Dataset Information

Genome-wide Transcription Response of Staphylococcus epidermidis to Heat Shock and Medically-Relevant Glucose Levels

ABSTRACT: Skin serves as both barrier and interface between body and environment. Skin microbes are intermediaries evolved to respond, transduce, or act in response to changing environmental or physiological conditions. Here, we quantify genome-wide changes in gene expression levels for one abundant skin commensal, Staphylococcus epidermidis, in response to an internal physiological signal, glucose levels, and an external environmental signal, temperature. We find 85 of 2354 genes change up to ~34-fold in response to medically-relevant changes in glucose concentration (0 mM to 17 mM; adj P value ≤ 0.05). We observed carbon catabolite repression in response to a range of glucose spikes, as well as upregulation of genes involved in glucose utilization in response to persistent glucose. We observed 366 differentially expressed genes in response to a physiologically-relevant change in temperature (37°C to 45°C; adj P value ≤ 0.05) and an S. epidermidis heat-shock response that mostly resembles the heat-shock response of related staphylococcal species. DNA motif analysis also revealed CtsR and CIRCE operator sequences arranged in tandem upstream of dnaK and groESL operons. We further identified 38 glucose-responsive genes as candidate ON or OFF genes for use in controlling synthetic genetic systems. Such systems might be used to instrument the in-situ skin microbiome or help control microbes bioengineered to serve as embedded diagnostics, monitoring, or treatment platforms.

ORGANISM(S): Staphylococcus epidermidis ATCC 12228

PROVIDER: GSE261664 | GEO | 2024/03/19

REPOSITORIES: GEO

ACCESS DATA

Similar Datasets

Project description:Recombinant Escherichia coli cultures are used to manufacture numerous therapeutic proteins and industrial enzymes, where many of these processes use elevated temperatures to induce recombinant protein production. The heat-shock response in wild-type E. coli has been well studied. In this study, the transcriptome profiles of recombinant E. coli subjected to a heat-shock and to a dual heat-shock recombinant protein induction were examined. Most classical heat-shock protein genes were identified as regulated in both conditions. The major transcriptome differences between the recombinant and reported wild-type cultures were heavily populated by hypothetical and putative genes, which indicates recombinant cultures utilize many unique genes to respond to a heat-shock. Comparison of the dual stressed culture data with literature recombinant protein induced culture data revealed numerous differences. The dual stressed response encompassed three major response patterns: induced-like, in-between, and greater than either individual stress response. Also, there were no genes that only responded to the dual stress. The most interesting difference between the dual stressed and induced cultures was the amino acid-tRNA gene levels. The amino acid-tRNA genes were elevated for the dual cultures compared to the induced cultures. Since tRNAs facilitate protein synthesis via translation, this observed increase in amino acid-tRNA transcriptome levels, in concert with elevated heat-shock chaperones, might account for improved productivities often observed for thermo-inducible systems. Most importantly, the response of the recombinant cultures to a heat-shock was more profound than wild-type cultures, and further, the response to recombinant protein induction was not a simple additive response of the individual stresses. The objective of the present work is to gain a better understanding of the heat-shock response in recombinant cultures and how this response might impact recombinant protein production. To accomplish this objective, the transcriptome response of recombinant cultures subjected to a heat-shock and a dual heat-shock recombinant protein induction were analyzed. The transcriptome levels were determined using Affymetrix E. coli Antisense DNA microarrays, such that the entire genome was evaluated. These two transcriptome responses were also compared to recombinant cultures at normal growth temperature that were not over-expressing the recombinant protein and a set of literature recombinant culture data that were chemically induced to over-express the recombinant protein. Additionally, the heat-shock response of the recombinant cultures was compared to the literature report of the heat-shock response in wild-type cultures. The results of the global transcriptome analysis demonstrated that recombinant cultures respond differently to a heat-shock stress than wild-type cultures, where the transcriptome response of the recombinant cultures is further modified by production of a recombinant protein. Experiment Overall Design: The heat-shock and recombinant protein production phases were synchronized to the cell density of 11.5 OD, which is referred to as Sample Time 0. For the heat-shocked cultures, the temperature was increased from 37°C to 50°C over 8 minutes beginning at Sample Time 0. The temperature and duration used in this study are the same conditions used to evaluate the heat-shock in wild-type cultures. The temperature was then decreased from 50°C to 37°C over 4 minutes. For the dual heat-shocked recombinant protein production cultures, 5 mM IPTG was added 8 minutes after Sample Time 0. The unstressed recombinant cultures were conducted similarly, except without the heat-shock or IPTG-addition. Each sample condition was obtained from at least two separate fermentations (two biological replicates). RNA from each biological replicate was purified and processed independently. Prior to hybridization, where only two biological replicates existed, one of the processed samples was divided (two technical replicates), resulting in three separate hybridized chips. The heat-shocked and dual stressed culture samples all consisted of three technical replicates from two biological duplicates. For the unstressed culture samples, triplicate samples were obtained for the 11.5 OD and duplicates for the 14 OD conditions. There were no statistical differences between the 11.5 and 14 OD unstressed samples (p ≤ 0.001). Thus, the unstressed culture transcriptome profile consisted of six technical replicates from five biological replicates and four independent fermentations.

Project description:Voit2003 - Trehalose Cycle This model is described in the article: Biochemical and genomic regulation of the trehalose cycle in yeast: review of observations and canonical model analysis. Voit EO. J. Theor. Biol. 2003 Jul; 223(1): 55-78 Abstract: The physiological hallmark of heat-shock response in yeast is a rapid, enormous increase in the concentration of trehalose. Normally found in growing yeast cells and other organisms only as traces, trehalose becomes a crucial protector of proteins and membranes against a variety of stresses, including heat, cold, starvation, desiccation, osmotic or oxidative stress, and exposure to toxicants. Trehalose is produced from glucose 6-phosphate and uridine diphosphate glucose in a two-step process, and recycled to glucose by trehalases. Even though the trehalose cycle consists of only a few metabolites and enzymatic steps, its regulatory structure and operation are surprisingly complex. The article begins with a review of experimental observations on the regulation of the trehalose cycle in yeast and proposes a canonical model for its analysis. The first part of this analysis demonstrates the benefits of the various regulatory features by means of controlled comparisons with models of otherwise equivalent pathways lacking these features. The second part elucidates the significance of the expression pattern of the trehalose cycle genes in response to heat shock. Interestingly, the genes contributing to trehalose formation are up-regulated to very different degrees, and even the trehalose degrading trehalases show drastically increased activity during heat-shock response. Again using the method of controlled comparisons, the model provides rationale for the observed pattern of gene expression and reveals benefits of the counterintuitive trehalase up-regulation. To induce a heat shock, set the parameter heat_shock from 0 to 1. This changes the parameter values of X8 to X19 from 1 to the values given in table 3 of the original publication. As this is an S-systems model, it does not contain any reactions encoded in SBML. This model is hosted on BioModels Database and identified by: BIOMD0000000266. To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

Dataset Information

Genome-wide Transcription Response of Staphylococcus epidermidis to Heat Shock and Medically-Relevant Glucose Levels

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure