Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Growth of Cupriavidus metallidurans CH34 in the presence of basalt

ABSTRACT: The weathering of volcanic minerals makes a significant contribution to the global silicate weathering budget, influencing carbon dioxide drawdown and climate control. Basalt rocks may account for over 30% of the global carbon dioxide drawdown in silicate weathering. Yet the genetics of biological rock weathering are unknown. For the first time, we apply a DNA microarray to investigate the genes involved in weathering by the heavy metal resistant organism, Cupriavidus metallidurans CH34; in particular we investigate the sequestering of iron. The results show that the bacterium sequesters iron in the ferrous state (FeII); therefore, not requiring siderophores. Instead an energy efficient process involving upregulation of large porins is employed concomitantly with genes associated with biofilm formation. We hypothesise that rock weathering is induced by changes in chemical equilibrium at the microbe-mineral interface, reducing the saturation state of iron. We also demonstrate that low concentrations of metals in the basalt induce heavy metal resistant genes. Volcanic environments are analogous to some of the earliest environments on Earth. These results not only elucidate the mechanisms by which microorganisms might have sequestered nutrients on the early Earth but they also provide an explanation for the evolution of multiple heavy metal resistance genes long before the creation of contaminated industrial biotopes by human activity. Cultures of Cupriavidus metallidurans CH34 were grown in Tris buffered medium MM284 media (with iron), MM284 without iron and MM284 without iron with sterilized basalt at 25 rpm, 30°C until mid-log phase. RNA was extracted from the cells. Three biological replicates of both samples were differentially labeled (resp. Cy3 and Cy5) and hybridized to three CH34 60-mer oligonucleotide glass-spotted microarray carrying three technical repeats.

ORGANISM(S): Ralstonia metallidurans CH34

SUBMITTER: Natalie Leys

PROVIDER: E-GEOD-12133 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Background: The high number of heavy metal resistance genes in the soil bacterium Cupriavidus metallidurans CH34 makes it an interesting model organism to study microbial responses to heavy metals. Results: In this study the transcriptional response of this bacterium was measured after challenging it to a wide range of sub-lethal concentrations of various essential or toxic metals. Considering the global transcriptional responses for each challenge as well as by identifying the overlap in upregulated genes between different metal responses, the sixteen metals could be clustered in three different groups. Additionally, next to the assessment of the transcriptional response of already known metal resistance genes, new metal response gene clusters were identified. The majority of the metal response loci showed similar expression profiles when cells were exposed to different metals, suggesting complex cross-talk at transcriptional level between the different metal responses. The highly redundant nature of these metal resistant regions – illustrated by the large number of paralogous genes – combined with the phylogenetic distribution of these metal response regions within evolutionary related and other metal resistant bacteria, provides important insights on the recent evolution of this naturally soil dwelling bacterium towards a highly metal-resistant strain found in harsh and anthropogenic environments. Conclusions: The metal-resistant soil bacterium Cupriavidus metallidurans CH34 displays myriads of gene expression patterns when exposed to a wide range of heavy metals at non-lethal concentrations. The interplay between the different gene expression clusters points towards a complex cross-regulated regulatory network governing heavy metal resistance in C. metallidurans CH34. Keywords: Cupriavidus metallidurans CH34, transcriptional regulation, heavy metal resistance Two-condition experiments. Comparing samples after induction with heavy metals versus non-induced samples. Biological duplicate or triplicate. Each array contains 3 or 4 technical replicates.

Project description:Various environmental bacteria were adapted to the presence of toxic and recalcitrant organic solvents. Cupriavidus metallidurans CH34, a β-proteobacterium that was found in industrial environments is known as a bacterial model to study heavy metal resistance. Interestingly, genome screening of CH34 also reveals the existence of genes involved in the degradation of recalcitrant organic solvents, such acetone and aromatic compounds. Here, we showed that this bacterium could resist a large variety of organic solvents, and was also able to metabolize some of them. In particular, investigations were focused on acetone and isopropanol catabolism. Integrative studies based on transcriptomic (DNA microarrays), proteomic (2D-DIGE and Isotope-Coded Protein Label technology) and biochemical analyses (enzyme purification and characterization) showed a similar catabolic pathway for both molecules which involved the AcxABC acetone carboxylase. First, isopropanol is oxidized into acetone by the Adh alcohol dehydrogenase. Acetoacetate production from acetone is then catalyzed by the acetone carboxylase. The generated acetoacetate molecules are then transformed by the PacIJ 3-oxoacid CoA-transferase, to acetoacetyl-CoA and succinate. Finally, an acetyl-CoA acetyltransferase catalyses the hydrolysis of acetoacetyl-CoA into 2 acetyl-CoA that are introduced into the glyoxylate cycle. As demonstrated, key enzymes of the acetone/isopropanol catabolism (encoded by acx and ald genes) are under the control of a σ54-dependent RNA polymerase. Moreover, the catabolic pathway involved in acetone and isopropanol consumption was repressed when gluconate was given as alternative carbon substrate, displaying a new example of diauxie. The results presented here provide a comprehensive picture of acetone and isopropanol biodegradation in Cupriavidus metallidurans CH34 and strongly support the fact that CH34 can be considered as a solvent tolerant bacterium. Two-condition experiments. Comparing samples after induction with acetone versus non-induced samples. Biological triplicate. Each array contains 3 technical replicates.

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Growth of Cupriavidus metallidurans CH34 in the presence of basalt

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