Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

45 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genes differentially expressed Haloarcula hispanica strains: PHB (M-NM-^TphaEC mutant) vs 960 (wild type)

ABSTRACT: Transcriptional profiling of Haloarcula hispanica comparing PHB with 960. PHB represents the PHA synthase genes mutant (i.e., M-NM-^TphaEC) which is deficient in PHBV accumulation when grown in MG medium. 960 represents the wild-type strain which can produce PHBV when grown in MG medium. Goal was to explore the PHBV biosynthesis and its impact on central metabolism in H. hispanica. Total RNA from PHB and 960 were used to generate target cDNA, and then hybridized to 8*15K Haloarcula hispanica genome array genechips, representing about 3800 genes.

ORGANISM(S): Haloarcula hispanica

SUBMITTER: Hailong Liu

PROVIDER: E-GEOD-42799 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Proteome reference map of Haloarcula hispanica and comparative proteomic and transcriptomic analysis of polyhydroxyalkanoate biosynthesis under genetic and environmental perturbations.

Liu Hailong H Luo Yuanming Y Han Jing J Wu Jinhua J Wu Zhenfang Z Feng Deqin D Cai Shuangfeng S Li Ming M Liu Jingfang J Zhou Jian J Xiang Hua H

Journal of proteome research 20130125 3

Many haloarchaea are known as polyhydroxyalkanoates (PHAs) producers, but a global and integrated view of the PHA biosynthesis is still lacking in this group of archaea. In this study, a combined proteomic and transcriptomic approach was employed in Haloarcula hispanica, a model haloarchaeon that accumulates poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) under nutrient-limiting conditions with excess carbon source. First, a comprehensive proteome reference map was established for H. hispani ...[more]

PMID: 23301558

Similar Datasets

Genes differentially expressed Haloarcula hispanica strains: PHB (ΔphaEC mutant) vs 960 (wild type)

Project description:Transcriptional profiling of Haloarcula hispanica comparing PHB with 960. PHB represents the PHA synthase genes mutant (i.e., ΔphaEC) which is deficient in PHBV accumulation when grown in MG medium. 960 represents the wild-type strain which can produce PHBV when grown in MG medium. Goal was to explore the PHBV biosynthesis and its impact on central metabolism in H. hispanica.

2013-01-22 | GSE42799 | GEO

Haloarcula hispanica wild-type strain cultured in different media: MG vs 168

Project description:Transcriptional profiling of Haloarcula hispanica wild-type strain cultured in different media comparing MG medium with 168 medium. H. hispanica wild-type strain can accumulate PHBV in MG medium, while can not in 168 medium. Goal was to explore the PHA biosynthesis and its impact on central metabolism in H. hispanica. Total RNA from MG and 168 were used to generate target cDNA, and then hybridized to 8*15K Haloarcula hispanica genome array genechips, representing about 3800 genes.

2013-01-22 | E-GEOD-42798 | biostudies-arrayexpress

Genes differentially expressed Haloferax mediterranei strains: control wild-type strain vs M-NM-^TphaA1 strain

Project description:Transcriptional profiling of Haloferax mediterranei comparing control wild-type strain with M-NM-^TphaA1 strain, in which phaA1 gene are knockouted. M-NM-^TphaA1 strain can accumulate PHB only. Goal was to explore the PHA biosynthetic pathway and to determine their impact on primary metabolism in H. mediterranei. Total RNA from the control Haloferax mediterranei and its M-NM-^TphaA1 strain were used to generate target cDNA, and then hybridized to 8*15K Haloferax mediterranei genome array genechips, representing about 3800 genes.

2012-04-19 | E-GEOD-37420 | biostudies-arrayexpress

Proteome reference map of Haloarcula hispanica and comparative proteomic and transcriptomic analysis of polyhydroxyalkanoate biosynthesis under genetic and environmental perturbations

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-01-22 | E-GEOD-42800 | biostudies-arrayexpress

Genes differentially expressed Haloferax mediterranei strains: control wild-type strain vs M-NM-^TphaEC strain

Project description:Transcriptional profiling of Haloferax mediterranei comparing control wild-type strain with M-NM-^TphaEC strain, in which PHA synthase genes are knockouted. M-NM-^TphaEC strain is deficient in PHBV accumulation. Goal was to explore the PHBV biosynthetic pathway and to determine their impact on primary metabolism in H. mediterranei. Total RNA from the control Haloferax mediterranei and its M-NM-^TphaEC strain were used to generate target cDNA, and then hybridized to 8*15K Haloferax mediterranei genome array genechips, representing about 3800 genes.

2012-04-19 | E-GEOD-37421 | biostudies-arrayexpress

Physiological and transcriptional response of Bacillus cereus treated with low-temperature nitrogen gas plasma

Project description:Aims: To investigate the inactivation kinetics of Bacillus cereus vegetative cells upon exposure to low-temperature nitrogen gas plasma and to reveal the mode of inactivation by transcriptome profiling. Methods and results: Exponentially growing B. cereus cells were filtered and put on agar plates. The plates, carrying the filters with the vegetative cells, were placed into nitrogen gas plasma at atmospheric pressure and cold temperature (~37°C). After different exposure times the cells were harvested for RNA extraction and enumeration. The RNA was used to perform whole transcriptome profiling using DNA microarrays. The transcriptome profile showed a large overlap with profiles obtained from conditions generating reactive oxygen species inside B. cereus. However, excess radicals such as peroxynitrite, hydroxyl and or superoxide were not found. Conclusions: Antibacterial activity of nitrogen gas plasmas is not based on UV radiation but on the formation of reactive oxygen or nitrogen species in the plasma jet rather than inside the targeted cells. Significance and impact of the study: This study represents the ﬁrst investigation of differential gene expression on a genome-wide scale in B. cereus following nitrogen gas plasma exposure. This study may help to design cheap, safe, and effective plasma decontamination devices. Plasma treated sampes compared with nitrogen gas flow treated samples and plasma treated samples compared to untreated control samples. Nitrogen flow samples in duplicate, plasma treated samples 4 replicates. Replicates hybridized with dyes swapped.

2013-05-06 | E-GEOD-35060 | biostudies-arrayexpress

Systems-wide understanding of the osmotic response and metabolic rearrangement in Bacillus megaterium

Project description:For many years now, Bacillus megaterium has served as a microbial industrial strain for high-level production of recombinant proteins in the g/L-scale. Nevertheless, the impact of process-related stress has only been poorly characterized so far. Taking advantage of the recent technical developments for quantifying the cell at various molecular levels, we interrogated the osmotic stress response of B. megaterium using transcriptome, proteome, metabolome and fluxome analyses. Under osmotic upshift conditions, several stress response enzymes, iron scavenging, and reactive oxygen species (ROS) fighting proteins were upregulated. The downregulation of genes of the upper part of glycolysis resulted in the activation of the pentose phosphate pathway (PPP), generating an oversupply of NADPH. The (NADH/NAD+) ratio indicating the redox state of the cell was also altered, which was partially compensated by the higher production of lactate accompanied by the reduction of acetate secretion. NADH was produced mainly within the tricarboxylic acid cycle (TCA) cycle elucidated from the higher mRNA and protein levels of enzymes involved within this pathway. This adaptation mainly focused on the massive de novo synthesis of the compatible solute proline recruiting an osmo-dependent pathway to fulfil this requirement. 13C flux analyses confirmed these findings. Giving the high flux towards acetyl-CoA and large pool of NADPH, B. megaterium cells redirected the produced acetyl-CoA to the polyhydroxybutyrate (PHB) biosynthetic pathway under non-limiting nutrient condition, amassing around 30% of the CDW as PHB. This direct relation between osmotic stress and intracellular PHB content has been evidenced for the first time, thus opening new avenues for synthesizing this valuable biopolymer using varying salt concentrations under non-limiting nutrient conditions.

2020-05-26 | PXD015605 | Pride

Effects of TiO2 and Ag nanoparticles on polyhydroxybutyrate biosynthesis by activated sludge bacteria

Project description:Manufactured nanomaterials (MNMs) are increasingly incorporated into consumer products that are disposed into sewage. In wastewater treatment, MNMs adsorb to activated sludge biomass where they may impact biological wastewater treatment performance, including nutrient removal. Here, we studied MNM effects on bacterial polyhydroxyalkanoate (PHA), specifically polyhydroxybutyrate (PHB), biosynthesis because of its importance to enhanced biological phosphorus (P) removal (EBPR). Activated sludge was sampled from an anoxic selector of a municipal wastewater treatment plant (WWTP), and PHB-containing bacteria were concentrated by density gradient centrifugation. After starvation to decrease intracellular PHB stores, bacteria were nutritionally augmented to promote PHB biosynthesis while being exposed to either MNMs (TiO2 or Ag) or to Ag salts (each at a concentration of 5 mg L-1). Cellular PHB concentration and PhyloChip community composition were analyzed. The final bacterial community composition differed from activated sludge, demonstrating that laboratory enrichment was selective. Still, PHB was synthesized to near-activated sludge levels. Ag salts altered final bacterial communities, although MNMs did not. PHB biosynthesis was diminished with Ag (salt or MNMs), indicating the potential for Ag-MNMs to physiologically impact EBPR through the effects of dissolved Ag ions on PHB producers.

2014-12-03 | GSE63781 | GEO

Transcriptome analysis of Geobacter sulfurreducens grown with different nitrogen sources

Project description:Investigation of comprehensive information about the expression level of RNA transcripts across the entire G.sulfurreducens genome with different nitrogen sources, including NH3, Gln, Asp and N2. A twelve chip study using total RNA recovered from four separate culture conditions of G.Sulfurreducens. G.Sulfurreducens PCA were harvested at mid-exponential phase. The high-density oligonucleotide tiling arrays used were consisted of 381,174 oligonucleotide probes spaced 20 bp apart (30-bp overlap between two probes) across the G.sulfurreducens genome (NimbleGen). Experiments were conducted as three bioliogical replicates (different cultures)

2010-06-30 | E-GEOD-17834 | biostudies-arrayexpress

The YmdB phosphodiesterase is a global regulator of biofilm-specific mRNA levels in Bacillus subtilis

Project description:Detailed description (other than provided below) of growth conditions, RNA preparation, cDNA synthesis and hybridization conditions can be found in the submitted paper. GSM956794-GSM956801: Bacillus subtilis 168 wild type and its ymdB derivative strain were grown in CSE-Glu medium and cells were harvested at mid exponential (OD600 ~0.8) and early stationary phase (OD600 ~2.2-2.4). For both time points, 4 biological replicates were used, resulting 4 slides for both exponential and stationary phase. Dye swaps are included in both experiments. GSM1011025-GSM1011032: Bacillus subtilis GP966 antibiotic tagged synthetic wild type and its ymdB E39Q point mutant strain GP969 were grown in CSE-Glu medium and cells were harvested at mid exponential (OD600 ~0.8) and early stationer phase (OD600 ~2.2-2.4). For both time points, 4 biological replicates were used, resulting 4 slides for both exponential and stationer phase. Dye swaps are included in both experiments.

2013-12-11 | E-GEOD-39142 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data