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

MACCHI, M.; VALACCO, M. P.; MACCHI, M.; TAUIL, R. M. NEME; VALACCO, M. P.; COPPOTELLI, B. M.; TAUIL, R. M. NEME; COPPOTELLI, B. M.; MARTINEZ, M.; MORELLI, I. S.; MARTINEZ, M.; MORELLI, I. S.

WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY

SPRINGER

Año: 2018 vol. 34

0959-3993

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 toexperimental 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 phenanthrenedegradation, but exogenous-HNA addition did not affect further degradation. Genomic analysis predicted 126 putative genesencoding enzymes for all the steps of phenanthrene degradation, which loci could also participate in the metabolism of otherPAH. Proteomic analysis identified enzymes involved in 19 of the 23 steps needed for the transformation of phenanthrene totrichloroacetic-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, withmost catabolic proteins being overexpressed at 96 h?e. g., the biphenyl dioxygenase and a multispecies (2Fe?2S)-bindingprotein. These results provided the first clues about regulation of expression of phenanthrene degradative enzymes in strain20006FA and enabled an elucidation of the metabolic pathway utilized by the bacterium. To our knowledge the present workrepresents the first investigation of genomic, proteomic, and physiological studies of a PAH-degrading Sphingomonas strain.