Dataset Information

The Pd (II) reduction mechanisms in Bacillus megaterium Y-4 revealed by proteomic analysis

ABSTRACT: Many studies have been conducted on microbial reduction of Pd (II) to palladium nanoparticles (PdNPs) due to the environmental friendliness, low cost and the decreased toxicity of Pd (II) ions. In this study, we investigate the reduction mechanism of Pd (II) by Bacillus megaterium Y-4 through proteomics. Our results revealed that B. megaterium Y-4 may use the endogenous electron donor (NAD(P)H) generated by nirB, tdh and fabG and reductase to reduce Pd (II) to PdNPs. The expression levels of fabG, tdh, gudB and rocG that generates NAD(P)H were further increased, and the amount of reduced PdNPs was further increased in the presence of exogenous electron donor sodium formate. Endogenous electron mediators such as quinones and flavins in B. megaterium Y-4, can further enhance Pd (II) reduction. The findings provided invaluable information regarding the reduction mechanism of Pd (II) by B. megaterium Y-4 at the proteome level.

INSTRUMENT(S): Thermo Fisher Scientific instrument model

ORGANISM(S): Environmental Samples <bacteria

TISSUE(S): Cell Suspension Culture

SUBMITTER: Yuan Chen

LAB HEAD: Yuan Chen

PROVIDER: PXD049711 | Pride | 2024-05-24

REPOSITORIES: Pride

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			Action	DRS
	HFX1_FFRA22H004093-1A.raw	Raw
	HFX1_FFRA22H004094-1A.raw	Raw
	HFX1_FFRA22H004095-1A.raw	Raw
	HFX1_FFRA22H004096-1A.raw	Raw
	HFX1_FFRA22H004097-1A.raw	Raw

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Publications

The Pd (II) Reduction Mechanisms in Bacillus megaterium Y-4 Revealed by Proteomic Analysis.

Chen Yuan Y Wang Jiaxing J Chen Daidi D Wang Boxi B Wu Jinchuan J Liu Rongrong R Li Qingxin Q

Nanomaterials (Basel, Switzerland) 20240312 6

Many studies have been conducted on the microbial reduction of Pd (II) to palladium nanoparticles (Pd-NPs) due to the environmental friendliness, low cost, and the decreased toxicity of Pd (II) ions. In this study, we investigate the reduction mechanism of Pd (II) by Bacillus megaterium Y-4 through proteomics. The data are available via ProteomeXchange with identifier PXD049711. Our results revealed that B. megaterium Y-4 may use the endogenous electron donor (NAD(P)H) generated by ...[more]

PMID: 38535660

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Project description:Anaerobic benzene oxidation coupled to the reduction of Fe(III) was studied in Ferroglobus placidus in order to learn more about how such a stable molecule could be metabolized under strict anaerobic conditions. F. placidus conserved energy to support growth at 85°C in a medium with benzene provided as the sole electron donor and Fe(III) as the sole electron acceptor. The stoichiometry of benzene loss and Fe(III) reduction, as well as the conversion of [14C]-benzene to [14C]-carbon dioxide, was consistent with complete oxidation of benzene to carbon dioxide with electron transfer to Fe(III). Benzoate, but not phenol or toluene, accumulated at low levels during benzene metabolism and [14C]-benzoate was produced from [14C]-benzene. Analysis of gene transcript levels revealed increased expression of genes encoding enzymes for anaerobic benzoate degradation during growth on benzene versus growth on acetate, but genes involved in phenol degradation were not up-regulated during growth on benzene. A gene for a putative carboxylase that was more highly expressed in benzene- versus benzoate-grown cells was identified. These results suggest that benzene is carboxylated to benzoate and that phenol is not an important intermediate in the benzene metabolism of F. placidus. This is the first demonstration of a microorganism in pure culture that can grow on benzene under strict anaerobic conditions and for which there is strong evidence for degradation of benzene via clearly defined anaerobic metabolic pathways. Thus, F. placidus provides a much needed pure culture model for further studies on the anaerobic activation of benzene in microorganisms. A five-chip study using total RNA recovered from three separate cultures of Ferroglobus placidus DSM 10642 grown with 0.5 mM phenol (experimental condition) and two separate cultures of Ferroglobus placidus DSM 10642 grown on 1 mM benzoate (control condition). Each chip measures the expression level of 2,613 genes from Ferroglobus placidus DSM 10642 with nine 45-60-mer probe pairs (PM/MM) per gene, with three-fold technical redundancy.

Project description:Anaerobic benzene oxidation coupled to the reduction of Fe(III) was studied in Ferroglobus placidus in order to learn more about how such a stable molecule could be metabolized under strict anaerobic conditions. F. placidus conserved energy to support growth at 85°C in a medium with benzene provided as the sole electron donor and Fe(III) as the sole electron acceptor. The stoichiometry of benzene loss and Fe(III) reduction, as well as the conversion of [14C]-benzene to [14C]-carbon dioxide, was consistent with complete oxidation of benzene to carbon dioxide with electron transfer to Fe(III). Benzoate, but not phenol or toluene, accumulated at low levels during benzene metabolism and [14C]-benzoate was produced from [14C]-benzene. Analysis of gene transcript levels revealed increased expression of genes encoding enzymes for anaerobic benzoate degradation during growth on benzene versus growth on acetate, but genes involved in phenol degradation were not up-regulated during growth on benzene. A gene for a putative carboxylase that was more highly expressed in benzene- versus benzoate-grown cells was identified. These results suggest that benzene is carboxylated to benzoate and that phenol is not an important intermediate in the benzene metabolism of F. placidus. This is the first demonstration of a microorganism in pure culture that can grow on benzene under strict anaerobic conditions and for which there is strong evidence for degradation of benzene via clearly defined anaerobic metabolic pathways. Thus, F. placidus provides a much needed pure culture model for further studies on the anaerobic activation of benzene in microorganisms. A six-chip study using total RNA recovered from three separate cultures of Ferroglobus placidus DSM 10642 grown with 1 mM benzene (experimental condition) and three separate cultures of Ferroglobus placidus DSM 10642 grown on 0.5 mM phenol (control condition). Each chip measures the expression level of 2,613 genes from Ferroglobus placidus DSM 10642 with nine 45-60-mer probe pairs (PM/MM) per gene, with three-fold technical redundancy.

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Project description:Anaerobic benzene oxidation coupled to the reduction of Fe(III) was studied in Ferroglobus placidus in order to learn more about how such a stable molecule could be metabolized under strict anaerobic conditions. F. placidus conserved energy to support growth at 85°C in a medium with benzene provided as the sole electron donor and Fe(III) as the sole electron acceptor. The stoichiometry of benzene loss and Fe(III) reduction, as well as the conversion of [14C]-benzene to [14C]-carbon dioxide, was consistent with complete oxidation of benzene to carbon dioxide with electron transfer to Fe(III). Benzoate, but not phenol or toluene, accumulated at low levels during benzene metabolism and [14C]-benzoate was produced from [14C]-benzene. Analysis of gene transcript levels revealed increased expression of genes encoding enzymes for anaerobic benzoate degradation during growth on benzene versus growth on acetate, but genes involved in phenol degradation were not up-regulated during growth on benzene. A gene for a putative carboxylase that was more highly expressed in benzene- versus benzoate-grown cells was identified. These results suggest that benzene is carboxylated to benzoate and that phenol is not an important intermediate in the benzene metabolism of F. placidus. This is the first demonstration of a microorganism in pure culture that can grow on benzene under strict anaerobic conditions and for which there is strong evidence for degradation of benzene via clearly defined anaerobic metabolic pathways. Thus, F. placidus provides a much needed pure culture model for further studies on the anaerobic activation of benzene in microorganisms. A five-chip study using total RNA recovered from three separate cultures of Ferroglobus placidus DSM 10642 grown with 1 mM benzene (experimental condition) and two separate cultures of Ferroglobus placidus DSM 10642 grown on 1 mM benzoate (control condition). Each chip measures the expression level of 2,613 genes from Ferroglobus placidus DSM 10642 with nine 45-60-mer probe pairs (PM/MM) per gene, with three-fold technical redundancy.

Dataset Information

The Pd (II) reduction mechanisms in Bacillus megaterium Y-4 revealed by proteomic analysis

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Publications

The Pd (II) Reduction Mechanisms in <i>Bacillus megaterium</i> Y-4 Revealed by Proteomic Analysis.

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