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

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.

Figure 1

Circular maps and genetic features of PP1Y replicons. The principal genomic features of PP1Y Chr (A) and its plasmids (B, C and D) are shown. For each of them, we report, from outside to the center, genes on the forward and on reverse strands (red and blue), GC content (black) and GC skew (green and violet).

Figure 2

Open reading frame (ORF) annotation. Fraction of ORFs that resemble another protein based on BLAST matches with the Uniref50 and KEGG databases and that have a predicted function according to COG categories (A). The distribution of Chr and Mpl genes is reported with respect to COG functional categories (B) and according to Kegg pathways (C). D, Cell cycle control, cell division, chromosome partitioning. M, Cell wall/membrane/envelope biogenesis; N, Cell motility; O, Posttranslational modification, protein turnover, chaperones; T: Signal transduction mechanisms; U: Intracellular trafficking, secretion, and vesicular transport; V, Defense mechanisms; J: Translation, ribosomal structure and biogenesis; K: Transcription; L: Replication, recombination and repair; C, Energy production and conversion; E, Amino acid transport and metabolism; F, Nucleotide transport and metabolism; G, Carbohydrate transport and metabolism; H, Coenzyme transport and metabolism; I, Lipid transport and metabolism; P, Inorganic ion transport and metabolism; Q, Secondary metabolite biosynthesis, transport and catabolism; R, General function prediction only; S. Function unknown.

Figure 3

Neighbor-Joining tree summarizing the relationships among the alpha subunits of the dioxygenases of strains PP1Y, F199 and US6-1. Colours indicate the localization of the ORFs: blue PP1Y/chromosome; green, PP1Y/megaplasmid; red, F199/chromosome; magenta, F199/pNL1; brown, F199/pNL2; black, US6-1/chromosome; gray, US6-1/pLA1. The numbers following the name of the oxygenases refer to the gi accession numbers of the NCBI protein database. The analysis involved 164 amino acid sequences (the sequences used to prepare the tree in Additional file 1: Figure S4 plus 18 sequences from strain US6-1). All positions containing gaps were eliminated. There was a total of 150 positions in the final dataset. For clarity all the branches not containing sequences from strains PP1Y, F199 and US6-1 were compressed.

Figure 4

PP1Y growth, measured as total protein and total carbohydrate content in the culture medium, in the presence of millimolar concentrations of heavy metals. (A) 2.5 mM NiCl₂; (B) 10 mM PbCl₂; (C) 10 mM CuCl₂; (D) 5 mM ZnCl₂. The control growth shown in all graphs was performed in 1% glutamic acid. Empty squares and circles: total proteins and total carbohydrates, respectively in the control culture. Filled squares and circles: total proteins and total carbohydrates, respectively in the cultures containing metals. Error bars are omitted for clarity; relative error was invariably lower than 8%.