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Metaproteomic analysis of two bacterial species

ABSTRACT: The species of two bacterial colonies were determined by sequencing their DNA and comparing it with databases. Their adaptation to extreme conditions (conditions similar to those found in the planet Mars) were studied by proteomics, comparing the proteome obtained from a culture under standard laboratory conditions with the proteome obtained from a culture under extreme conditions. The techniques used were 2-DE electrophoresis, Difference in gel electrophoresis (2-D DIGE) and protein analysis by mass spectrometry Matrix Assisted Laser Desorption/ Ionization – Time of Flight (MALDI-TOF).

INSTRUMENT(S): autoflex

ORGANISM(S): Environmental Samples

SUBMITTER: Eva Garcia

LAB HEAD: Garcia Lopez Eva; Cid Sanchez Cristina

PROVIDER: PXD027249 | Pride | 2023-07-17

REPOSITORIES: Pride

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Metaproteomic analysis of two bacterial species

Project description:The species of two bacterial colonies were determined by sequencing their DNA and comparing it with databases. Their adaptation to extreme conditions (conditions similar to those found in the planet Mars) were studied by proteomics, comparing the proteome obtained from a culture under standard laboratory conditions with the proteome obtained from a culture under extreme conditions. The techniques used were 2-DE electrophoresis, Difference in gel electrophoresis (2-D DIGE) and protein analysis by mass spectrometry Matrix Assisted Laser Desorption/ Ionization – Time of Flight (MALDI-TOF).

2023-07-17 | PXD027245 | Pride

Functional characterization of microbial communities from glacial ecosystems

Project description:Glaciers are populated by a large number of microorganisms including bacteria, archaea and microeukaryotes. Several factors such as solar radiation, nutrient availability and water content greatly determine the diversity and abundance of these microbial populations, the type of metabolism and the biogeochemical cycles. In order to study their metabolic potentials, samples of glacial ice were taken from several glacial ecosystems. Microorganisms were analyzed by a polyphasic approach that combines a set of -omic techniques: 16S rRNA sequencing, culturomics and metaproteomics. This combination provides key information about diversity and functions of microbial populations, especially in rare habitats. Several whole essential proteins and enzymes related to metabolism and energy production, recombination and translation were found that demonstrate the existence of cellular activity at subzero temperatures.

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Metaproteomic analysis of glacial ecosystem

Project description:Glaciers are populated by a large number of microorganisms including bacteria, archaea and microeukaryotes. From an ecological point of view, three ecosystems can be differentiated in glaciers: the supraglacial ecosystem, the subglacial ecosystem and the englacial ecosystem. Several factors such as solar radiation, nutrient availability and water content greatly determine the diversity and abundance of microbial populations, the type of metabolism and the biogeochemical cycles. Firstly, the supraglacial ecosystem, sunlit and oxygenated, is predominantly populated by autotrophic microorganisms. Secondly, the subglacial ecosystem contains a majority of chemoautrotophs that are fed on the mineral salts of the rocks and basal soil. Lastly, the englacial ecosystem is the less studied and the one that contains the smallest number of microorganisms. However, these unknown englacial microorganisms establish a true trophic chain and appear to have an active metabolism. In order to study their metabolic potentials, samples of englacial ice were taken from an Antarctic glacier. The cells were harvested and their proteins were extracted and analyzed by matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI/TOF/TOF). Several proteins and enzymes were found that demonstrate the existence of cellular activity at subzero temperatures. In this way it is shown that the englacial microorganisms are not quiescent, but that they maintain an active metabolism and play an important role in the glacial microbial community.

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Metaproteomic analysis of glacial ecosystem

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Transcription profiling of Pseudomonas aeruginosa treated with hydrogen peroxide

Project description:Background: Pseudomonas aeruginosa, a pathogen infecting those with cystic fibrosis, encounters toxicity from phagocyte-derived reactive oxidants including hydrogen peroxide during active infection. P. aeruginosa responds with adaptive and protective strategies against these toxic species to effectively infect humans. Despite advances in our understanding of the responses to oxidative stress in many specific cases, the connectivity between targeted protective genes and the rest of cell metabolism remains obscure. Results: Herein, we performed a genome-wide transcriptome analysis of the cellular responses to hydrogen peroxide in order to determine a more complete picture of how oxidative stress-induced genes are related and regulated. Our data reinforce the previous conclusion that DNA repair proteins and catalases may be among the most vital antioxidant defense systems of P. aeruginosa. Our results also suggest that sublethal oxidative damage reduces active and/or facilitated transport and that intracellular iron might be a key factor for a relationship between oxidative stress and iron regulation. Perhaps most intriguingly, we revealed that the transcription of all F-, R-, and S-type pyocins was upregulated by oxidative stress and at the same time, a cell immunity protein (pyocin S2 immunity protein) was downregulated, possibly leading to self-killing activity. Conclusions: This finding proposes that pyocin production might be another novel defensive scheme against oxidative attack by host cells. Experiment Overall Design: We conducted four and five independent microarray experiments with biological replicates in the absence (control) and the presence (experimental) of hydrogen peroxide, respectively.

2007-07-19 | E-GEOD-3090 | biostudies-arrayexpress

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2008-06-15 | E-GEOD-7402 | biostudies-arrayexpress

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Project description:In the present study, we employed Affymetrix Pseudomonas aeruginosa GeneChip arrays to investigate the dynamics of global gene expression profiles during the cellular response of Pseudomonas aeruginosa to Chlorhexidine diacetate, which involved initial growth inhibition and metabolism. Experiment Overall Design: We conducted three independent microarray experiments (biological replicates) in the absence (control) and the presence (experimental) of Chlorhexidine diacetate. We calculated fold change as the ratio between the signal averages of three untreated (control) and three chlorhexidine diacetate-treated (experimental) cultures for 0, 10 and 60 min exposures.

2009-01-17 | E-GEOD-14253 | biostudies-arrayexpress

Microarray Analysis of Toxicogenomic Effects of Ortho-Phenylphenol on Staphylococcus aureus

Project description:In the present study, we employed Affymetrix Staphylococcus aureus GeneChip arrays to investigate the dynamics of global gene expression profiles during the cellular response of Staphylococcus aureus to Ortho-Phenylphenol, which involved initial growth inhibition and metabolism. Keywords: Time course We conducted five independent microarray experiments (biological replicates) in the absence (control) and the presence (experimental) of Ortho-Phenylphenol. We calculated fold change as the ratio between the signal averages of five untreated (control) and five ortho-phenylphenol-treated (experimental) cultures for 0, 20 and 60 min exposures.

2008-04-01 | E-GEOD-10605 | biostudies-arrayexpress

TAU - Ben-Jacob - P. vortex - Gene Prediction Validation - 105k

Project description:Validation of the de-novo sequenced Paenibacillus vortex annotation using microarray.

2010-11-29 | E-MEXP-3019 | biostudies-arrayexpress