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, 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 carbon source, the proteome of this strain is analyzed in the presence of succinate, phenol, and o‐, m‐, and p‐cresol as the sole carbon source. As a reference proteome, the bacteria are grown in succinate and then compared with the respective proteomes of bacteria grown on phenol and different cresols. In total, 2295 proteins are identified; 1908 proteins are used for quantification between different growth conditions. The carbon source affects 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, show higher abundance in the presence of monocyclic aromatic compounds. The results provide, for the first time, comprehensive information on the proteome response of this strain to monocyclic aromatic compounds.

Polyhydroxyalkanoate (PHA) Production in Pseudomonas sp. phDV1 Strain Grown on Phenol as Carbon Sources

“…Mass spectrometry-based proteomics has been used to understand the aromatic biodegradation pathways in Pseudomonas sp. strain phDV1 [ 10 , 11 , 13 , 14 , 15 ]. These studies have shown that Pseudomonas sp.…”

“…These studies have shown that Pseudomonas sp. strain phDV1 can metabolize 2.2 mM phenol and 1.9 mM cresols, respectively, via the meta -cleavage pathway [ 10 , 13 , 15 ]. Recent studies show that monocyclic aromatic substrates influence the central carbon metabolism.…”

Label-Free Quantitative Proteomic Analysis of the Global Response to Indole-3-Acetic Acid in Newly Isolated Pseudomonas sp. Strain LY1

“…LY1. Lyratzakis et al, 2021). As shown in Figure 5, IAA-up DAPs were mainly grouped into three biological processes: IAA degradation, stress response, and membrane-related processes, and the three biological processes have interactions with each other.…”

“…Proteomic analysis is a useful tool to elucidate the global protein response to pollutant degradation ( Armengaud, 2016 ; Lyratzakis et al, 2021 ). As shown in Figure 5 , IAA-up DAPs were mainly grouped into three biological processes: IAA degradation, stress response, and membrane-related processes, and the three biological processes have interactions with each other.…”

“…Proteomics has been widely applied in the identification and quantification of proteins presented in a biological sample and provided a necessary foundation to generate insights into the complexities and molecular mechanisms under these complex systems ( Armengaud, 2016 ; Kellie et al, 2019 ). These approaches have been used to investigate catabolic pathways and screen metabolic genes involved in these metabolic pathways ( Li et al, 2016 ; Otzen et al, 2018 ; Lyratzakis et al, 2021 ). In addition, high-throughput proteomics analysis can be used to identify the global change in abundance of proteins due to adaptive responses of the microorganism using different substrates or under different environments.…”