Differential protein expression during growth on model and commercial mixtures of naphthenic acids in Pseudomonas fluorescens Pf‐5

Abstract

Naphthenic acids (NAs) are carboxylic acids with the formula (C n H 2n + Z O 2 ) and are among the most toxic, persistent constituents of oil sands process‐affected waters (OSPW), produced during oil sands extraction. Currently, the proteins and mechanisms involved in NA biodegradation are unknown. Using LC‐MS/MS shotgun proteomics, we identified proteins overexpressed during the growth of Pseudomonas fluorescens Pf‐5 on a model NA (4′‐ n ‐butylphenyl)‐4‐butanoic acid ( n ‐BPBA) and commercial NA mixture (Acros). By day 11, >95% of n ‐BPBA was degraded. With Acros, a 17% reduction in intensity occurred with 10–18 carbon compounds of the Z family −2 to −14 (major NA species in this mixture). A total of 554 proteins ( n ‐BPBA) and 631 proteins (Acros) were overexpressed during growth on NAs, including several transporters (e.g., ABC transporters), suggesting a cellular protective response from NA toxicity. Several proteins associated with fatty acid, lipid, and amino acid metabolism were also overexpressed, including acyl‐CoA dehydrogenase and acyl‐CoA thioesterase II, which catalyze part of the fatty acid beta‐oxidation pathway. Indeed, multiple enzymes involved in the fatty acid oxidation pathway were upregulated. Given the presumed structural similarity between alkyl‐carboxylic acid side chains and fatty acids, we postulate that P . fluorescens Pf‐5 was using existing fatty acid catabolic pathways (among others) during NA degradation.

Construction of whole cell bacterial biosensors as an alternative environmental monitoring technology to detect naphthenic acids in oil sands process-affected water

“…This may have been a limitation of using duplicates for the transcriptome studies, but the use of transcriptional lux fusions validated many of the upregulated genes identified by RNA-seq. Many fatty acid degradation genes that likely contribute to β-oxidation of naphthenic acids were identified, which is consistent with the results of a proteomic study with Pseudomonas fluorescens Pf-5 (53). This study identified transcriptional repressors that may act as naphthenic acid sensing proteins.…”

“…We identified several strong inducible promoters capable of NA sensing, driving the expression of genes involved in degradation or protection from NA. A transcriptome approach was used for the discovery of NA-induced genes, although there were relatively few significantly induced genes when exposed to various NA extracts, compared to other genomic studies (53). This may have been a limitation of using duplicates for the transcriptome studies, but the use of transcriptional lux fusions validated many of the upregulated genes identified by RNA-seq.…”

The Use of Surface-Modified Nanocrystalline Cellulose Integrated Membranes to Remove Drugs from Waste Water and as Polymers to Clean Oil Sands Tailings Ponds

“…Naphthenic acids present as pollutants in oil sand tailings ponds are a series of aliphatic and alicyclic carboxylic acids with a pKa in the 5-6 range so at the pH of oil sands (approximately 8) these compounds are generally negatively charged but also vary significantly in their degree of hydrophobicity [25,27,29]. In these studies, we used a more aromatic naphthyloxy butanoic acid and a more complex mixed aliphatic/aromatic compound often used in oil sands naphthenic acid toxicity studies, butyl phenyl butanoic acid [51,52]. Naphthenic acids pollutants are present in oil sands tailings ponds at up to 120 µg/mL concentrations [53,54] and so in these binding studies the naphthenic acids were used at similar concentrations.…”

Microbial degradation of naphthenic acids using constructed wetland treatment systems: metabolic and genomic insights for improved bioremediation of process-affected water

“…metagenomics, metatranscriptomics) to scan the degradation potential of unculturable microorganisms. Experiments targeting gene or protein expression analyses (McKew et al 2021 ) have so far provided important insight on the diversity of NA-degrading microorganisms, genes, and pathways. This, coupled with the ever-growing accumulation of sequence data, provides the opportunity to explore the NA degradation potential in a range of environments where metagenomic data is available.…”