation for developing interventions against pathogenic Burkholderia species.

2025-07-13 | GSE279483 | GEO

Transcriptome-proteome profiling in Burkholderia thailandensis during the transition from exponential to stationary phase

2025-07-16 | PXD056625 | Pride

GAS M3 serotype, exponential versus stationary phase

Project description:MGAS315 is a wild type strain. RNA isolated in exponential phase and stationary phase were compared Keywords: Growth phase comparison

2007-06-28 | GSE5179 | GEO

Salmonella enterica serovar Typhimurium gene expression in exponential and stationary phase cultures

Project description:Transcriptional profiling of Salmonella Typhimurium strains SL1344 in exponential and stationary phase cultures

2017-03-29 | GSE97161 | GEO

RNA-seq of wild type Mycobacterium smegmatis mc2 155 (exponential and stationary phase) and Ms1 deletion strain (exponential and stationary phase)

Project description:RNA-seq of wild type Mycobacterium smegmatis mc2 155 (exponential and stationary phase) and Ms1 deletion strain (exponential and stationary phase)

| PRJEB27728 | ENA

RNA-seq of wild type Mycobacterium smegmatis mc2 155 (exponential and stationary phase) and Ms1 deletion strain (exponential and stationary phase)

Project description:Ms1 RNA is ~300 nt sRNA that is highly expressed in stationary phase of growth and binds to the RNA polymerase (RNAP) core. We assume that by binding to RNAP, Ms1 could regulate transcription. Our aim was to reveal the most prominent changes in the transcriptome upon entry into stationary phase that might be dependent on Ms1. We performed RNA-seq data to characterize exponential (Ms_WT_exp) and stationary phase (Ms_WT_stat) transcriptome in M. smegmatis in wild type cells. In addition, we compared the transcriptome of the Ms1 knockout cells (Ms_KO_stat) with wild type cells in stationary phase and in exponential phase (Ms_KO_exp).

2018-11-12 | E-MTAB-7004 | biostudies-arrayexpress

Comparison of Bacillus subtilis wild type and cshA mutant at exponential versus stationary phase

Project description:Comparison of Bacillus subtilis wild type and cshA mutant at exponential versus stationary phase. Detailed description (other than provided below) of growth conditions, RNA preparation, cDNA synthesis and hybridization conditions can be found in the submitted paper.

2012-11-26 | GSE36877 | GEO

Proteome dynamics during transition from exponential to stationary phase in yeast

Project description:Glycolysis is the central pathway for sugar metabolism in most living organisms. The single celled eukaryote yeast is a widely used model organism for higher eukaryotes in which the regulation of glycolysis is widely studied. S. cerevisiae is one of the few eukaryotic organisms that can efficiently grow under both aerobic and anaerobic conditions. Furthermore, this yeast switches from proliferation into a resting phase when nutrients are exhausted. However, little is known about the proteome dynamics that takes place during this transition, particularly under anaerobic conditions. Moreover, like many other organisms including humans, the genome of S. cerevisiae contains duplications which result in the expression of so called ‘isoenzymes’ in central metabolic pathways including glycolysis. Interestingly, the role of those ‘isoenzymes’ remains elusive to date. Here we describe a large-scale quantitative proteome study combining shotgun experiments using a nano-LC coupled to a QE plus Orbitrap mass spectrometer (Thermo, Germany), to capture the proteome dynamics during transition from proliferation into stationary phase, under both aerobic and anaerobic growth. Furthermore, we explore the proteome dynamics of a mutant yeast where the glycolytic isoenzymes are deleted.

2023-04-15 | PXD031412 | Pride

The small transcriptome of Escherichia coli in exponential and stationary phase

Project description:We have deep sequenced the small transcriptome of Escherichia coli growing in LB and in MOPS, in exponential and stationary phase, and analyzed the resulting reads by a novel pipeline STARPA (Stable RNA Processing Product Analyzer). Our analysis reveals over 14,000 small transcripts enriched during both growth stages. RNA samples were collected from total RNA pools or from crude ribosome pools and then size selected by electrophoresis to limit the products to 20-300nt.

2020-11-21 | GSE161907 | GEO

Transcription differences of Micrococcus luteus at late-exponential and stationary phase

Project description:Investigation of transcriptomic changes in M.luteus at 12hrs and 24hrs. Differences in fatty acid profiles of M. luteus at exponential and stationary phase is attributed to transcriptional changes of branched amino acid biosynthesis and degradation genes. This study is described by Pereira, J.H., E.B. Goh, J.D. Keasling, H.R. Beller and P.A. Adams in Crystal structure of FabH and factors affecting the distribution of branched fatty acids in Micrococcus luteus, which has been submitted to Acta Crystallographica Section D

2012-09-24 | GSE38040 | GEO

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