The Nocardia cyriacigeorgica GUH-2 genome shows ongoing adaptation of an environmental Actinobacteria to a pathogen's lifestyle

Abstract

Background: Nocardia cyriacigeorgica is recognized as one of the most prevalent etiological agents of human nocardiosis. Human exposure to these Actinobacteria stems from direct contact with contaminated environmental matrices. The full genome sequence of N. cyriacigeorgica strain GUH-2 was studied to infer major trends in its evolution, including the acquisition of novel genetic elements that could explain its ability to thrive in multiple habitats.

Results: N. cyriacigeorgica strain GUH-2 genome size is 6.19 Mb-long, 82.7% of its CDS have homologs in at least another actinobacterial genome, and 74.5% of these are found in N. farcinica. Among N. cyriacigeorgica specific CDS, some are likely implicated in niche specialization such as those involved in denitrification and RuBisCO production, and are found in regions of genomic plasticity (RGP). Overall, 22 RGP were identified in this genome, representing 11.4% of its content. Some of these RGP encode a recombinase and IS elements which are indicative of genomic instability. CDS playing part in virulence were identified in this genome such as those involved in mammalian cell entry or encoding a superoxide dismutase. CDS encoding non ribosomal peptide synthetases (NRPS) and polyketide synthases (PKS) were identified, with some being likely involved in the synthesis of siderophores and toxins. COG analyses showed this genome to have an organization similar to environmental Actinobacteria.

Conclusion: N. cyriacigeorgica GUH-2 genome shows features suggesting a diversification from an ancestral saprophytic state. GUH-2 ability at acquiring foreign DNA was found significant and to have led to functional changes likely beneficial for its environmental cycle and opportunistic colonization of a human host.

Figure 1

Histological observations of mice tissue infected byN. cyriacigeorgicaGUH-2. Photograph illustrating the immunohistochemistry analysis of kidney cells from a case of fatal septicemia; white arrows indicate filamentous bacteria.

Figure 2

Circular representation of the N. cyriacigeorgica chromosome. Scale is in megabases and indicated on the outer black circle. The orange bar indicates position of the replication terminus. Black arrows show correspondence between RGP and low G + C content. Moving inward, the second circle indicates putative virulence genes (red); the third circle indicates conserved synteny groups (≥ 5 CDS) between N. cyriacigeorgica, N. farcinica, R. jostii and M. tuberculosis (blue); the fourth circle indicates tRNA genes (black), phage related genes (soft pink) and IS (purple); the fifth circle indicates selected regions of genomic plasticity i. e. RGP-Cy1 to RGP-Cy22 (green; also see Table 2); the sixth circle indicates the largest CDS observed (pink) and the seventh circle shows GC plot of the N. cyriacigeorgica genome.

Figure 3

Percentage of N. cyriacigeorgica CDS shared with eight selected Actinobacteria genomes (A. mediterranei, C. diphtheriae, C. glutamicum, M. tuberculosis, M. smegmatis, N. farcinica, N. cyriacigeorgica, R. equi, and R. jostii). CDS belonging to pangenomes are in orange and were related to phylogenetic suborders and families shown in Figure 4. N. cyriacigeorgica CDS shared by two to seven Actinobacteria belonging to different families (Nocardiaceae, Mycobacteriaceae, Corynebacteriaceae, Pseudonocardiaceae) are in purple, CDS shared with only one genome are in green and N. cyriacigeorgica specific CDS are in blue (threshold of 40% identity).

Figure 4

NJ phylogenetic tree of the Actinobacteria inferred from concatenated gyrB-rrs-secA1-hsp65-rpoB DNA sequences. Phylogenetic order, suborders and families are indicated in red, orange and purple respectively.

Figure 5

Correspondance analysis of COGs in the genomes of Nocardia cyriacygeorgica and relatives identified on the Mage platform. COGs were retrieved for (Am) A. mediterranei, (Cd) C. diphtheriae, (Cg) C. glutamicum, (Mt) M. tuberculosis, (Ms) M. smegmatis, (Nc) N. cyriacigeorgica, (Nf) N. farcinica, (Re), R. equi, (Rj) R. jostii. The pathogens are highlighted in red, the non-pathogens or saprophytic bacteria in blue and the Nocardia in orange. The COGs comprise (A) RNA processing and modification, (B) Chromatin structure and dynamics, (C) Energy production and conversion, (D) Cell cycle control, cell division, chromosome partitioning, (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, (J) Translation, ribosomal structure and biogenesis, (K) Transcription, (L) Replication, recombination and repair, (M) Cell wall/membrane/envelope biogenesis, (N) Cell motility, (O) Posttranslational modification, protein turnover, chaperones, (P) Inorganic ion transport and metabolism, (Q) Secondary metabolites biosynthesis, transport and catabolism, (R) General function prediction only, (S) Function unknown, (T) Signal transduction mechanisms, (U) Intracellular trafficking, secretion, and vesicular transport, (V) Defense mechanisms. The first two principal components that represent respectively 47.7% (horizontal axis) and 23.5% (vertical axis) of the total variance of the dataset are plotted against one another.

Figure 6

Lineplot based on conserved synteny results (≥ 5 CDS) between N. cyriacigeorgica and N. farcinica genomes. Strand conservations (in green) and strand inversions (in red) are shown. Above the lineplot, orange bar indicates approximate terminus replication location and pink bars indicate transposases and insertion sequences. Blue bars indicate rRNA and green ones tRNA.

Figure 7

Cladogram illustrating the distribution of 22 RGP observed in the N. cyriacigeorgica GUH-2 genome among a panel of 83 N. cyriacigeorgica strains. PCR screenings targeted three markers among each of the 22 RGP. Strains indicated in red harbored 5 or more RGP and those in black harbored less than 5 RGP. “*” indicates strains moving from one cluster to another depending on the number of markers analyzed per RGP. The scale indicates the number of changes in the RGP patterns between pairs of strains.

Figure 8

Relation between isoelectric point (x-axis) and molecular weight (y-axis) of N. cyriacigeorgica proteins.