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GroEL-proteotypbing-based stable isotope probing of Thauera aromatica K172, Pseudomonas putida KT2440, and Escherichia coli BL21(DE3)

ABSTRACT: This dataset has been used to establish GroEL-SIP, coupling a targeted proteotyping approach for assessing bacterial community compositions using the taxonomic marker protein GroEL with stable isotope probing to link the identified taxa to substrate assimilation. This dataset contains raw data of four experiments: 1.) Pure cultures of T. aromatica cultivated with 13C or 12C benzoate mixed in defined ratios. 2.) Pure cultures of P. putida cultivated with 13C or 12C benzoate mixed in a 1:1 ratio. 3.) Pure cultures of E. coli cultivated with 12C acetate and 13C or 12C benzoate mixed in a 1:1 ratio. 4.) Co-cultivated biculture of T. aromatica and P. putida cultivated with 13C or 12C benzoate and mixed in a 1:1 ratio. 5.) Co-cultivated biculture of T. aromatica and E. coli cultivated with 12c acetate and 13C or 12C benzoate and mixed in a 1:1 ratio. 1)-3) were analyzed after in-solution digestion 4)-5) were analyzed after in-gel digestion of the 60 kDa band

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Thauera Aromatica K172 Escherichia Coli Bl21(de3) Bacteria Pseudomonas Putida Kt2440

TISSUE(S): Cell Culture

SUBMITTER: Simon Klaes

LAB HEAD: Lorenz Adrian

PROVIDER: PXD048255 | Pride | 2024-10-17

REPOSITORIES: Pride

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Project description:Anaerobic activation of benzene is expected to represent a novel biochemistry of environmental significance but research into the mechanisms has been stymied by a lack of a genetically tractable pure culture which unequivocally does not use molecular oxygen to activate benzene. Geobacter metallireducens grew in a medium in which benzene was the sole electron donor and Fe(III) was the sole electron acceptor with a stoichiometry of benzene loss and Fe(III) reduction consistent with benzene oxidation to carbon dioxide coupled with Fe(III) reduction. Phenol labeled with 18O was produced when the medium was labeled with H218O, as expected for a true anaerobic conversion of benzene to phenol. Gene expression patterns indicated that benzene was metabolized through a phenol intermediate rather than benzoate or toluene. Deletion of ppcB, which encodes a subunit of the phenylphosphate carboxylase, an enzyme required for phenol metabolism, inhibited metabolism of benzene. Deleting genes specific for benzoate or toluene metabolism did not. Comparison of gene expression patterns in cells grown on benzene versus cells grown on phenol revealed genes specifically expressed in benzene-grown cells. Deletion of one of these, Gmet_3376, inhibited anaerobic benzene oxidation, but not the metabolism of phenol, benzoate, or toluene. The availability of a genetically tractable pure culture that can anaerobically convert benzene to phenol with oxygen derived from water should significantly accelerate elucidation of the mechanisms by which benzene can be activated in the absence of molecular oxygen. Total RNA from three separate cultures of G. metallireducens grown with 250 ÂµM benzene three separate cultures of G. metallireducens grown with 500 ÂµM phenol three separate cultures of G. metallireducens grown with 1 mM benzoate three separate cultures of G. metallireducens grown with 500 ÂµM toluene three separate cultures of G. metallireducens grown with 10 mM acetate were used to study [1] Anaerobic oxidation of benzene by G. metallireducens (Benzene vs. acetate, Benzene vs. benzoate, Benzene vs. phenol, Benzene vs. toluene) [2] Anaerobic oxidation of benzoate by G. metallireducens (Benzoate vs. acetate) [3] Anaerobic oxidation of phenol by G. metallireducens (Phenol vs. acetate) [4] Anaerobic oxidation of toluene by G. metallireducens (Toluene vs. acetate) Each chip measures the expression level of 3,627 genes from G. metallireducens DSM 7210 with nine 45-60-mer probe pairs (PM/MM) per gene, with three-fold technical redundancy.

			Action	DRS
	01_EC44_01.raw	Raw
	01_TP14_01.raw	Raw
	02_EC44_02.raw	Raw
	03_EC44_03.raw	Raw
	03_TP15_03.raw	Raw

Dataset Information

GroEL-proteotypbing-based stable isotope probing of Thauera aromatica K172, Pseudomonas putida KT2440, and Escherichia coli BL21(DE3)

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