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. 2013 Jun 3;8(6):e65425.
doi: 10.1371/journal.pone.0065425. Print 2013.

Complete genome sequence analysis of Nocardia brasiliensis HUJEG-1 reveals a saprobic lifestyle and the genes needed for human pathogenesis

Lucio Vera-Cabrera  1 , Rocio Ortiz-Lopez, Ramiro Elizondo-Gonzalez, Jorge Ocampo-Candiani
Affiliations

Complete genome sequence analysis of Nocardia brasiliensis HUJEG-1 reveals a saprobic lifestyle and the genes needed for human pathogenesis

Lucio Vera-Cabrera et al. PLoS One. .

Abstract

Nocardia brasiliensis is an important etiologic agent of mycetoma. These bacteria live as a saprobe in soil or organic material and enter the tissue via minor trauma. Mycetoma is characterized by tumefaction and the production of fistula and abscesses, with no spontaneous cure. By using mass sequencing, we determined the complete genomic nucleotide sequence of the bacteria. According to our data, the genome is a circular chromosome 9,436,348-bp long with 68% G+C content that encodes 8,414 proteins. We observed orthologs for virulence factors, a higher number of genes involved in lipid biosynthesis and catabolism, and gene clusters for the synthesis of bioactive compounds, such as antibiotics, terpenes, and polyketides. An in silico analysis of the sequence supports the conclusion that the bacteria acquired diverse genes by horizontal transfer from other soil bacteria, even from eukaryotic organisms. The genome composition reflects the evolution of bacteria via the acquisition of a large amount of DNA, which allows it to survive in new ecological niches, including humans.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Mycetoma of the foot from Nocardia brasiliensis showing the characteristic triad of tumefaction, fistulae and microcolonies.
Central image, an X-ray analysis of the ankle and foot region showing the severe destruction of bones. Right image, a microcolony of N. brasiliensis stained with PAS surrounded by a PMN infiltrate.
Figure 2
Figure 2. Physical map of the N. brasiliensis chromosome and gene clusters for putative virulence genes.
The outer scale is numbered in megabases starting from the dnaA gene. The outermost two circles represent the position and strand direction of putative virulence genes and transposases. Circles 3, 4, and 5 represent a BLAST comparison with the complete genome of Nocardia farcinica IFM 10152 (NC_6361.1, red), Rhodococcus equi 103S (NC_014659.1, cyan) and Mycobacterium tuberculosis H37Rv (NC_000962.2, yellow), respectively. Circle 6, GC content; circle 7, GC bias. In magenta, we show the fragment with different G+C% (between nucleotide 5,126,000 and nucleotide 5,800,000).
Figure 3
Figure 3. Syntenic dot plot of N. brasiliensis ATCC 700358 genome against Nocardia farcinica IFM10152 (a), Nocardia cyriacigeorgica GUH-2 (b), Rhodococcus equi 103S, Amycolatopsis mediterranei U32, Streptomyces coelicolor A(2), and Mycobacterium tuberculosis H37Rv genomes.
Dots represent a reciprocal best match by BLASTP comparison. The x-axis corresponds to the N. brasiliensis genome plotted against the rest of the genomes (y-axis). Inclination to the right corresponds to ORFs in same direction. An inclination to the left corresponds to an opposite direction. The highest homology in the Nocardia species was found at about the dnaA site. In each case, genome coverage was 30, 30, 11, 7, 5 and 4%.
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CONACYT grant No. 155892. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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