Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Functional genomic analysis of three nitrogenase isozymes in the photosynthetic bacterium Rhodopseudomonas palustris

ABSTRACT: To address the question of how photosynthetic bacterium Rhodopseudomonas palustris differentially regulates gene expression of three nitrogenase isozymes (Mo, V, and Fe nitrogenases), we constructed Mo strain (Mo nitrogenase only strain), V strain (V nitrogenase only strain), and Fe strain (Fe nitrogenase only strain), and analyzed the whole genome transcriptome profiles of each mutant and wild-type cells grown under nitrogen-fixing conditions. Keywords: Genetic modification

ORGANISM(S): Rhodopseudomonas palustris

PROVIDER: GSE3030 | GEO | 2005/11/10

SECONDARY ACCESSION(S): PRJNA93035

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Functional genomic analysis of three nitrogenase isozymes in the photosynthetic bacterium Rhodopseudomonas palustris

Project description:To address the question of how photosynthetic bacterium Rhodopseudomonas palustris differentially regulates gene expression of three nitrogenase isozymes (Mo, V, and Fe nitrogenases), we constructed Mo strain (Mo nitrogenase only strain), V strain (V nitrogenase only strain), and Fe strain (Fe nitrogenase only strain), and analyzed the whole genome transcriptome profiles of each mutant and wild-type cells grown under nitrogen-fixing conditions. RNA was isolated from various Rhodopseudomonas palustris strains that were grown to the mid-logarithmic phase of growth. Fluorescently labeled cDNA was prepared by direct incorporation of either Cy3-dCTP or Cy5-dCTP during a first-strand reverse transcription reaction. The hybridization mixtures containing the two labeled cDNA samples to be compared were applied to microarray slides that had been covered with Lifterslips (Erie Scientific Company, Portsmouth, NH). The slides were assembled with hybridization chambers (Corning, Corning, NY) and submerged in a 65ÂºC water bath. After 14-16 h of hybridization, the slides were washed and scanned with a ScanArray 4000XL scanner (PerkinElmer, Boston, MA). Images (Cy3 and Cy5) were captured as TIFF files and were analyzed with the image processing software ImaGene version 5.6 (BioDiscovery, Inc., El Segundo, CA). The software package lcDNA was used for data normalization and assessment of the statistical confidence intervals of gene expression. Duplicate calibration experiments and three comparative experiments using RNA from three separately grown cultures (three biological replicates) with duplicate slides for each (10 slides in total) were used to generate each data set.

2010-06-30 | E-GEOD-3030 | biostudies-arrayexpress

How post-translational modification of nitrogenase is circumvented in Rhodopseudomonas palustris strains that produce hydrogen gas constitutively

Project description:Characterization of post-translational modification of nitrogenase in Rhodopseudomonas palustris strains that produce hydrogen gas constitutively.

2012-03-15 | GSE32292 | GEO

Rhodopseudomonas palustris

Project description:Functional genomic analysis of three nitrogenase isozymes in the photosynthetic bacterium Rhodopseudomonas palustris

| PRJNA93035 | ENA

How post-translational modification of nitrogenase is circumvented in Rhodopseudomonas palustris strains that produce hydrogen gas constitutively

Project description:Characterization of post-translational modification of nitrogenase in Rhodopseudomonas palustris strains that produce hydrogen gas constitutively. To characterize the effect of yeast extract as nitrogen source on gene expression under nitrogen fixing conditions, expression profiles of wild-type cells grown on either NF plus yeast extract and succinate and PM plus ammonium sulfate and succinate were compared using Affymetrix GeneChip. Using NF plus yeast extract and succinate media, transcriptome profiles of various mutants and wild-type cells were compared using glass spotted microarrays.

2012-03-15 | E-GEOD-32292 | biostudies-arrayexpress

Anaerobic degradation of syringic acid by an adapted strain of Rhodopseudomonas palustris

Project description:Rhodopseudomonas palustris strain SA008.1.07 can use syringic acid as sole organic carbon source anaerobically. Grew all anaerobically in various carbon sources: syringic acid, succinate, and p-hydroxybenzoic acid.

2019-11-25 | GSE135630 | GEO

Characterization of anaerobic catabolism of p-coumarate in Rhodopseudomonas palustris

Project description:To address the question of how photosynthetic bacterium Rhodopseudomonas palustris metabolize lignin derived compound p-coumarate, transcriptomics and quantitative proteomics were combined to characterize gene expression profiles at both the mRNA level and protein level in Rhodopseudomonas palustris grown with succinate, benzoate, and p-coumarate as the carbon source. Keywords: Comparison of transcriptome profiles

2008-05-07 | GSE6221 | GEO

Characterization of anaerobic catabolism of p-coumarate in Rhodopseudomonas palustris

2008-05-07 | E-GEOD-6221 | biostudies-arrayexpress

Gene expression patterns of a Rhodopseudomonas palustris ΔregSR strain under photoheterotrophic growth conditions

Project description:The redox-sensing two-component signal transduction system, RegSR, in Rhodopseudomonas palustris has been shown to regulate an uptake hydrogenase in response to varying cellular redox states; however, its role is still largely undefined. Here, we used RNA sequencing to compare gene expression patterns in wild type R. palustris strain CGA010 to a ΔregSR derivative, CGA2023, under varying metabolic conditions. Growth conditions were chosen to utilize the different metabolic capabilites of R. palustris and, thus, present a variety of different redox challenges to the cell.

2021-07-31 | GSE150608 | GEO

Phosphoproteomic analysis of Rhodopseudomonas palustris

Project description:This study is to compare the phosphoproteome of Rhodopseudomonas palustris under photoheterotrophic and chemoheterotrophic states

2012-12-12 | PXD000025 | Pride

Rhodopseudomonas palustris proteome grown under aerobic and anaerobic conditions

Project description:Rhodopseudomonas palustris proteome grown under three conditions to investigate the expression of essential genes.

2022-03-01 | PXD010001 | Pride