Dataset Information

Proteomic characterization of the Pseudomonas sp. strain phDV1 response to monocyclic aromatic compounds

ABSTRACT: The degradation of aromatic compounds comprises an important step in the removal of pollutants and re-utilization of plastics and other non-biological polymers. Here we set out to study Pseudomonas sp. strain phDV1, a gram-negative bacterium that was selected for its ability to degrade aromatic compounds. In order to understand how the aromatic compounds and their degradation products are reintroduced in the metabolism of the bacteria and the systematic/metabolic response of the bacterium to the new carbon source, the proteome of this strain was analysed in the presence of succinate, phenol and o-, m-, p-cresol as sole carbon source. We then applied label-free quantitative proteomics to monitor overall proteome remodeling during metabolic adaptation to different carbon sources. As a reference proteome, we grew the bacteria in succinate and then compared the respective proteomes of bacteria grown on phenol and different cresols. In total, we identified 2295 proteins; 1908 proteins were used for quantification between different growth conditions. We found that 70, 100, 150 and 155 proteins were significantly differentially expressed in cells were grown in phenol, o-, m- and p-cresol-containing medium, respectively. The carbon source affected the synthesis of enzymes related to aromatic compound degradation, and in particular, the enzyme involved in the meta-pathway of monocyclic aromatic compounds degradation. In addition, proteins involved in the production of polyhydroxyalkanoate (PHA), an attractive biomaterial, showed higher expression levels in the presence of monocyclic aromatic compounds.Our results provide for the first time comprehensive information on the proteome response of this strain to monocyclic aromatic compounds.

INSTRUMENT(S): impact II

ORGANISM(S): Pseudomonas Sp. Phdv1

SUBMITTER: Julian Langer

LAB HEAD: Julian Langer

PROVIDER: PXD021237 | Pride | 2020-10-22

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	20180115_1480_GeTsiotis_bruker40_cartridge_90min_lin2-35_4ul_01_01.baf	Other
	20180115_1480_GeTsiotis_bruker40_cartridge_90min_lin2-35_4ul_01_02.baf	Other
	20180115_1480_GeTsiotis_bruker40_cartridge_90min_lin2-35_4ul_01_03.baf	Other
	20180115_1480_GeTsiotis_bruker40_cartridge_90min_lin2-35_4ul_02_01.baf	Other
	20180115_1480_GeTsiotis_bruker40_cartridge_90min_lin2-35_4ul_02_02.baf	Other

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Proteomic Characterization of the Pseudomonas sp. Strain phDV1 Response to Monocyclic Aromatic Compounds.

Lyratzakis Alexandros A Valsamidis Giannis G Kanavaki Iliana I Nikolaki Antigoni A Rupprecht Fiona F Langer Julian D JD Tsiotis Georgios G

Proteomics 20201119 2

The degradation of aromatic compounds comprises an important step in the removal of pollutants and re-utilization of plastics and other non-biological polymers. Here, Pseudomonas sp. strain phDV1, a gram-negative bacterium that is selected for its ability to degrade aromatic compounds is studied. In order to understand how the aromatic compounds and their degradation products are reintroduced in the metabolism of the bacteria and the systematic/metabolic response of the bacterium to the new carb ...[more]

PMID: 33108051

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Project description:The efficacy of inoculation of single pure bacterial cultures into complex microbiomes, for example, in order to achieve increased pollutant degradation rates in contaminated material (i.e., bioaugmentation), has been frustrated by insufficient knowledge on the behaviour of the inoculated bacteria under the specific abiotic and biotic boundary conditions. Here we present a comprehensive analysis of global gene expression of the bacterium Sphingomonas wittichii RW1 in contaminated sand, compared to regular suspended batch growth in liquid culture. RW1 is a well-known bacterium capable of mineralizing polycyclic aromatic hydrocarbons such as dioxins, dibenzofurans and other chlorinated congeners. We tested the reactions of the cells both during the immediate transition phase from liquid culture to sand with or without dibenzofuran, as well during growth and stationary phase in sand. Cells during transition resemble going through stationary phase, showing evidence of stress responses and nutrient scavenging, and even of major adjustments in their primary metabolism if they were not pre-cultured on the same contaminant as found in the soil. Cells growing and surviving in soil show very different signatures as in liquid or in liquid culture exposed to chemicals inducing drought stress, and we obtain evidence for numerous soil-specific expressed genes. We conclude that studies focusing on inoculation efficacy should test behavior under conditions as closely as possible mimicking the intended microbiome conditions We were interested to study the global reactions of bacteria with biodegradative properties under near-environmental as compared to laboratory culture conditions. we compared here the genome-wide responses of RW1 between regular laboratory batch growth on the aromatic substrates DBF and salicylate with growth in sandy soil with or without the same aromatic compounds. We analysed the cellular reactions immediately after introduction into the sand, during lag phase, all in carefully controlled and replicated experimental conditions.