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

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...

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Bibliographic Details
Published in:	World journal of microbiology & biotechnology Vol. 34; no. 1; pp. 7 - 14
Main Authors:	Macchi, M., Martinez, M., Tauil, R. M. Neme, Valacco, M. P., Morelli, I. S., Coppotelli, B. M.
Format:	Journal Article
Language:	English
Published:	Dordrecht Springer Netherlands 01-01-2018 Springer Nature B.V
Subjects:	Anthracene Anthracenes - metabolism Applied Microbiology Bacteria Bacterial Proteins - genetics Biochemistry Biodegradation Biodegradation, Environmental Biomedical and Life Sciences Biotechnology Biphenyl Biphenyl 2,3-dioxygenase Catabolism Computer Simulation Degradation Dibenzothiophene Dioxygenases - metabolism DNA, Bacterial Environmental Engineering/Biotechnology Enzymes Fluoranthene Fluorenes - metabolism Genetic transformation Genomes Genomic analysis Glucose - metabolism Hydrocarbon-degrading bacteria Hydroxybenzoates - metabolism Intermediates Life Sciences Metabolic Networks and Pathways - genetics Metabolic Networks and Pathways - physiology Metabolism Metabolites Microbiology Naphthols - metabolism Original Paper Phenanthrene Phenanthrenes - metabolism Physiology Polycyclic aromatic hydrocarbons Polycyclic Aromatic Hydrocarbons - metabolism Predictions Proteins Proteome - metabolism Proteomics Salicylates - metabolism Salicylic acid Soil Microbiology Soil Pollutants - metabolism Sphingomonas Sphingomonas - enzymology Sphingomonas - genetics Sphingomonas - growth & development Sphingomonas - metabolism Thiophenes - metabolism Trichloroacetic Acid - metabolism Whole Genome Sequencing Strain 20006FA HNA accumulation Phenanthrene pathway Genomics Proteomics
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Summary:	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.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	0959-3993 1573-0972
DOI:	10.1007/s11274-017-2391-6