Cobalt resistance via detoxification and mineralization in the iron-reducing bacterium Geobacter sulfurreducens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA660261 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12547039.fastq.gz | Fastqsanger.gz | |||
| SRR12547040.fastq.gz | Fastqsanger.gz | |||
| SRR12547041.fastq.gz | Fastqsanger.gz | |||
| SRR12547042.fastq.gz | Fastqsanger.gz |
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Project description:We gained insights into the environmental controls of Geobacter activities in cobamide-driven microbiomes by investigating the adaptive responses of the model representative G. sulfurreducens to growth and reproduction in the presence of CoII. Consistent with environmental exposure, we demonstrate high CoII resistance in this species and describe from genomic rand transcriptomic data multiple pathways for protein and DNA repair, cell envelope modifications, and biofilm formation that allow the cells to effectively cope with CoII stress. Importantly, we show that metal acclimation also involves respiratory chains for the reductive precipitation of the metal on the cell’s surface. These adaptive responses allow Geobacter species to grow in CoII-rich environments, sustaining the productivity of the native microbiomes and contributing to hitherto abiotic reactions of the Co cycle.
2020-12-21 | GSE157146 | GEO
Project description:Bacteria in the genus Geobacter thrive in iron- and manganese-rich environments where the divalent cobalt cation (CoII) accumulates to potentially toxic concentrations. Consistent with selective pressure from environmental exposure, the model laboratory representative Geobacter sulfurreducens grew with CoCl2 concentrations (1 mM) typically used to enrich for metal-resistant bacteria from contaminated sites. We reconstructed from genomic data canonical pathways for CoII import and assimilation into cofactors (cobamides) that support the growth of numerous syntrophic partners. We also identified several metal efflux pumps, including one that was specifically upregulated by CoII. Cells acclimated to metal stress by downregulating non-essential proteins with metals and thiol groups that CoII preferentially targets. They also activated sensory and regulatory proteins involved in detoxification as well as pathways for protein and DNA repair. In addition, G. sulfurreducens upregulated respiratory chains that could have contributed to the reductive mineralization of the metal on the cell surface. Transcriptomic evidence also revealed pathways for cell envelope modification that increased metal resistance and promoted cell-cell aggregation and biofilm formation in stationary phase. These complex adaptive responses confer on Geobacter a competitive advantage for growth in metal-rich environments that are essential to the sustainability of cobamide-dependent microbiomes and the sequestration of the metal in hitherto unknown biomineralization reactions.
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Project description:Geobacter sulfurreducens is capable of reducing Pd(II) to Pd(0) using pyruvate as an electron donor; however, the biochemical and genetic mechanisms involved in this process have not been described. In this work, we carried out transcriptome profiling analyes to identify genes involved in Pd(II) reduction in this bacteria. Our results showed that 254 genes were upregulated while 142 were downregulated during Pd(II) reduction. Among the upregulated genes, 12 were related to energy metabolism and electron transport; 50 were classified as involved in protein synthesis; 42 were associated with regulatory functions and transcription, and 47 have no homologs with known function. RT-qPCR data confirmed upregulation during Pd(II) reduction of genes encoding PilA, the structural protein for the electrically conductive pili, and c-type cytochromes GSU1062, GSU2513, GSU2808, GSU2934, GSU3107, OmcH, OmcM, PpcA, PpcD. ΔpilA and ΔpilR mutant strains showed 20% and 40%, decrease in the Pd(II) reduction respectively, compared to the wild type strain, indicating the central role of the pili in this process. RT-qPCR data also confirmed downregulation during Pd(II) reduction of the omcB, omcC, omcZ, and omcS genes, which have been shown to be involved in Fe(III) reduction and electrodes. Based on these results, we propose mechanisms involved in Pd(II) reduction by G. sulfurreducens.
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Project description:Protein validation of Geobacter Sulfurreducens using LC-MS/MS
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Project description:Geobacter sulfurreducens is a dissimilatory metal-reducing bacterium capable of forming thick electron-conducting biofilms on solid electrodes in the absence of alternative electron acceptors. The remarkable ability of such biofilms to transfer electrons, liberated from soluble organic electron donors, over long distances has attracted scientific interest as to the mechanism for this process, and technological interest for application to microbial fuel and electrolysis cells and sensors. Here, we employ comparative proteomics to identify key metabolic pathways involved in G. sulfurreducens respiration by planktonic cells versus electron-conducting biofilms, in an effort to elucidate long-range electron transfer mechanisms.
2018-02-16 | PXD002667 | Pride
Project description:Geobacter sulfurreducens Raw sequence reads
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Project description:Geobacter sulfurreducens Genome sequencing and assembly
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Project description:In this study we further investigate the previously observed syntrophic interaction between Geobacter sulfurreducens and Pseudomonas aeruginosa. In early coculture establishment, two genetic variants of G. sulfurreducens emerged that were strongly selected for throughout coculture evolution. Single nucleotide polymorphism (SNP) variants occurred in fabI and tetR genes of G. sulfurreducens. The tetR variants displayed upregulation of adenylate cyclase transporter, CyaE and of RND efflux pump proteins as determined through SWATH-MS proteomics.
2020-04-20 | PXD013990 | Pride
Project description:Gene expression in a Geobacter sulfurreducens strain overexpressing the two-component system GsuTCS1
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Project description:Geobacter sulfurreducens was originally considered a strict anaerobe. However, this bacterium was later shown to not only tolerate but also to use oxygen as terminal electron acceptor. Research performed has so far only revealed the general ability of G. sulfurreducens to reduce oxygen, but the oxygen consumption rate has not been quantified, nor has evidence been provided as to how the bacterium achieves oxygen consumption. The microaerobic growth of G. sulfurreducens under more controlled operating conditions was investigated here and a transcriptome analysis was performed to elucidate possible metabolic mechanisms important for oxygen consumption in G. sulfurreducens. The experiments revealed that growth with oxygen is possible to the same extent as with fumarate when a maximum oxygen load per cell of 95 mgO2gcdw-1h-1 is applied. When oxygen concentrations are too high, growth is completely inhibited and there is no partial consumption. Transcriptome analysis suggests a menaquinol oxidase to be the enzyme responsible for oxygen reduction. Transcriptome analysis has further revealed three different survival strategies, depending on the oxygen concentration present. When prompted with small amounts of oxygen, G. sulfurreducens will try to escape the microaerobic area; if concentrations are higher cells will focus on rapid and complete reduction; and ultimately cells will form protective layers if a complete reduction becomes impossible. The results presented here have important implications for understanding how G. sulfurreducens survives exposure to oxygen.
2020-01-02 | GSE124792 | GEO