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Open Access Research article

Complete sequencing of Novosphingobium sp. PP1Y reveals a biotechnologically meaningful metabolic pattern

Valeria D’Argenio12, Eugenio Notomista3, Mauro Petrillo12, Piergiuseppe Cantiello1, Valeria Cafaro3, Viviana Izzo4, Barbara Naso12, Luca Cozzuto1, Lorenzo Durante3, Luca Troncone3, Giovanni Paolella12, Francesco Salvatore15* and Alberto Di Donato3

  • * Corresponding author: Francesco Salvatore salvator@unina.it

  • † Equal contributors

Author Affiliations

1 CEINGE-Biotecnologie Avanzate, Napoli, Italy

2 Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Napoli, Italy

3 Dipartimento di Biologia, Università di Napoli Federico II, Napoli, Italy

4 Dipartimento di Medicina e Chirurgia, Università degli Studi di Salerno, Salerno, Italy

5 IRCCS-Fondazione SDN, Naples, Italy

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BMC Genomics 2014, 15:384  doi:10.1186/1471-2164-15-384

Published: 19 May 2014

Abstract

Background

Novosphingobium sp. strain PP1Y is a marine α-proteobacterium adapted to grow at the water/fuel oil interface. It exploits the aromatic fraction of fuel oils as a carbon and energy source. PP1Y is able to grow on a wide range of mono-, poly- and heterocyclic aromatic hydrocarbons. Here, we report the complete functional annotation of the whole Novosphingobium genome.

Results

PP1Y genome analysis and its comparison with other Sphingomonadal genomes has yielded novel insights into the molecular basis of PP1Y’s phenotypic traits, such as its peculiar ability to encapsulate and degrade the aromatic fraction of fuel oils. In particular, we have identified and dissected several highly specialized metabolic pathways involved in: (i) aromatic hydrocarbon degradation; (ii) resistance to toxic compounds; and (iii) the quorum sensing mechanism.

Conclusions

In summary, the unraveling of the entire PP1Y genome sequence has provided important insight into PP1Y metabolism and, most importantly, has opened new perspectives about the possibility of its manipulation for bioremediation purposes.

Keywords:
De novo sequencing; Novosphingobium sp. PP1Y; Sphingomonads; Next generation sequencing; Aromatic pollutant compounds/bioremediation