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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todo:paper_09593993_v34_n1_p_Macchi2023-10-03T15:52:54Z Insights into the genome and proteome of Sphingomonas paucimobilis strain 20006FA involved in the regulation of polycyclic aromatic hydrocarbon degradation Macchi, M. Martinez, M. Tauil, R.M.N. Valacco, M.P. Morelli, I.S. Coppotelli, B.M. Genomics HNA accumulation Phenanthrene pathway Proteomics Strain 20006FA Anthracene Aromatic compounds Bacteria Enzymes Genes Hydrocarbons Metabolism Metabolites Molecular biology Physiology Polycyclic aromatic hydrocarbons Proteins Trichloroacetic acid 1-Hydroxy-2-naphthoic acid Genomics HNA accumulation Intermediate metabolites Phenanthrene pathway Polycyclic aromatic hydrocarbon (PAH) Proteomics Sphingomonas paucimobilis Aromatic hydrocarbons 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. © 2017, Springer Science+Business Media B.V., part of Springer Nature. JOUR info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by/2.5/ar http://hdl.handle.net/20.500.12110/paper_09593993_v34_n1_p_Macchi |
| institution |
Universidad de Buenos Aires |
| institution_str |
I-28 |
| repository_str |
R-134 |
| collection |
Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) |
| topic |
Genomics HNA accumulation Phenanthrene pathway Proteomics Strain 20006FA Anthracene Aromatic compounds Bacteria Enzymes Genes Hydrocarbons Metabolism Metabolites Molecular biology Physiology Polycyclic aromatic hydrocarbons Proteins Trichloroacetic acid 1-Hydroxy-2-naphthoic acid Genomics HNA accumulation Intermediate metabolites Phenanthrene pathway Polycyclic aromatic hydrocarbon (PAH) Proteomics Sphingomonas paucimobilis Aromatic hydrocarbons |
| spellingShingle |
Genomics HNA accumulation Phenanthrene pathway Proteomics Strain 20006FA Anthracene Aromatic compounds Bacteria Enzymes Genes Hydrocarbons Metabolism Metabolites Molecular biology Physiology Polycyclic aromatic hydrocarbons Proteins Trichloroacetic acid 1-Hydroxy-2-naphthoic acid Genomics HNA accumulation Intermediate metabolites Phenanthrene pathway Polycyclic aromatic hydrocarbon (PAH) Proteomics Sphingomonas paucimobilis Aromatic hydrocarbons Macchi, M. Martinez, M. Tauil, R.M.N. Valacco, M.P. Morelli, I.S. Coppotelli, B.M. Insights into the genome and proteome of Sphingomonas paucimobilis strain 20006FA involved in the regulation of polycyclic aromatic hydrocarbon degradation |
| topic_facet |
Genomics HNA accumulation Phenanthrene pathway Proteomics Strain 20006FA Anthracene Aromatic compounds Bacteria Enzymes Genes Hydrocarbons Metabolism Metabolites Molecular biology Physiology Polycyclic aromatic hydrocarbons Proteins Trichloroacetic acid 1-Hydroxy-2-naphthoic acid Genomics HNA accumulation Intermediate metabolites Phenanthrene pathway Polycyclic aromatic hydrocarbon (PAH) Proteomics Sphingomonas paucimobilis Aromatic hydrocarbons |
| description |
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. © 2017, Springer Science+Business Media B.V., part of Springer Nature. |
| format |
JOUR |
| author |
Macchi, M. Martinez, M. Tauil, R.M.N. Valacco, M.P. Morelli, I.S. Coppotelli, B.M. |
| author_facet |
Macchi, M. Martinez, M. Tauil, R.M.N. Valacco, M.P. Morelli, I.S. Coppotelli, B.M. |
| author_sort |
Macchi, M. |
| title |
Insights into the genome and proteome of Sphingomonas paucimobilis strain 20006FA involved in the regulation of polycyclic aromatic hydrocarbon degradation |
| title_short |
Insights into the genome and proteome of Sphingomonas paucimobilis strain 20006FA involved in the regulation of polycyclic aromatic hydrocarbon degradation |
| title_full |
Insights into the genome and proteome of Sphingomonas paucimobilis strain 20006FA involved in the regulation of polycyclic aromatic hydrocarbon degradation |
| title_fullStr |
Insights into the genome and proteome of Sphingomonas paucimobilis strain 20006FA involved in the regulation of polycyclic aromatic hydrocarbon degradation |
| title_full_unstemmed |
Insights into the genome and proteome of Sphingomonas paucimobilis strain 20006FA involved in the regulation of polycyclic aromatic hydrocarbon degradation |
| title_sort |
insights into the genome and proteome of sphingomonas paucimobilis strain 20006fa involved in the regulation of polycyclic aromatic hydrocarbon degradation |
| url |
http://hdl.handle.net/20.500.12110/paper_09593993_v34_n1_p_Macchi |
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