Open Access Highly Accessed Research article

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

Anthony Zoropogui1, Petar Pujic2, Philippe Normand2, Valérie Barbe4, Patrick Belli3, Arnault Graindorge1, David Roche4, David Vallenet4, Sophie Mangenot4, Patrick Boiron13, Véronica Rodriguez-Nava13, Sebastien Ribun13, Yves Richard14, Benoit Cournoyer14 and Didier Blaha13*

Author Affiliations

1 Research group on “Bacterial Opportunistic Pathogens and Environment”, Université de Lyon, Lyon, France

2 Research group on “Actinorhizal symbiosis”, Université de Lyon, Lyon, France

3 Research group on “Environmental Microbiology Lyon – Biological Resource Center”, UMR5557 Ecologie Microbienne, Université de Lyon, Université Lyon 1, CNRS, and VetAgro Sup Veterinary Campus, Lyon, France

4 Commissariat à l’Energie Atomique, Genoscope 91057, Evry cedex, France

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BMC Genomics 2013, 14:286  doi:10.1186/1471-2164-14-286

Published: 27 April 2013

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.

Keywords:
Nocardia cyriacigeorgica; Regions of genomic plasticity; Insertion sequences; COG; Evolution; Opportunistic pathogen