Genome Organization and Adaptive Potential of Archetypal Organophosphate Degrading Sphingobium fuliginis ATCC 27551

Abstract

Sphingobium fuliginis ATCC 27551, previously classified as Flavobacterium sp. ATCC 27551, degrades neurotoxic organophosphate insecticides and nerve agents through the activity of a membrane-associated organophosphate hydrolase. This study was designed to determine the complete genome sequence of S. fuliginis ATCC 27551 to unravel its degradative potential and adaptability to harsh environments. The 5,414,624 bp genome with a GC content of 64.4% is distributed between two chromosomes and four plasmids and encodes 5,557 proteins. Of the four plasmids, designated as pSF1, pSF2, pSF3, and pSF4, only two (pSF1 and pSF2) are self-transmissible and contained the complete genetic repertoire for a T4SS. The other two plasmids (pSF3 and pSF4) are mobilizable and both showed the presence of an oriT and relaxase-encoding sequences. The sequence of plasmid pSF3 coincided with the previously determined sequence of pPDL2 and included an opd gene encoding organophosphate hydrolase as a part of the mobile element. About 15,455 orthologous clusters were identified from among the cumulatively annotated genes of 49 Sphingobium species. Phylogenetic analysis done using the core genome consisting of 802 orthologous clusters revealed a close relationship between S. fuliginis ATCC 27551 and bacteria capable of degradation of polyaromatic hydrocarbon compounds. Genes coding for transposases, efflux pumps conferring resistance to heavy metals, and TonR-type outer membrane receptors are selectively enriched in the genome of S. fuliginis ATCC 27551 and appear to contribute to the adaptive potential of the organism to challenging and harsh environments.

Keywords: biodegradation; genome sequence; horizontal gene transfer; mobile elements; organophosphate hydrolase; plasmids.

Fig. 1.

—Circular maps of the chromosomes (A and B) and plasmids (C- F) of Sphingobium fuliginis ATCC 27551. The innermost circle depicts the GC-skew of the reverse and forward strands in dodger blue and dark green, respectively. The second innermost circle represents the GC-content of the reverse and forward strands represented in violet and dark yellow, respectively. The third innermost (in pink) represents VNTRs. The fourth circle represents RNA genes (rRNAs in dark blue and tRNAs in light blue). Hypothetical and annotated proteins of the reverse strand are shown in blue and dark orange, respectively, in the fifth circle. The hypothetical (in red) and annotated proteins (in vivid green) of the forward strand are shown in the sixth circle. Island patches have been shown in pink color in the outermost circle. VNTRs are not shown in plasmids. The fourth circle is absent in plasmids(C- F) as the genes coding rRNAs and tRNAs are not present.

Fig. 2.

—Graphical representation of the pair-wise alignment of SMRT-generated pSF3 sequence with pPDL2 is shown along with ∼6 kb duplicated region in panel (A). The genetic organization of the duplication region is shown in panel (B).