Insights into the genome and proteome of Sphingomonas paucimobilis strain 20006FA involved in the regulation of polycyclic aromatic hydrocarbon degradation

Abstract

In order to study the mechanisms regulating the phenanthrene degradation pathway and the intermediate-metabolite accumulation in strain S. paucimobilis 20006FA, we sequenced the genome and compared the genome-based predictions to experimental proteomic analyses. Physiological studies indicated that the degradation involved the salicylate and protocatechuate pathways, reaching 56.3% after 15 days. Furthermore, the strain degraded other polycyclic aromatic hydrocarbons (PAH) such as anthracene (13.1%), dibenzothiophene (76.3%), and fluoranthene. The intermediate metabolite 1-hydroxy-2-naphthoic acid (HNA) accumulated during phenanthrene catabolism and inhibited both bacterial growth and phenanthrene degradation, but exogenous-HNA addition did not affect further degradation. Genomic analysis predicted 126 putative genes encoding enzymes for all the steps of phenanthrene degradation, which loci could also participate in the metabolism of other PAH. Proteomic analysis identified enzymes involved in 19 of the 23 steps needed for the transformation of phenanthrene to trichloroacetic-acid intermediates that were upregulated in phenanthrene cultures relative to the levels in glucose cultures. Moreover, the protein-induction pattern was temporal, varying between 24 and 96 h during phenanthrene degradation, with most catabolic proteins being overexpressed at 96 h-e. g., the biphenyl dioxygenase and a multispecies (2Fe-2S)-binding protein. These results provided the first clues about regulation of expression of phenanthrene degradative enzymes in strain 20006FA and enabled an elucidation of the metabolic pathway utilized by the bacterium. To our knowledge the present work represents the first investigation of genomic, proteomic, and physiological studies of a PAH-degrading Sphingomonas strain.

The genome of Alcaligenes aquatilis strain BU33N: Insights into hydrocarbon degradation capacity

“…To further interrogate the genomic basis for the ability of BU33N to utilize complex aromatic hydrocarbons, the phenanthrene biodegradation pathway was identified and reconstructed ( Fig 8 ). On the basis of the identified genes, BU33N could be predicted to catabolize phenanthrene via the ortho-cleavage pathway [47, 48] to yield 3-carboxy-cis cis-muconate and subsequently beta-ketoadipate [49] through the β-ketoadipate pathway ( Fig 8 ). Unlike the benzoate degradation pathway described above, the enzymes involved in phenanthrene biodegradation are encoded in different genomic regions and only genes for (EC 1.14.12.10: benzoate 1,2-dioxygenase), (EC 1.3.1.25:1,2-dihydroxycyclohexa-3,5-diene-1-carboxylate dehydrogenase), (EC 1.2.1.10: Acetaldehyde dehydrogenase) and (EC 4.1.3.39: 4-hydroxy-2-oxovalerate aldolase) were positioned within the major aromatic compound degradation gene clusters.…”

Design and evaluation of synthetic bacterial consortia for optimized phenanthrene degradation through the integration of genomics and shotgun proteomics

“…6 a and Tables S9 and S10). Proteins with antioxidant function help in combating oxidative and osmotic stress [ 74 ] and were previously observed during PAH metabolism [ 26 ] as a result of the production of oxidative damage by oxygenases involved in the degradation of these compounds [ 75 ]. Membrane transport proteins like TonB-dependent active transporter, play a crucial role in aromatic degradation in Gram-negative bacteria, allowing the transport of large molecules across the cell membrane [ 76 , 77 ].…”

“…Genomes of the five isolates were sequenced with Illumina sequencing technology (HiSeq 1500, 2 × 100-bp paired-end reads) at INDEAR (Rosario, Argentina) and raw data were analysed as described in previous works [ 23 , 26 ]. Draft genome sequences have been deposited at the GenBank nucleotide database under accession nos.…”

Sphingosinithalassobacter tenebrarum sp. nov., isolated from a deep-sea cold seep

“…Polycyclic aromatic hydrocarbons (PAH) constitute ubiquitous and serious worldwide pollutants since they are extremely harmful to human health. Sphingomonas paucimobilis 20006FA was considered to be a good candidate to effectively degrade polycyclic aromatic hydrocarbons (PAH) including salicylate, protocatechuate, dibenzothiophene, anthracene and fluoranthene [17]. It has been found that Sphingomonas paucimobilis EPA505 could grow on 2,3-dimethylnaphthalene, anthracene, phenanthrene and fluoranthene and catalyze incomplete degradation of biphenyl, fluorene, anthraquinone, pyrene, and chrysene [18].…”