Draft Genome Sequence of Nocardia jinanensis, an Opportunistic Bacterial Pathogen That Causes Cellulitis.

The draft genome sequence of Nocardia jinanensis, an opportunistic pathogen that can cause skin infections, reveals genes that may contribute to the lifestyle and pathogenicity of N. jinanensis The genome also reveals the biosynthetic capacity of N. jinanensis in producing mycolic acids, siderophores, and other polyketide and nonribosomal peptide-derived secondary metabolites.

GENOME ANNOUNCEMENT

Nocardia is a genus of rare actinomycetes that is partially acid-fast in nature and characterized by a microscopic appearance of branching hyphae (1). Various Nocardia strains have been isolated from aquatic and terrestrial habitats as well as the tissue of infected patients. Nocardia are capable of producing secondary metabolites, some of which are likely to contribute to the pathogenicity of pathogenic Nocardia strains. The Nocardia jinanensis strain NBRC 108249 (CGMCC 4.3508, DSM 45048) was isolated from soil samples and is considered an opportunistic pathogenic strain that causes a form of skin infection called cellulitis (2). The pathogenesis of N. jinanensis seems to differ from that of the pathogenic Nocardia strains N. farcinica and N. brasiliensis. We sequenced the genome of N. jinanensis to gain a better understanding of the pathogenicity of N. jinanensis and its biosynthetic capacity.

The genomic DNA of N. jinanensis was isolated and purified using the TIANamp bacteria DNA kit. Genome sequencing was performed using a whole-genome shotgun technique (HiSeq Illumina platform), and the DNA fragments were assembled using SOAPdenovo by Macrogen, Inc. (South Korea). The draft genome of N. jinanensis has a G+C content of 67.3% and a size of 5.04 Mb. The genome seems to be relatively small compared to the genomes of N. farcinica (6.3 Mb), N. cyriacigeorgica (6.2 Mb), and N. brasiliensis (9.4 Mb). Phylogenetic analysis of Nocardia spp. based on 16S RNA sequences suggests that N. jinanensis belongs to the same clade as the pathogenic N. farcinica and N. cyriacigeorgica in the phylogenetic tree consisting of 78 Nocardia species. The genome of N. jinanensis contains the orthologs of a large number of putative pathogenic genes of N. farcinica (3), such as the Mce and YbrE virulence factors used for mammalian cell invasion and infection, superoxide dismutases, antigenic proteins/transporters, esterases, and hemolysin. The presence of the putative pathogenic genes provides support for the lifestyle and pathogenicity of N. jinanensis as an opportunistic pathogen.

Mining of biosynthetic gene clusters using antiSMASH 3.0 (4) suggests that the genome contains more than 20 biosynthetic gene clusters that encode polyketide synthase (PKS), nonribosomal peptide synthase (NRPS), terpene cyclase, glycosyltransferases, and other enzymes. The genome contains several unique biosynthetic gene clusters that indicate that N. jinanensis can produce secondary metabolites that are unique to the strain. We identified eight NRPS gene clusters and two PKS gene clusters in the genome. One of the PKS gene clusters shares high similarity with the mycolic acid gene cluster from Mycobacterium tuberculosis. This cluster is likely to be involved in the biosynthesis of mycolic acids, considering that it contains all the genes required for mycolic acid biosynthesis, including the genes that code for the iterative PKS, AMP-dependent ligase, carboxyl transferase, and other essential enzymes (5). The genome also contains two PKS-NRPS hybrid gene clusters. One of the PKS-NRPS gene clusters bears resemblance to the nocobactin cluster of N. farcinica and is also conserved in N. cyriacigeorgica GUH-2 (6).

Nucleotide sequence accession numbers.

The genome sequence can be found in GenBank with the accession numbers LNDA01000001 to LNDA01000107.