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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Global Transcriptional Analysis of Stress-Response Strategies in Acidithiobacillus ferrooxidans ATCC 23270 Exposed to Organic Extractant - Lix984n

ABSTRACT: Acidithiobacillus ferrooxidans (A. ferrooxidans) ATCC 23270 is a model bacteria for bioleaching research. Because of the use of extractant in metal extraction industry, A. ferrooxidans needs to cope with the water-organic two-phase system. To get insight into the molecular response of A. ferrooxidans to organic solvent, global gene expression pattern was examined in A. ferrooxidans ATCC 23270 cells subjected to Lix984n (an organic extractant) using the method of whole-genome DNA microarray. The data suggested that the global response of A. ferrooxidans to Lix984n stress was characterized by the up-regulation of genes involved in pentose phosphate pathway, fatty acid and glutamate biosynthesis contrary to the significant down-regulation of the majority motility-related genes. In further study, compared to heterotrophic bacteria in dealing with short-time stress, A. ferrooxidans has a special strategy of continuously enhancing the expression of genes encoding proteins involved in electron transport, such as petI, petII, cyo and cyd. Besides, acrAB-tolC operon encoding organic solvent efflux pump and its positive regulator gene ostR were addressed. In this work, the whole-genome array was employed to conduct the time-course transcriptome analysis of A. ferrooxidans ATCC 23270 in response to 1% (v/v) Lix984n for 5, 20, 40, and 80 min.

ORGANISM(S): Acidithiobacillus ferrooxidans ATCC 23270

SUBMITTER: xueduan liu

PROVIDER: E-GEOD-28538 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Global Transcriptional Analysis of Stress-Response Strategies in Acidithiobacillus ferrooxidans ATCC 23270 Exposed to Organic Extractant - Lix984n

Project description:Acidithiobacillus ferrooxidans (A. ferrooxidans) ATCC 23270 is a model bacteria for bioleaching research. Because of the use of extractant in metal extraction industry, A. ferrooxidans needs to cope with the water-organic two-phase system. To get insight into the molecular response of A. ferrooxidans to organic solvent, global gene expression pattern was examined in A. ferrooxidans ATCC 23270 cells subjected to Lix984n (an organic extractant) using the method of whole-genome DNA microarray. The data suggested that the global response of A. ferrooxidans to Lix984n stress was characterized by the up-regulation of genes involved in pentose phosphate pathway, fatty acid and glutamate biosynthesis contrary to the significant down-regulation of the majority motility-related genes. In further study, compared to heterotrophic bacteria in dealing with short-time stress, A. ferrooxidans has a special strategy of continuously enhancing the expression of genes encoding proteins involved in electron transport, such as petI, petII, cyo and cyd. Besides, acrAB-tolC operon encoding organic solvent efflux pump and its positive regulator gene ostR were addressed.

2011-04-14 | GSE28538 | GEO

Response of the Biomining Acidithiobacillus ferrooxidans to high Cadmium Concentrations

Project description:Cadmium is one of several heavy metals present in contaminated soils. Apparently, it has no biological role but can produce DNA damage, overexpression of stress response proteins and misfolded proteins, amongst other deleterial effects. Acidithiobacillus ferrooxidans is an acidophilic bacterium capable of resisting very high concentrations of heavy metals such as cadmium. This is important for industrial bioleaching processes where Cd+2 concentrations can be in the range of 5-100 mM. Cadmium resistance mechanisms in these microorganisms have not been fully characterized. A. ferrooxidans ATCC 53993 contains genes coding for possible metal resistance determinants such as efflux systems belonging to three families: P-type ATPases, RND transporters and cation diffusion facilitators (CDF). In addition, it has some extra copies of these genes in its exclusive genomic island (GI). Several of these putative genes were characterized in the present report by determining their transcriptional expression profiles and functionality. Moreover, a global quantitative proteomic analysis was carried out to further explore new cadmium resistance determinants in this biomining acidophile. Changes in iron oxidation pathways, upregulation of transport proteins (P-type ATPases and CDFs) and changes in ribosomal protein levels were seen. Finally, increased concentrations of exclusive putative cadmium ATPases present in strain ATCC 53993 GI and other non-identified proteins such as Lferr_0210, which forms part of a possible operon, could explain its greater resistance to cadmium compared to other acidophiles such as A. ferrooxidans ATCC 23270.

2022-02-28 | PXD012041 | Pride

The differentially expressed genes of A. ferrooxidans ATCC 23270 at different time after introduced fluoride

Project description:The deleterious fluoride ions, which released from fluoride in uranium during its bioleaching, strongly influenced microbial growth, energy intake, enzyme activity and relative metabolism. Whole-genome microarrays were used to obtain a comprehensive description of the molecular response by A. ferrooxidans ATCC 23270 at 4.8 mM fluoride stress. The experimental group was introduced 4mM fluoride at the mid-log phase. RNA from control samples were compared to the experimental samples taken at 10, 30, 60, 120 and 240 min after fluoride added. It was used to analyze the genome-wide expression profiling at different time after fluoride was introduced.

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Study of the quorum sensing regulon of the acidophilic Acidithiobacillus ferrooxidans ATCC23270 with cDNA microarrays

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20% (w/v) Glucose osmotic stress (YP20) vs 1M Sorbitol osmotic stress (YPS)

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2015-01-01 | E-GEOD-59659 | biostudies-arrayexpress

The differentially expressed genes of A. ferrooxidans ATCC 23270 at different time after introduced fluoride

2016-01-01 | GSE76450 | GEO

Transcription profiling of Acidithiobacillus ferrooxidans type strain ATCC23270 grown in the presence of iron or elemental sulfur as energy source until mid logarithmic phase

Project description:Transcriptional profiles from Acidithiobacillus ferrooxidans type strain ATCC23270 grown in the presence of iron or elemental sulfur as energy source until mid logarithmic phase were compared. Cells were harvested after 48 hs of growth in 9K-FeII pH 1.6 and after 120 hs of growth in 9K-S0 pH 3.5. Pellets were washed to remove precipitates, frozen and stored at -80C until RNA extraction.<br><br>In toto 8 different hybridizations were performed using 4 independent biological samples of A. ferrooxidans (with dye-swap), 4 arrays of array design FCV-CNRS AFE Oligoarray v.1 and 4 arrays of array design FCV-CNRS AFE Oligoarray v.2. This experimental design produced 8 raw data files and 1 transformed and/or normalized data file.

2009-12-31 | E-MEXP-1990 | biostudies-arrayexpress

Genome-wide transcriptome profiling of Acidithiobacillus ferrooxidans ATCC 23270 in response to the cyc2 knockout

Project description:The outer-membrane c-type cytochrome Cyc2 is generally considered to be the initial electron acceptor in iron respiratory chain of Acidithiobacillus ferrooxidans ATCC 23270, a model microorganism in acidophilic bioleaching environment. In our work, however, the knockout of cyc2 did not result in impaired Fe(II) consumption or growth capacity. To screen the potential genes for alternative initial electron acceptors other than Cyc2, RNA-Seq was employed to compare global gene expressions in the A. ferrooxidans ATCC 23270 wild type and the Δcyc2 mutant grown on Fe(II) or switched energy source from S0 to Fe(II). The data focused on 29 up-regulated and 19 down-regulated genes in the mutant under both conditions, among which AFE_1428 was the most highest one. in-silico analysis also suggested that the product of AFE_1428 might act as an alternative initial electron acceptor when Cyc2 was absent, which needs to be further validated.

2022-04-26 | GSE124570 | GEO

Stress-Responsive MicroRNAs in Populus

Project description:MicroRNAs (miRNAs), a group of small non-coding RNAs, have recently become a subject of intense study. They are a class of post-transcriptional, negative regulators playing vital roles in plant development and growth. However, little is known about their regulatory roles in treeâs responses to the stressful environments incurred over its long-term growth. Here, we reported the cloning of small RNAs from abiotic stressed tissues of P. trichocarpa and the identification of 68 putative miRNA sequences that can be classified into 27 families based on sequence homology. Among them, 9 families are novel, raising the number of the known ptc-miRNA families from 33 to 42. Total 346 targets are predicted for the cloned ptc-miRNAs using penalty scores of â¤2.5 for mismatched patterns in the miRNA:mRNA duplexes as the criterion. Six selected targets are experimentally validated. The expression of a majority of the novel miRNAs is altered in response to cold, heat, salt, dehydration, and mechanical stresses. Microarray analysis of known ptc-miRNAs identified 19 additional cold stress responsive ptc-miRNAs that originate from 14 miRNA gene families. Interestingly, we found that miRNAs of the same family respond differentially to the same stress. This suggests that members of a miRNA family may have different functions. These results reveal possible roles for miRNAs in the regulatory networks associated with development and stress response and therefore critical to plant long-term growth; and provide useful information for developing trees with a greater level of stress-resistance. Keywords: microRNA, cold stress, time course MicroRNA abundance of 21 samples from 7 cold stress time point were analyzed, each cold stress time point contain three replicates. 0 hour cold stress treatment were used as control.

2010-05-26 | E-GEOD-10582 | biostudies-arrayexpress

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