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

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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.

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Acknowledgements

This research was partially supported by the Agencia Nacional de Promoción Científica y Tecnológica (PICT 2013-0103 and 2010-1983). Macchi M. has a doctoral fellowship supported by CONICET. Morelli I.S. is a research member of CIC-PBA. Coppotelli B.M. and Valacco MP are research members of CONICET. Dr. Donald F. Haggerty, a retired academic career investigator and native English speaker, edited the final version of the manuscript.

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Authors and Affiliations

  1. Laboratory of Microbial Degradation of Hydrocarbons, Centro de Investigación y Desarrollo en Fermentaciones Industriales, CINDEFI (UNLP; CCT-La Plata, CONICET), Street 50 No 227, 1900, La Plata, Argentina

    M. Macchi, M. Martinez, I. S. Morelli & B. M. Coppotelli

  2. Comisión de Investigaciones Científicas de la Provincia de Buenos Aires, La Plata, Argentina

    I. S. Morelli

  3. IQUIBICEN, FCEN-UBA, Buenos Aires, Argentina

    R. M. Neme Tauil & M. P. Valacco

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  1. M. Macchi
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  2. M. Martinez
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  3. R. M. Neme Tauil
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  4. M. P. Valacco
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  5. I. S. Morelli
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  6. B. M. Coppotelli
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Correspondence to B. M. Coppotelli.

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Macchi, M., Martinez, M., Tauil, R.M.N. et al. Insights into the genome and proteome of Sphingomonas paucimobilis strain 20006FA involved in the regulation of polycyclic aromatic hydrocarbon degradation. World J Microbiol Biotechnol 34, 7 (2018). https://doi.org/10.1007/s11274-017-2391-6

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