BACKGROUND
nocardia is part of the well-known cmn actinobacterial group that also includes corynebacterium and mycobacterium in the corynebacteriales order  <cit> .
these actinobacteria are characterized by long-chain mycolic acids in their cell wall  <cit> , making them acid-resistant according to the ziehl-neelsen staining procedure, and favoring resistance to hydrophilic chemicals and dehydration.
all cmn genera include pathogenic strains causing human diseases that affect millions of individuals such as leprosy, tuberculosis, and diphtheria.
besides, the cmn group also includes saprophytes that thrive in soils, waters, and polluted environments.
the nocardia genus comprises about  <dig> species  <cit> .
n. cyriacigeorgica was defined as a species in  <dig> following the isolation and characterization of strain immib d-1627 t from a bronchial discharge in a chronic bronchitis patient in gelsenkirchen, germany  <cit> .
n. cyriacigeorgica can be differentiated from other species by 16s rdna sequence analysis, their ability at growing on acetamide but inability at using proline as carbon and nitrogen sources.
definition of this species was confirmed by conville et al.
during their investigation of nocardia strains with a type vi drug resistance pattern   <cit> .
n. cyriacigeorgica differs from n. farcinica strains by their ability at synthesizing a nitrate reductase and hydrolyzing xantine but their inability at synthesizing a urease, at hydrolyzing esculin and growing on l-rhamnose  <cit> .
n. cyriacigeorgica strains were described as etiological agents of human pneumonia, brain abscesses, and kidney, heart and eye infections  <cit> .
it is the most prevalent species involved in human nocardiosis in north america  <cit>  and its prevalence in france was estimated at 12% among human nocardial infections declared between  <dig> and  <dig>  <cit> .
nocardiosis can be fatal for immunosuppressed individuals  <cit> .
there is no report of nocardia cross-contaminations in human populations, suggesting that environmental exposure is the main cause of infection.
however, n. cyriacigeorgica has rarely been reported among environmental samples.
nevertheless, n. cyriacigeorgica strains have been recovered from oil contaminated soils  <cit> , and were shown to oxidize a variety of aliphatic compounds  <cit> .
in this work, the n. cyriacigeorgica guh- <dig> genome sequence is presented, and compared with those of other actinobacteria.
the guh- <dig> strain was isolated from a primary human kidney infection with systemic progression, which had a fatal outcome at georgetown university hospital, washington, d.c  <cit> .
the ability of this strain to induce parkinson-like symptoms in inoculated mouse and monkey models  <cit>  made it the model strain to study nocardia biology and pathogenesis.
these latter observations led to investigations on its possible role in some human parkinson cases  <cit> .
animals infected by n. cyriacigeorgica were found to develop abnormal behaviors like rhythmic vertical “yes-yes” head–shaking movements, stooped posture, hesitation to move forward, retropulsion, and restlessness  <cit> .
these parkinsonian-like symptoms appeared to be related to  a decrease in dopamine receptors and  a programmed cell death of dopaminergic neurons within the substantia nigra in mice  <cit> .
intraperitoneal injection of antiparkinsonian drugs such as l-dopa temporarily alleviated these symptoms  <cit> .
n. cyriacigeorgica guh- <dig> was also reported, in several independent experiments, to produce a substance that can induce apoptosis and dopamine depletion  <cit> .
inferences on the likely nature of this substance  were made from the cds sequence presented in this paper.
a transposon mutagenesis screening of mycobacterium tuberculosis showed the structural proteasomal genes of this closely related bacterium to be involved in their response toward oxidative and nitrosative stresses  <cit> .
the nocardial proteasome could thus play a role in virulence.
the guh- <dig> genomic sequence was also used to identify key evolutionary events in the emergence of n. cyriacigeorgica.
other members of the cmn group were shown to have evolved through important dna reshuffling.
insertion sequences  have largely contributed to genome rearrangements in the corynebacterium and mycobacterium genera, favoring deletion of genes, inversions, and functional specialization  <cit> .
important levels of cds duplications and domains reshuffling were reported in mycobacteria   <cit> .
statistical tests were performed to identify biases in n. cyriacigeorgica guh- <dig> cds and cog contents.
a phylogenomic approach was developed to track the origin of some cds or cds clusters.
these comparisons highlighted regions of genomic plasticity  among the n. cyriacigeorgica guh- <dig> genome.
selection of these rgp was probably a driving force in the emergence of n. cyriacigeorgica guh- <dig>  these results revealed highly dynamic genomic evolutionary patterns in n. cyriacigeorgica caused by a significant ability at acquiring foreign dna.
RESULTS
virulence status of n. cyriacigeorgica guh-2
virulence of n. cyriacigeorgica guh- <dig> strain was confirmed by intravenous injection of approximately 107 cfu in the tail of balb/c mice.
the death rate rose to 60% 7 days after infection.
autopsy indicated death to be due to septicemia with formation of nodules in several organs: kidneys, liver, brain, spleen, lungs and heart .
microscopic analysis of nodules showed high numbers of poly- and mono-nucleated inflammatory cells, and n. cyriacigeorgica guh- <dig> cells.
some mice were injected a lower number  of n. cyriacigeorgica guh- <dig> cells and developed abnormal behavior: rigidity, stooped posture, hemiparesis and vertical yes-yes head shaking probably due to a brain infection.
general features of the nocardia cyriacigeorgica genome
the  <dig> -mb genome of n. cyriacigeorgica was sequenced and annotated during this work.
it was found to harbor a single circular chromosome, and to have a ~ <dig> % g + c content.
three rrn operons containing the genes for the 16s, 23s and 5s rrnas,  <dig>  predicted protein-coding sequences ,  <dig> trna genes, and  <dig> pseudogenes i.e.
truncated genes, were detected.
a function could be predicted for most cds .
other cds were detected among other bacterial groups  or showed no homology with known sequences  .
n. cyriacigeorgica guh- <dig> strain did not harbor a plasmid.
the genome coding density was estimated at  <dig> %, which is markedly lower than the 91% value observed in related genomes .
guh- <dig> chromosome harbors eleven insertion sequences , and  <dig> cds encoding putative phage proteins.
putative virulence genes are scattered along the chromosome without distinguishable pathogenicity island .
several syntons of  <dig> cds or more were found conserved between n. cyriacigeorgica, n. farcinica, rhodococcus jostii and mycobacterium tuberculosis .
non-conserved regions frequently showed distinct g + c % biases.
regions encoding the largest putative proteins from the genome were found to have features of non ribosomal peptide synthetases  and showed a high g + c content.
the only exception is nocyr_ <dig> cds which has a g + c content slightly lower than the averaged one, and encodes a putative dipeptidyl carboxypeptidase dcp located near a transposase-related cds .
to better understand the events that had led to the present-day n. cyriacigeorgica guh- <dig> genomic structure, its core genome was delimited by identifying cds conserved in a panel of closely related actinobacteria .
15%  of the cds was found in a putative common ancestor to all genomes except frankia sp.
cci <dig> .
of these cds, 80% could be assigned a function and, as expected, a large proportion was inferred to play part in basic bacterial functions such as synthesis of proteins, nucleosides and nucleotides, amino acids, co-factor prosthetic groups and carriers, and of the cell envelope .
interestingly, the only cds exclusively shared between n. cyriacigeorgica and m. tuberculosis were those of is <dig>  an insertion sequence, suggesting a likely transfer of this is between these species.
the n. cyriacigeorgica and n. farcinica genomes were found to share  <dig> % of their cds, delimiting a nocardia pangenome of about  <dig>  mb.
<dig> cds  of n. cyriacigeorgica were not found in the n. farcinica genome.
most of these cds are of unknown function  but some are likely involved in phosphonate transport and metabolism , synthesis of fatty acids, glutamate metabolism, nitrite/nitrate transport, and rubisco production.
conversely,  <dig> cds of n. farcinica were not found in the n. cyriacigeorgica genome .
again, a high proportion of these cds  were “unk” cds  and a few could be related to particular activities like synthesis of thiocyanate  , catabolism of urea , of auxins  and lignin, heavy metal resistance and virulence .
these differences were in line with biochemical tests such as measurement of nitrate reductase and urease activities, performed to differentiate these two species.
<dig> % cds  of n. farcinica and n. cyriacigeorgica genomes were not recorded in other actinobacterial sequenced genomes .
these two nocardia strains have an equivalent genome size which is longer than the ones of primary actinobacterial pathogens .
<dig> %  of n. cyriacigeorgica cds content was not recorded in any other organisms referenced in the databases.
these cds were sometimes related to mobile and extrachromosomal elements but most of them were of “unknown function”.
a search for amplified cds among n. cyriacigeorgica genome revealed  <dig> occurrences, of which  <dig> are duplicated,  <dig> are triplicated and  <dig> are quadruplicated.
more than 29% of these cds could not be given a particular function, and 79% were also found in n. farcinica.
is , mce , transcriptional regulators  and nitrate reductase  were part of these amplified regions.
more than 23% of these cds were found among regions of genomic plasticity  .
out of the  <dig> cds present in n. cyriacigeorgica genome,  <dig> cds  could be assigned to a cog .
the proportion of these cogs among actinobacteria was similar, with a slightly higher occurrence of cds among the “transcription”  and “signal transduction”  cogs of the nocardia genomes.
correspondence analysis of the number of cds per cog among a set of actinobacterial species was performed, to identify a possible bias related to the pathogenic nature of the species.
this analysis showed that the number of cds per cog could differentiate primary pathogens from non-pathogens.
this “pathogen pattern” was more significant than the cog organization bias inferred from species belonging to a same genus.
on the other hand, all non-pathogens had closer cog patterns even though some were part of different genus or part of a genus showing pathogenic species.
cog patterns of the nocardia genomes were found similar to those of non-pathogens .
a correspondence analysis on the functional domains inferred from the cds of the “transcription” cog was performed .
this analysis did not segregate the dataset according to the pathogenic nature of the species regardless of their genus.
instead, the numbers of cds per sub-division were found similar between the nocardia genomes and similar to those observed among m. tuberculosis.
regions of genomic plasticity
a lineplot graph between n. farcinica and n. cyriacigeorgica genomes, representing synteny results of series of  <dig> cds or more, was performed in order to visualize the distribution of variable and conserved regions .
this analysis showed the number of conserved cds between these chromosomes to increase towards their respective origin of replication.
the lowest concentration of these cds was observed around the chromosomal terminus of replication.
overall, the organization of these variations was quite similar between the two halves of the circular chromosome creating a mirror-like effect indicative of increasing evolutionary constraints from the terminus towards the origin of replication .
the chromosomal terminus is partially visible on the circular map of n. cyriacigeorgica genome, and shows a large segment with a distinct g + c content according to the gc plot .
the artemis comparison tool  was used to refine these analyses and identify dna segments > <dig>  kb or containing more than  <dig> cds.
these dna regions were not showing all the features of genomic islands such as a trna gene at one end, an integrase cds or a g + c bias distinct from the one of the genome.
twenty-two rgp could be detected using this approach  .
twenty-one of these rgp were also detected with the rgpfinder tool of the mageplateform.
rgp-cy <dig> was not detected in this latter analysis because of its length of  <dig>  kb.
of these rgp, four could be considered genomic islets , and the largest rgp was of about 80 kb.
these rgp represented a total of 704 kb i.e.
<dig> % of the genome and encoded  <dig> cds.
the average g + c% content of these rgp is of  <dig> %, with values ranging from  <dig> % to  <dig> %.
rgp boundaries were analyzed.
trna or tmrna genes were detected at the extremity of ten of these.
direct dna repeats were observed for rgp-cy <dig> from positions  <dig> to  <dig> and  <dig> to  <dig>  at its left and right ends, respectively.
four rgp showed is sequences.
five rgp contain cds implicated in dna modification processes such as integrases, recombinases, endonucleases and excisionases.
these cds were probably involved in the acquisition of these rgp.
ten rgp did not show any of the above features.
most cds on these selected rgp encode putative proteins and transcriptional regulators of unknown function .
some cds, likely representing a benefit for n. cyriacigeorgica guh- <dig>  could be identified and predicted to encode a catalase , a limonene monooxygenase , and a sulfonate abc transporter .
furthermore, cds involved in nitrate metabolism were identified on the rgp-cy <dig>  a cobalamin-independent methionine synthase  and three cds involved in citrate metabolism were found on rgp-cy <dig> while pgly and pglz involved in phage defense were found on cy <dig> .
pcr screenings were designed to investigate the distribution of these rgp among 83 n. cyriacigeorgica strains .
prevalence of these rgp was quite variable, with some not being detected in other strains, and some being found among up to 69% of the strains.
rgp-cy <dig> and rgp-cy <dig> were only found in the n. cyriacigeorgica guh- <dig> genome and showed all the features of mobile elements.
a cladogram was built using the rgp distribution patterns based on the positive and negative pcr results .
dataset of inner rgp and rgp-ends dna targets were analyzed separately or together, and gave similar cladograms.
all strains harboring  <dig> or more rgp were grouped in the “guh- <dig> complex”.
other strains belonged to a “type strain complex”.
in fact, rgp patterns of  <dig> strains were found to be in the “guh- <dig> complex”, while patterns of  <dig> strains were allocated to the “type strain complex”.
among the “guh- <dig> complex”, some of the selected rgp were highly prevalent: rgp-cy <dig>  rgp-cy <dig>  rgp-cy <dig>  rgp-cy <dig>  rgp-cy <dig>  rgp-cy <dig> and rgp-cy <dig> were found in  <dig>   <dig>   <dig>   <dig>   <dig>   <dig>  and  <dig> strains respectively.
strain n <dig> harbored the highest number of rgp found in the n. cyriacigeorgica guh- <dig> genome .
among the type strain complex, rgp- cy <dig>  -cy <dig>  -cy <dig>  -cy <dig>  -cy <dig>  -cy <dig>  -cy <dig>  -cy <dig>  -cy <dig>  -cy <dig>  and -cy <dig> were not recorded.
no rgp seemed to be representative of this latter complex, and rgp-cy <dig>  rgp-cy <dig> and rgp-cy <dig> were the most prevalent.
rgp-cy <dig> was the most broadly distributed  among the n. cyriacigeorgica species.
pcr screenings targeting the left and right ends of rgp were defined to estimate the level of conservation of their respective proximal dna region.
the left  and right  ends of rgp-cy <dig>  -cy <dig>  and -cy <dig> were broadly detected whereas only one end could be detected for rgp-cy <dig> , -cy <dig> , -cy <dig> , -cy <dig> , -cy <dig> , -cy <dig> , -cy <dig> , -cy <dig> , -cy <dig> , -cy <dig> , and -cy <dig>  among all the strains tested.
the l and r ends of the rgp-cy <dig>  cy <dig>  cy <dig>  and cy <dig> were detected among the “guh- <dig> complex”, while only rgp-cy <dig> , -cy <dig> , -cy <dig> , -cy <dig> , -cy <dig> , -cy <dig> , -cy <dig>  could be detected among the “guh- <dig> complex” .
it is noteworthy that an attempt was made at comparing this rgp classification with phylogenetic relationships inferred from 16s rdna sequences.
however, significant sub-groups among n. cyriacigeorgica could not be resolved with this marker .
rgp represent gains in cds likely to confer novel properties but cds losses can also represent adaptations to particular habitats.
193 n. farcinica cds were found mising in the n. cyriacigeorgica guh- <dig> genome.
among these, 35% encode putative proteins of unknown function but four clusters of cds involved in glutamine metabolism, in phenyl acid acetic degradation, in thiocyanate degradation and nitrogen metabolism, and in urease synthesis were found mising .
the particular case of insertion sequences
on the n. cyriacigeorgica genome, eleven is belonging to five different families were detected .
a re-evaluation of the n. farcinica is genome content was performed, and led to the identification of fifteen is belonging to five families  .
only isnfa <dig> and isncy <dig> of the is <dig> family were found located in the same dna site of these two actinobacteria.
these is share 86% dna identity.
n cyriacigeorgica genome showed dna signatures of two tn <dig> transposons but one appeared to be truncated.
n. farcinica genome also showed the presence of a tn <dig> in which the transposase cds shares 85% dna identity with the one of n. cyriacigeorgica transposon  <dig>  inverted repeats  and/or direct repeats  were identified for five n. cyriacigeorgica is and for three n. farcinica is.
isncy <dig> copies  in n. cyriacigeorgica genome were found related to is <dig>  which was only previously detected in the m. tuberculosis and m. bovis genomes.
the n. cyriacigeorgica guh- <dig> genome harbors the isncy <dig> in four copies with one being partial and three being identical.
three is were found in several copies in n. farcinica.
isnfa <dig> of the is <dig> family was found in two copies with 99% dna identity; isnfa <dig> of the is <dig> family in eight copies with identities going from 72% to 99%; and isnfap <dig>  a partial element of the tn <dig> family, having 85% dna identity with a copy found on n. farcinica larger plasmid.
the distribution of six of these is/tn elements was investigated among a sub-set  of the n. cyriacigeorgica strains screened in the rgp section, a set  of n. farcinica strains, and a panel of nocardia species type strains  .
only isncy <dig>  and isnfa <dig>  were detected among both n. cyriacigeorgica and n. farcinica but their prevalence was quite different from one species to another.
in fact, both of these elements were more prevalent among the panel of strains of n. farcinica than n. cyriacigeorgica strains selected for this study.
isncy <dig>  was the most prevalent among n. cyriacigeorgica but was absent from the n. farcinica strains tested.
this isncy <dig> was also found among the n. otitidiscaviarum type strain.
isncy <dig> was not detected in n. farcinica.
its prevalence was higher among the guh- <dig> complex of n. cyriacigeorgica .
a similar situation was observed for isncy <dig>  isncy <dig> and isncy <dig> were not detected among the nocardia type strains that were selected for this analysis, suggesting a distribution restricted to n. cyriacigeorgica.
isnfa <dig> and isnfa <dig> were not detected in n. cyriacigeorgica and appeared to be restricted to n. farcinica strain  <dig>  isncy <dig>  and isnfa <dig>  share 89% identity, and were detected among several strains of n. farcinica and n. cyriacigeorgica.
a cladogram was built from this is distribution pattern analysis and was found to match the rgp distribution patterns .
virulence-related functions
several genes were previously found involved in virulence among actinobacteria.
blast and keyword-based searches allowed identification of some of these cds among the n. cyriacigeorgica genome.
six complete mce  loci containing yrbe and mas  cds were found.
analysis of cds encoding cell wall components involved in virulence revealed 85-kda antigens family proteins , lipoproteins  and pe_pgrs/ppe family proteins .
two superoxide dismutase cds  and three catalase ones were also identified.
nitrate reductase cds , trehalose  <dig> ’-dimycolate transferase  and rubisco  were detected and found to be clustered.
extracellular enzymes were identified by searching for particular domains including a peptide leader and low number of transmembrane domains.
the inferred secretome of n. cyriacigeorgica guh- <dig> was compared with the ones of other actinobacteria, and showed a majority  of putative proteins of unknown function, several proteases, lipases as well as a transcriptional regulator and members of the mce genes .
comparison of the putative proteins of the n. cyriacigeorgica and n. farcinica secretomes showed high identities , much higher than those observed with other actinobacteria .
the n. cyriacigeorgica guh- <dig> genome shows a good potential for the synthesis of a number of metabolites that could be antimicrobials or proteasome inhibitors.
seven cds were predicted to encode polyketides synthases , and  <dig> cds were predicted to encode nrps .
among n. farcinica,  <dig> pks and  <dig> nrpss were found including the cluster of cds previously described as producing a lipid-soluble iron-binding nocobactin.
a cluster of nine cdss similar to the coelibactine synthesis cluster in streptomyces coelicolor was also identified in n. cyriacigeorgica guh-2’s genome.
nocyr_ <dig> was found to be the longest cds of the genome  and likely to encode a nrps with twelve modules.
two other nrps operons containing two and three cds could synthesize molecules containing thirteen and eleven building blocks, respectively.
a 2-amino- <dig>  epoxi-8-oxodecanoic acid was predicted for nocyr_ <dig>  this putative acid shows a structure similar to the epoxomicin proteasome inhibitor  but chemical assays will be required to confirm its synthesis.
other softwares did not find this structure.
it is noteworthy that a correlation was observed between the isoelectric point and the molecular weight of the inferred proteins of the n. cyriacigeorgica guh- <dig> genome.
the largest proteins of the genome, constituted mainly by nrps and pks, showed similar isoelectric points, suggesting a compartmentalization inside the cytosol that could allow a coordinated functioning of these enzymes .
genetic potentials and metabolic profiling
phenotypic microarray datasets including antibiotic resistances were compared with the functional predictions made from the annotated n. cyriacigeorgica guh- <dig> genome.
phenotypic profiling was performed by testing n. cyriacigeorgica ability to grow with various carbon and nitrogen sources.
kegg pathways were used to find the cds involved in these pathways but also as a reference for explaining an absence of growth under certain conditions.
.
only seven amino acids  could be used as carbon and/or nitrogen sources.
the absence of some cds previously shown in other bacteria to be involved in the substrate catabolism or transport could explain several negative results.
however, the lack of growth with l-aspartic acid, l-lysine and l-proline could not be explained by the absence of particular cds.
the osmoadaptation capacity n. cyriacigeorgica guh- <dig> was also tested and found to be high under high salt concentrations.
this property could involve cds encoding transport proteins and/or osmoprotectants like ectoine and betaine .
growth tests were also performed under various ph.
n. cyriacigeorgica guh- <dig> was shown to grow at ph  <dig> and  <dig> but not ph  <dig> .
this dataset was completed by an analysis of the antibiotics resistance pattern of n. cyriacigeorgica guh- <dig> using plate assays.
n. cyriacigeorgica guh- <dig> was confirmed to have a type vi pattern with resistance against several sulfonamides, aminoglycosides, tetracyclines and penicillins.
it was found sensitive to cefamandole, cefotaxime, amikacin, and imipenem.
many cds likely playing part in these antibiotic resistances were found in the n. cyriacigeorgica genome.
a mutation in the gyrase a gene that can prevent ciprofloxacin binding, was detected.
several cds were inferred as encoding β-lactamases in the guh- <dig> genome, and could be responsible for the observed ampicillin, carbenicillin, oxacillin and penicillin resistances.
the paromomycin and tobramycin resistances observed can be due to the expression of one of the three aminoglycoside phosphotransferases detected by the annotation process.
macrolide resistances could involve one of the six ribosomal rna methyltransferases encoded by the guh- <dig> genome.
these may cause a decrease in the affinity of macrolides for the 50s ribosomal unit.
the fourteen drug or multidrug efflux transporters encoded by this genome could be involved in tetracycline, penimepicycline, polymyxin b, paromomycin, d,l-serine hydroxamate, sisomicin, sulfamethazine, novobiocin and/or sulfadiazine resistance  by extruding these molecules.
discussion
nocardia cyriacigeorgica is an opportunistic pathogen causing many infections including deadly brain abscesses and granulomatous diseases among immune-compromised and healthy individuals.
however, the bacterial properties involved in these infections are poorly understood.
here, the content, organization, plasticity, and functional potentialities of n. cyriacigeorgica guh- <dig> full genome sequence are presented.
a particular attention was paid to the analysis of cds likely involved in virulence including antibiotic resistances.
these analyses led to the identification of several rgp and is elements that were then tracked among a panel of n. cyriacigeorgica strains.
these screenings revealed an important ability of this species at acquiring dna by horizontal transfer events.
virulence determinants
the n. cyriacigeorgica guh- <dig> genome analyses revealed several genetic determinants related to virulence.
some of these are part of rgp but some were also part of the nocardia or actinobacteria pangenomes inferred from comparisons with the full genome sequence of n. farcinica and other actinobacteria.
the genome of n. cyriacigeorgica harbors virulence-related cds such as mce coding genes described as important virulence factors of m. tuberculosis <cit> .
mce can act as transmembrane transporters favoring macrophage invasion  <cit> .
these cdss are organized in operons containing two yrbe cds followed by six mce cds and sometimes two mce associated  cdss.
there are six copies of the complete mce operon in n. cyriacigeorgica and n. farcinica whereas four copies are identified in m. tuberculosis genome.
although, the importance of these cdss in m. tuberculosis virulence has been shown  <cit> , their detection in multicopies among m. smegmatis and r. jostii  suggests a function not limited to cell entry  <cit> .
having access to the n. cyriacigeorgica mce cds will allow transcriptomics experiments to identify the mce cdss which are turned on during host cell colonization.
other n. cyriacigeorgica cdss besides mce have been described as important in the infection and cell invasion processes.
in particular, the expression of superoxide dismutase and catalase cds were observed during n. cyriacigeorgica macrophage invasion and were suggested to be involved in resistance towards oxidative stresses  <cit> .
two sod and three kat cds were found in the n. cyriacigeorgica genome.
the kata cds is harbored by the rgp-cy <dig> but the other two kat cdss are found on conserved genomic regions.
other cdss can also have a complementary action during nocardia growth in macrophages.
the trehalose  <dig> ’-dimycolate transferase cds was found related to the 85-kda antigen family protein  <cit>  that can promote m. tuberculosis survival in macrophages by decreasing both phagosomal acidification and phagolysosomal fusion  <cit> .
an encoded n. cyriacigeorgica hemolysin which can disrupt the phagolysosome membrane was also annotated and could also favor survival in macrophages  <cit> .
the isocitrate lyase cds observed on rgp-cy <dig> could also be part of the n. cyriacigeorgica macrophage invasion process by preventing host cell apoptosis as observed in m. tuberculosis <cit> .
an intracellular pathogen not only requires defense mechanisms against macrophage antibacterial processes but also needs to survive under low oxygen pressure such as the one observed in poorly irrigated tissue of the mammal body  <cit> .
cds involved in such processes can thus also be defined as virulence-related determinants.
n. cyriacigeorgica contains denitrification cdss  of which five are harbored by rgp-cy <dig>  n. cyriacigeorgica was initially described as an obligate aerobe but presence denitrifying cds suggests an ability to grow under anaerobic conditions.
however, the conditions allowing growth under low oxygen pressure remain to be defined.
several metabolites, proteins, enzymes and lipids which are not directly involved in colonization but are at the frontline during host infection can also play a role in virulence such as cell wall constituents and some extracellular enzymes/metabolites.
the cell wall is a protection for bacteria but can also be a target for the immune system.
for example, pe/ppe serine α/β hydrolases membrane proteins are important in mycobacterium pathogenic species to avoid detection or killing during their intracellular life in a variety of host cells  <cit> .
however, their low number in n. cyriacigeorgica and n. farcinica could be an effect of their opportunistic status  and could explain their poor ability to escape the immune system of a healthy host.
nocardia can also secrete several enzymes that may interfere with the host cell metabolism  <cit> , in particular sods  <cit> , lipases  <cit>  and proteases  <cit> .
cdss encoding such enzymes were observed in the n. cyriacigeorgica guh- <dig> genome.
eight cdss were found encoding extracellular lipases and  <dig> encoding extracellular proteases.
nevertheless, much more cdss encoding putative secreted enzymes have been reported in mycobacterium such as the esat  proteins  <cit> .
n. cyriacigeorgica guh- <dig> genome harbored three esat cdss.
another major group of secreted molecules that can play a role in virulence are siderophores.
nocardia strains can produce several siderophores like formobactin  <cit> , amamistatin  <cit> , brasilibactin  <cit> , asterobactin  <cit>  and nocobactin  <cit> .
nocobactin synthesis was previously found encoded by two genetic clusters, with cluster i positioned 195 kb from cluster ii.
the n. cyriacigeorgica guh- <dig> genome showed a cluster i organization different from the one observed in the n. farcinica genome.
the gene nbth is absent in the n. cyriacigeorgica guh- <dig> genome and replaced by a putative formyltransferase cds, which could play a role in preventing the transfer of an acyl chain to the ϵ-amino group of lysine.
the n. cyriacigeorgica guh- <dig> cluster ii shows high identities with the one of n. farcinica but additional cds encoding nrps and an exported protein of unknown function were recorded.
the nrps cdss could play a role in the synthesis of this siderophore and change some of its properties.
a coelibactin-like siderophore is also likely to be produced by n. cyriacigeorgica guh- <dig>  a conserved synteny was observed with s. coelicolor cds involved in its synthesis except for a supplementary cds encoding a cytochrome p <dig> protein.
these actinobacteria are also known to synthesize other extracellular metabolites through nrps and pks-related processes.
the n. cyriacigeorgica guh- <dig> genome was found to encode  <dig> pks-related cdss and  <dig> nrps-related ones.
it is considered that the substance produced by n. cyriacigeorgica guh- <dig> which can cause brain damages by inducing apoptosis and a dopamine depletion would be encoded by a nrps or pks  <cit> .
here, a putative metabolite produced by an operon of three nrpss could be predicted to have a structure similar to the one of epoxomicin  <cit> .
such molecules have epoxy groups that could inhibit the functioning of proteasomes.
nrps and pks are also involved in the synthesis of antibiotics, and could have been involved in the synthesis of transvalencin z  <cit> , da- <dig>  <cit> , and nocardithiocin  <cit> .
however, the molecules produced by these synthases are often difficult to obtain in large quantities and are hard to purify from culture filtrates without genetic manipulations.
phenotypic and genomic plasticities
metabolic profilings showed n. cyriacigeorgica guh- <dig> abilities at growing on a variety of substrates.
in most cases, the cdss involved in transport and catabolism of these substrates were found in the genome.
however, some metabolic activities inferred from the genome could not be confirmed by growth tests e. g. the growth on l-glycine, l-lysine, and l-proline.
interestingly, cdss involved in l-lysine and l-proline catabolism were detected outside rgp but showed a codon adaption index  below the average .
this codon bias could be related to the low expression of these cdss, and might be the consequence of a recent acquisition.
an overexpression of these genes by genetic manipulations of n. cyriacigeorgica guh- <dig> would be needed to test this hypothesis.
low cai was also observed for cdss identified when in vivo activity was assessed.
in this case the presence of multiple cds  assigned to this function probably allowed a sufficient gene expression level to observe the expected phenotype.
a high turnover of rgp appears to occur among n. cyriacigeorgica.
n. cyriacigeorgica guh- <dig> closest rgp profile among a collection of  <dig> strains showed the absence of  <dig> rgp and the conservation of  <dig> ones.
rgp profilings thus suggest a good n. cyriacigeorgica competence towards dna acquisition but the mechanisms involved remain to be determined.
rgp-cy <dig> appeared to have been recently acquired by n. cyriacigeorgica guh- <dig>  and was found to harbor all the trademarks of mobile genomic islands.
this rgp could be a good candidate for the design of a dna cloning vector  <cit> .
no rgp was found related to prophage-like elements.
this is different from the situation observed in corynebacterial and mycobacterial pathogenic genomes, where such prophage-like dna contains virulence genes  <cit> .
a high turnover of is elements was also observed among nocardia.
however, while several is were found among the n. cyriacigeorgica  and n. farcinica  genomes in this work, previous studies had only identified two is among the nocardia: isnfa <dig>   <cit>  and is <dig>   <cit> .
these low numbers suggested nocardia strains to have a poor propensity at acquiring exogenous dna which are often acting as is shuttles.
here, we clearly demonstrate the opposite.
the nocardia genomes were found to be rich in is elements and diversity.
is of eight families were recorded suggesting a high genomic tolerance towards these elements and a frequent acquisition by these actinobacteria.
however, about 45% of the observed is did not show ir and dr. a lack of such sequences could be indicative of a loss of transposition autonomy or of selective pressures leading to their fixation at a particular site because of functional benefits.
this would need to be further investigated.
is were found involved in the emergence of pathogenic clones by reducing genome size  <cit> .
there are also some reports showing a good match between the presence of a particular is and infra-specific diversifications e.g.
<cit> .
distribution analysis also showed species-specific is elements among the nocardia e.g.
isncy <dig> and isnfa <dig> being restricted to n. cyriacigeorgica and n. farcinica, respectively.
furthermore, isncy <dig> was restricted to the n. cyriacigeorgica guh- <dig> complex, and isnfa <dig> of two particular clones of n. farcinica.
these data support the hypothesis of a good match between is acquisitions and infra-specific diversifications.
interestingly, distribution analysis indicated similar rgp/is repartition profiles among n. cyriacigeorgica strains.
these profiles divided n. cyriacigeorgica into two clusters:  those with patterns similar to strain guh- <dig>  and  those with patterns similar to the type strain.
these similarities in the evolutionary patterns of these elements suggest a strong association.
rgp could have been the genetic shuttles for some of these is elements.
in fact, even though most is elements were found distributed over the genome without particular insertion site preferences, some e.g.
isncy <dig>  isncy2-b, isncy <dig>  & isncy1-a <dig>  were found harbored by rgp.
for example, isncy2-b could have been acquired with rgp-cy <dig>  this is is significantly different from the other isncy2-related copies found in the n. cyriacigeorgica guh- <dig> genome, and has dna signatures only detected on the copy found on this rgp.
interestingly, a division of n. cyriacigeorgica into two phylogenetic clusters was inferred by mctaggart et al.
<cit> .
however, the strain collection of this latter study was different from the one of this work.
it would be interesting to apply mctaggart et al.
<cit>  approach to see if the is/gi sub-groups would match such phylogenetic clusters.
these analyses would add further support for the role of is/gi elements in bacterial diversification and speciation.
no relation between the habitat nor the geographical origin of the strains used in our study and the observed rgp/is patterns could be inferred.
it is noteworthy that isncy <dig> was found similar to is <dig> of m. tuberculosis and m. bovis, and was not detected in other sequenced bacterial genomes.
in order to relate is divergences to the evolution of actinobacteria, the two orthologous is alleles named isnfa <dig> and isncy <dig>  found in n. farcinica and n. cyriacigeorgica, respectively, were used as molecular clocks.
these is have 86% identity.
using this value, one can consider isncy <dig> and is <dig> diversification  to be more ancient.
pcr screenings showed isncy <dig> to be broadly distributed among n. cyriacigeorgica whereas it was totally absent from n. farcinica and other nocardia type strains.
this would suggest an acquisition by n. cyriacigeorgica at the moment of its differentiation.
outdoor-related functional isues
although a significant number of virulence genes were identified, with some being harbored by rgp, the main drivers of n. cyriacigeorgica evolution appear to be related to its environmental cycle outside mammalian hosts.
nocardioses are without a doubt of environmental origin, and infections are mainly the consequence of exposure to soil or water sources of these opportunistic pathogens.
indeed, several characteristics of the n. cyriacigeorgica guh- <dig> genome reflect the environmental origin of this species.
for instance, n. cyriacigeorgica genome size is in the range of what is expected for saprophytic bacteria .
this higher size range is related to the selection of cds likely improving metabolic potentials and regulatory processes, and allowing growth under a wider range of environmental constraints  <cit> .
these observations were further supported by cog analyses which showed nocardia genomes to share a configuration similar to the ones observed among non-pathogenic actinobacteria.
interestingly, both nocardia genomes have a higher proportion of k and t cog cds.
these cogs encode dna and proteins with regulatory functions, suggesting an ongoing evolution towards regulatory fine tunings of their genetic potentials that likely lead to expression patterns favoring growth under more diverse conditions.
CONCLUSIONS
on one hand, primary pathogens are subjected to evolutionary forces driven by the host defense responses which can lead to a specialization for certain hosts and a genome size reduction as observed for b. mallei <cit> .
on the other hand, opportunistic pathogens are exposed to a multitude of environmental constraints that can favor an increased tolerance towards the acquisition of foreign dna and the selection of novel metabolic properties.
the n. cyriacigeorgica guh- <dig> genome is a clear reflection of these latter trends.
the n. cyriacigeorgica guh- <dig> genome shows a great plasticity as shown from its rgp and is patterns, which are strain-specific and appeared to have recently evolved.
in fact, this genome appears to be undergoing important genetic rearrangements, and, most surprisingly, to frequently acquire novel dna fragments.
so far, nocardia spp.
were thought to have a low mating frequency, not acquiring much novel dna from their neighbors.
this work shows a completely opposite trend.
n. cyriacigeorgica guh- <dig> is clearly competent towards dna or sexually active.
this property can favor the gain of novel functions, and lead to major changes in niche preference from one strain to another such as differences in the colonization of certain human tisues.

 nocardia is part of the well-known cmn actinobacterial group that also includes corynebacterium and mycobacterium in the corynebacteriales order. these actinobacteria are characterized by long-chain mycolic acids in their cell wall, making them acid-resistant according to the ziehl-neelsen staining procedure, and favoring resistance to hydrophilic chemicals and dehydration. all cmn genera include pathogenic strains causing human diseases that affect millions of individuals such as leprosy, tuberculosis, and diphtheria. besides, the cmn group also includes saprophytes that thrive in soils, waters, and polluted environments. the nocardia genus comprises about species. n. cyriacigeorgica was defined as a species in following the isolation and characterization of strain immib d-1627 t from a bronchial discharge in a chronic bronchitis patient in gelsenkirchen, germany. n. cyriacigeorgica can be differentiated from other species by 16s rdna sequence analysis, their ability at growing on acetamide but inability at using proline as carbon and nitrogen sources. definition of this species was confirmed by conville et al. during their investigation of nocardia strains with a type vi drug resistance pattern. n. cyriacigeorgica differs from n. farcinica strains by their ability at synthesizing a nitrate reductase and hydrolyzing xantine but their inability at synthesizing a urease, at hydrolyzing esculin and growing on l-rhamnose. n. cyriacigeorgica strains were described as etiological agents of human pneumonia, brain abscesses, and kidney, heart and eye infections. it is the most prevalent species involved in human nocardiosis in north america and its prevalence in france was estimated at 12% among human nocardial infections declared between and. nocardiosis can be fatal for immunosuppressed individuals. there is no report of nocardia cross-contaminations in human populations, suggesting that environmental exposure is the main cause of infection. however, n. cyriacigeorgica has rarely been reported among environmental samples. nevertheless, n. cyriacigeorgica strains have been recovered from oil contaminated soils, and were shown to oxidize a variety of aliphatic compounds. in this work, the n. cyriacigeorgica guh- genome sequence is presented, and compared with those of other actinobacteria. the guh- strain was isolated from a primary human kidney infection with systemic progression, which had a fatal outcome at georgetown university hospital, washington, d.c. the ability of this strain to induce parkinson-like symptoms in inoculated mouse and monkey models made it the model strain to study nocardia biology and pathogenesis. these latter observations led to investigations on its possible role in some human parkinson cases. animals infected by n. cyriacigeorgica were found to develop abnormal behaviors like rhythmic vertical “yes-yes” head–shaking movements, stooped posture, hesitation to move forward, retropulsion, and restlessness. these parkinsonian-like symptoms appeared to be related to a decrease in dopamine receptors and a programmed cell death of dopaminergic neurons within the substantia nigra in mice. intraperitoneal injection of antiparkinsonian drugs such as l-dopa temporarily alleviated these symptoms. n. cyriacigeorgica guh- was also reported, in several independent experiments, to produce a substance that can induce apoptosis and dopamine depletion. inferences on the likely nature of this substance were made from the cds sequence presented in this paper. a transposon mutagenesis screening of mycobacterium tuberculosis showed the structural proteasomal genes of this closely related bacterium to be involved in their response toward oxidative and nitrosative stresses. the nocardial proteasome could thus play a role in virulence. the guh- genomic sequence was also used to identify key evolutionary events in the emergence of n. cyriacigeorgica. other members of the cmn group were shown to have evolved through important dna reshuffling. insertion sequences have largely contributed to genome rearrangements in the corynebacterium and mycobacterium genera, favoring deletion of genes, inversions, and functional specialization. important levels of cds duplications and domains reshuffling were reported in mycobacteria. statistical tests were performed to identify biases in n. cyriacigeorgica guh- cds and cog contents. a phylogenomic approach was developed to track the origin of some cds or cds clusters. these comparisons highlighted regions of genomic plasticity among the n. cyriacigeorgica guh- genome. selection of these rgp was probably a driving force in the emergence of n. cyriacigeorgica guh- these results revealed highly dynamic genomic evolutionary patterns in n. cyriacigeorgica caused by a significant ability at acquiring foreign dna.  virulence status of n. cyriacigeorgica guh-2 virulence of n. cyriacigeorgica guh- strain was confirmed by intravenous injection of approximately 107 cfu in the tail of balb/c mice. the death rate rose to 60% 7 days after infection. autopsy indicated death to be due to septicemia with formation of nodules in several organs: kidneys, liver, brain, spleen, lungs and heart. microscopic analysis of nodules showed high numbers of poly- and mono-nucleated inflammatory cells, and n. cyriacigeorgica guh- cells. some mice were injected a lower number of n. cyriacigeorgica guh- cells and developed abnormal behavior: rigidity, stooped posture, hemiparesis and vertical yes-yes head shaking probably due to a brain infection. general features of the nocardia cyriacigeorgica genome the -mb genome of n. cyriacigeorgica was sequenced and annotated during this work. it was found to harbor a single circular chromosome, and to have a ~ % g + c content. three rrn operons containing the genes for the 16s, 23s and 5s rrnas, predicted protein-coding sequences, trna genes, and pseudogenes i.e. truncated genes, were detected. a function could be predicted for most cds. other cds were detected among other bacterial groups or showed no homology with known sequences. n. cyriacigeorgica guh- strain did not harbor a plasmid. the genome coding density was estimated at %, which is markedly lower than the 91% value observed in related genomes. guh- chromosome harbors eleven insertion sequences, and cds encoding putative phage proteins. putative virulence genes are scattered along the chromosome without distinguishable pathogenicity island. several syntons of cds or more were found conserved between n. cyriacigeorgica, n. farcinica, rhodococcus jostii and mycobacterium tuberculosis. non-conserved regions frequently showed distinct g + c % biases. regions encoding the largest putative proteins from the genome were found to have features of non ribosomal peptide synthetases and showed a high g + c content. the only exception is nocyr_ cds which has a g + c content slightly lower than the averaged one, and encodes a putative dipeptidyl carboxypeptidase dcp located near a transposase-related cds. to better understand the events that had led to the present-day n. cyriacigeorgica guh- genomic structure, its core genome was delimited by identifying cds conserved in a panel of closely related actinobacteria. 15% of the cds was found in a putative common ancestor to all genomes except frankia sp. cci. of these cds, 80% could be assigned a function and, as expected, a large proportion was inferred to play part in basic bacterial functions such as synthesis of proteins, nucleosides and nucleotides, amino acids, co-factor prosthetic groups and carriers, and of the cell envelope. interestingly, the only cds exclusively shared between n. cyriacigeorgica and m. tuberculosis were those of is an insertion sequence, suggesting a likely transfer of this is between these species. the n. cyriacigeorgica and n. farcinica genomes were found to share % of their cds, delimiting a nocardia pangenome of about  mb. cds of n. cyriacigeorgica were not found in the n. farcinica genome. most of these cds are of unknown function but some are likely involved in phosphonate transport and metabolism, synthesis of fatty acids, glutamate metabolism, nitrite/nitrate transport, and rubisco production. conversely, cds of n. farcinica were not found in the n. cyriacigeorgica genome. again, a high proportion of these cds were “unk” cds and a few could be related to particular activities like synthesis of thiocyanate, catabolism of urea, of auxins and lignin, heavy metal resistance and virulence. these differences were in line with biochemical tests such as measurement of nitrate reductase and urease activities, performed to differentiate these two species. % cds of n. farcinica and n. cyriacigeorgica genomes were not recorded in other actinobacterial sequenced genomes. these two nocardia strains have an equivalent genome size which is longer than the ones of primary actinobacterial pathogens. % of n. cyriacigeorgica cds content was not recorded in any other organisms referenced in the databases. these cds were sometimes related to mobile and extrachromosomal elements but most of them were of “unknown function”. a search for amplified cds among n. cyriacigeorgica genome revealed occurrences, of which are duplicated, are triplicated and are quadruplicated. more than 29% of these cds could not be given a particular function, and 79% were also found in n. farcinica. is, mce, transcriptional regulators and nitrate reductase were part of these amplified regions. more than 23% of these cds were found among regions of genomic plasticity. out of the cds present in n. cyriacigeorgica genome, cds could be assigned to a cog. the proportion of these cogs among actinobacteria was similar, with a slightly higher occurrence of cds among the “transcription” and “signal transduction” cogs of the nocardia genomes. correspondence analysis of the number of cds per cog among a set of actinobacterial species was performed, to identify a possible bias related to the pathogenic nature of the species. this analysis showed that the number of cds per cog could differentiate primary pathogens from non-pathogens. this “pathogen pattern” was more significant than the cog organization bias inferred from species belonging to a same genus. on the other hand, all non-pathogens had closer cog patterns even though some were part of different genus or part of a genus showing pathogenic species. cog patterns of the nocardia genomes were found similar to those of non-pathogens. a correspondence analysis on the functional domains inferred from the cds of the “transcription” cog was performed. this analysis did not segregate the dataset according to the pathogenic nature of the species regardless of their genus. instead, the numbers of cds per sub-division were found similar between the nocardia genomes and similar to those observed among m. tuberculosis. regions of genomic plasticity a lineplot graph between n. farcinica and n. cyriacigeorgica genomes, representing synteny results of series of cds or more, was performed in order to visualize the distribution of variable and conserved regions. this analysis showed the number of conserved cds between these chromosomes to increase towards their respective origin of replication. the lowest concentration of these cds was observed around the chromosomal terminus of replication. overall, the organization of these variations was quite similar between the two halves of the circular chromosome creating a mirror-like effect indicative of increasing evolutionary constraints from the terminus towards the origin of replication. the chromosomal terminus is partially visible on the circular map of n. cyriacigeorgica genome, and shows a large segment with a distinct g + c content according to the gc plot. the artemis comparison tool was used to refine these analyses and identify dna segments >  kb or containing more than cds. these dna regions were not showing all the features of genomic islands such as a trna gene at one end, an integrase cds or a g + c bias distinct from the one of the genome. twenty-two rgp could be detected using this approach. twenty-one of these rgp were also detected with the rgpfinder tool of the mageplateform. rgp-cy was not detected in this latter analysis because of its length of  kb. of these rgp, four could be considered genomic islets, and the largest rgp was of about 80 kb. these rgp represented a total of 704 kb i.e. % of the genome and encoded cds. the average g + c% content of these rgp is of %, with values ranging from % to %. rgp boundaries were analyzed. trna or tmrna genes were detected at the extremity of ten of these. direct dna repeats were observed for rgp-cy from positions to and to at its left and right ends, respectively. four rgp showed is sequences. five rgp contain cds implicated in dna modification processes such as integrases, recombinases, endonucleases and excisionases. these cds were probably involved in the acquisition of these rgp. ten rgp did not show any of the above features. most cds on these selected rgp encode putative proteins and transcriptional regulators of unknown function. some cds, likely representing a benefit for n. cyriacigeorgica guh- could be identified and predicted to encode a catalase, a limonene monooxygenase, and a sulfonate abc transporter. furthermore, cds involved in nitrate metabolism were identified on the rgp-cy a cobalamin-independent methionine synthase and three cds involved in citrate metabolism were found on rgp-cy while pgly and pglz involved in phage defense were found on cy. pcr screenings were designed to investigate the distribution of these rgp among 83 n. cyriacigeorgica strains. prevalence of these rgp was quite variable, with some not being detected in other strains, and some being found among up to 69% of the strains. rgp-cy and rgp-cy were only found in the n. cyriacigeorgica guh- genome and showed all the features of mobile elements. a cladogram was built using the rgp distribution patterns based on the positive and negative pcr results. dataset of inner rgp and rgp-ends dna targets were analyzed separately or together, and gave similar cladograms. all strains harboring or more rgp were grouped in the “guh- complex”. other strains belonged to a “type strain complex”. in fact, rgp patterns of strains were found to be in the “guh- complex”, while patterns of strains were allocated to the “type strain complex”. among the “guh- complex”, some of the selected rgp were highly prevalent: rgp-cy rgp-cy rgp-cy rgp-cy rgp-cy rgp-cy and rgp-cy were found in and strains respectively. strain n harbored the highest number of rgp found in the n. cyriacigeorgica guh- genome. among the type strain complex, rgp- cy -cy -cy -cy -cy -cy -cy -cy -cy -cy and -cy were not recorded. no rgp seemed to be representative of this latter complex, and rgp-cy rgp-cy and rgp-cy were the most prevalent. rgp-cy was the most broadly distributed among the n. cyriacigeorgica species. pcr screenings targeting the left and right ends of rgp were defined to estimate the level of conservation of their respective proximal dna region. the left and right ends of rgp-cy -cy and -cy were broadly detected whereas only one end could be detected for rgp-cy, -cy, -cy, -cy, -cy, -cy, -cy, -cy, -cy, -cy, and -cy among all the strains tested. the l and r ends of the rgp-cy cy cy and cy were detected among the “guh- complex”, while only rgp-cy, -cy, -cy, -cy, -cy, -cy, -cy could be detected among the “guh- complex”. it is noteworthy that an attempt was made at comparing this rgp classification with phylogenetic relationships inferred from 16s rdna sequences. however, significant sub-groups among n. cyriacigeorgica could not be resolved with this marker. rgp represent gains in cds likely to confer novel properties but cds losses can also represent adaptations to particular habitats. 193 n. farcinica cds were found mising in the n. cyriacigeorgica guh- genome. among these, 35% encode putative proteins of unknown function but four clusters of cds involved in glutamine metabolism, in phenyl acid acetic degradation, in thiocyanate degradation and nitrogen metabolism, and in urease synthesis were found mising. the particular case of insertion sequences on the n. cyriacigeorgica genome, eleven is belonging to five different families were detected. a re-evaluation of the n. farcinica is genome content was performed, and led to the identification of fifteen is belonging to five families. only isnfa and isncy of the is family were found located in the same dna site of these two actinobacteria. these is share 86% dna identity. n cyriacigeorgica genome showed dna signatures of two tn transposons but one appeared to be truncated. n. farcinica genome also showed the presence of a tn in which the transposase cds shares 85% dna identity with the one of n. cyriacigeorgica transposon inverted repeats and/or direct repeats were identified for five n. cyriacigeorgica is and for three n. farcinica is. isncy copies in n. cyriacigeorgica genome were found related to is which was only previously detected in the m. tuberculosis and m. bovis genomes. the n. cyriacigeorgica guh- genome harbors the isncy in four copies with one being partial and three being identical. three is were found in several copies in n. farcinica. isnfa of the is family was found in two copies with 99% dna identity; isnfa of the is family in eight copies with identities going from 72% to 99%; and isnfap a partial element of the tn family, having 85% dna identity with a copy found on n. farcinica larger plasmid. the distribution of six of these is/tn elements was investigated among a sub-set of the n. cyriacigeorgica strains screened in the rgp section, a set of n. farcinica strains, and a panel of nocardia species type strains. only isncy and isnfa were detected among both n. cyriacigeorgica and n. farcinica but their prevalence was quite different from one species to another. in fact, both of these elements were more prevalent among the panel of strains of n. farcinica than n. cyriacigeorgica strains selected for this study. isncy was the most prevalent among n. cyriacigeorgica but was absent from the n. farcinica strains tested. this isncy was also found among the n. otitidiscaviarum type strain. isncy was not detected in n. farcinica. its prevalence was higher among the guh- complex of n. cyriacigeorgica. a similar situation was observed for isncy isncy and isncy were not detected among the nocardia type strains that were selected for this analysis, suggesting a distribution restricted to n. cyriacigeorgica. isnfa and isnfa were not detected in n. cyriacigeorgica and appeared to be restricted to n. farcinica strain isncy and isnfa share 89% identity, and were detected among several strains of n. farcinica and n. cyriacigeorgica. a cladogram was built from this is distribution pattern analysis and was found to match the rgp distribution patterns. virulence-related functions several genes were previously found involved in virulence among actinobacteria. blast and keyword-based searches allowed identification of some of these cds among the n. cyriacigeorgica genome. six complete mce loci containing yrbe and mas cds were found. analysis of cds encoding cell wall components involved in virulence revealed 85-kda antigens family proteins, lipoproteins and pe_pgrs/ppe family proteins. two superoxide dismutase cds and three catalase ones were also identified. nitrate reductase cds, trehalose ’-dimycolate transferase and rubisco were detected and found to be clustered. extracellular enzymes were identified by searching for particular domains including a peptide leader and low number of transmembrane domains. the inferred secretome of n. cyriacigeorgica guh- was compared with the ones of other actinobacteria, and showed a majority of putative proteins of unknown function, several proteases, lipases as well as a transcriptional regulator and members of the mce genes. comparison of the putative proteins of the n. cyriacigeorgica and n. farcinica secretomes showed high identities, much higher than those observed with other actinobacteria. the n. cyriacigeorgica guh- genome shows a good potential for the synthesis of a number of metabolites that could be antimicrobials or proteasome inhibitors. seven cds were predicted to encode polyketides synthases, and cds were predicted to encode nrps. among n. farcinica, pks and nrpss were found including the cluster of cds previously described as producing a lipid-soluble iron-binding nocobactin. a cluster of nine cdss similar to the coelibactine synthesis cluster in streptomyces coelicolor was also identified in n. cyriacigeorgica guh-2’s genome. nocyr_ was found to be the longest cds of the genome and likely to encode a nrps with twelve modules. two other nrps operons containing two and three cds could synthesize molecules containing thirteen and eleven building blocks, respectively. a 2-amino- epoxi-8-oxodecanoic acid was predicted for nocyr_ this putative acid shows a structure similar to the epoxomicin proteasome inhibitor but chemical assays will be required to confirm its synthesis. other softwares did not find this structure. it is noteworthy that a correlation was observed between the isoelectric point and the molecular weight of the inferred proteins of the n. cyriacigeorgica guh- genome. the largest proteins of the genome, constituted mainly by nrps and pks, showed similar isoelectric points, suggesting a compartmentalization inside the cytosol that could allow a coordinated functioning of these enzymes. genetic potentials and metabolic profiling phenotypic microarray datasets including antibiotic resistances were compared with the functional predictions made from the annotated n. cyriacigeorgica guh- genome. phenotypic profiling was performed by testing n. cyriacigeorgica ability to grow with various carbon and nitrogen sources. kegg pathways were used to find the cds involved in these pathways but also as a reference for explaining an absence of growth under certain conditions.. only seven amino acids could be used as carbon and/or nitrogen sources. the absence of some cds previously shown in other bacteria to be involved in the substrate catabolism or transport could explain several negative results. however, the lack of growth with l-aspartic acid, l-lysine and l-proline could not be explained by the absence of particular cds. the osmoadaptation capacity n. cyriacigeorgica guh- was also tested and found to be high under high salt concentrations. this property could involve cds encoding transport proteins and/or osmoprotectants like ectoine and betaine. growth tests were also performed under various ph. n. cyriacigeorgica guh- was shown to grow at ph  and but not ph . this dataset was completed by an analysis of the antibiotics resistance pattern of n. cyriacigeorgica guh- using plate assays. n. cyriacigeorgica guh- was confirmed to have a type vi pattern with resistance against several sulfonamides, aminoglycosides, tetracyclines and penicillins. it was found sensitive to cefamandole, cefotaxime, amikacin, and imipenem. many cds likely playing part in these antibiotic resistances were found in the n. cyriacigeorgica genome. a mutation in the gyrase a gene that can prevent ciprofloxacin binding, was detected. several cds were inferred as encoding β-lactamases in the guh- genome, and could be responsible for the observed ampicillin, carbenicillin, oxacillin and penicillin resistances. the paromomycin and tobramycin resistances observed can be due to the expression of one of the three aminoglycoside phosphotransferases detected by the annotation process. macrolide resistances could involve one of the six ribosomal rna methyltransferases encoded by the guh- genome. these may cause a decrease in the affinity of macrolides for the 50s ribosomal unit. the fourteen drug or multidrug efflux transporters encoded by this genome could be involved in tetracycline, penimepicycline, polymyxin b, paromomycin, d,l-serine hydroxamate, sisomicin, sulfamethazine, novobiocin and/or sulfadiazine resistance by extruding these molecules. discussion nocardia cyriacigeorgica is an opportunistic pathogen causing many infections including deadly brain abscesses and granulomatous diseases among immune-compromised and healthy individuals. however, the bacterial properties involved in these infections are poorly understood. here, the content, organization, plasticity, and functional potentialities of n. cyriacigeorgica guh- full genome sequence are presented. a particular attention was paid to the analysis of cds likely involved in virulence including antibiotic resistances. these analyses led to the identification of several rgp and is elements that were then tracked among a panel of n. cyriacigeorgica strains. these screenings revealed an important ability of this species at acquiring dna by horizontal transfer events. virulence determinants the n. cyriacigeorgica guh- genome analyses revealed several genetic determinants related to virulence. some of these are part of rgp but some were also part of the nocardia or actinobacteria pangenomes inferred from comparisons with the full genome sequence of n. farcinica and other actinobacteria. the genome of n. cyriacigeorgica harbors virulence-related cds such as mce coding genes described as important virulence factors of m. tuberculosis. mce can act as transmembrane transporters favoring macrophage invasion. these cdss are organized in operons containing two yrbe cds followed by six mce cds and sometimes two mce associated cdss. there are six copies of the complete mce operon in n. cyriacigeorgica and n. farcinica whereas four copies are identified in m. tuberculosis genome. although, the importance of these cdss in m. tuberculosis virulence has been shown, their detection in multicopies among m. smegmatis and r. jostii suggests a function not limited to cell entry. having access to the n. cyriacigeorgica mce cds will allow transcriptomics experiments to identify the mce cdss which are turned on during host cell colonization. other n. cyriacigeorgica cdss besides mce have been described as important in the infection and cell invasion processes. in particular, the expression of superoxide dismutase and catalase cds were observed during n. cyriacigeorgica macrophage invasion and were suggested to be involved in resistance towards oxidative stresses. two sod and three kat cds were found in the n. cyriacigeorgica genome. the kata cds is harbored by the rgp-cy but the other two kat cdss are found on conserved genomic regions. other cdss can also have a complementary action during nocardia growth in macrophages. the trehalose ’-dimycolate transferase cds was found related to the 85-kda antigen family protein that can promote m. tuberculosis survival in macrophages by decreasing both phagosomal acidification and phagolysosomal fusion. an encoded n. cyriacigeorgica hemolysin which can disrupt the phagolysosome membrane was also annotated and could also favor survival in macrophages. the isocitrate lyase cds observed on rgp-cy could also be part of the n. cyriacigeorgica macrophage invasion process by preventing host cell apoptosis as observed in m. tuberculosis. an intracellular pathogen not only requires defense mechanisms against macrophage antibacterial processes but also needs to survive under low oxygen pressure such as the one observed in poorly irrigated tissue of the mammal body. cds involved in such processes can thus also be defined as virulence-related determinants. n. cyriacigeorgica contains denitrification cdss of which five are harbored by rgp-cy n. cyriacigeorgica was initially described as an obligate aerobe but presence denitrifying cds suggests an ability to grow under anaerobic conditions. however, the conditions allowing growth under low oxygen pressure remain to be defined. several metabolites, proteins, enzymes and lipids which are not directly involved in colonization but are at the frontline during host infection can also play a role in virulence such as cell wall constituents and some extracellular enzymes/metabolites. the cell wall is a protection for bacteria but can also be a target for the immune system. for example, pe/ppe serine α/β hydrolases membrane proteins are important in mycobacterium pathogenic species to avoid detection or killing during their intracellular life in a variety of host cells. however, their low number in n. cyriacigeorgica and n. farcinica could be an effect of their opportunistic status and could explain their poor ability to escape the immune system of a healthy host. nocardia can also secrete several enzymes that may interfere with the host cell metabolism, in particular sods, lipases and proteases. cdss encoding such enzymes were observed in the n. cyriacigeorgica guh- genome. eight cdss were found encoding extracellular lipases and encoding extracellular proteases. nevertheless, much more cdss encoding putative secreted enzymes have been reported in mycobacterium such as the esat proteins. n. cyriacigeorgica guh- genome harbored three esat cdss. another major group of secreted molecules that can play a role in virulence are siderophores. nocardia strains can produce several siderophores like formobactin, amamistatin, brasilibactin, asterobactin and nocobactin. nocobactin synthesis was previously found encoded by two genetic clusters, with cluster i positioned 195 kb from cluster ii. the n. cyriacigeorgica guh- genome showed a cluster i organization different from the one observed in the n. farcinica genome. the gene nbth is absent in the n. cyriacigeorgica guh- genome and replaced by a putative formyltransferase cds, which could play a role in preventing the transfer of an acyl chain to the ϵ-amino group of lysine. the n. cyriacigeorgica guh- cluster ii shows high identities with the one of n. farcinica but additional cds encoding nrps and an exported protein of unknown function were recorded. the nrps cdss could play a role in the synthesis of this siderophore and change some of its properties. a coelibactin-like siderophore is also likely to be produced by n. cyriacigeorgica guh- a conserved synteny was observed with s. coelicolor cds involved in its synthesis except for a supplementary cds encoding a cytochrome p protein. these actinobacteria are also known to synthesize other extracellular metabolites through nrps and pks-related processes. the n. cyriacigeorgica guh- genome was found to encode pks-related cdss and nrps-related ones. it is considered that the substance produced by n. cyriacigeorgica guh- which can cause brain damages by inducing apoptosis and a dopamine depletion would be encoded by a nrps or pks. here, a putative metabolite produced by an operon of three nrpss could be predicted to have a structure similar to the one of epoxomicin. such molecules have epoxy groups that could inhibit the functioning of proteasomes. nrps and pks are also involved in the synthesis of antibiotics, and could have been involved in the synthesis of transvalencin z, da-, and nocardithiocin. however, the molecules produced by these synthases are often difficult to obtain in large quantities and are hard to purify from culture filtrates without genetic manipulations. phenotypic and genomic plasticities metabolic profilings showed n. cyriacigeorgica guh- abilities at growing on a variety of substrates. in most cases, the cdss involved in transport and catabolism of these substrates were found in the genome. however, some metabolic activities inferred from the genome could not be confirmed by growth tests e. g. the growth on l-glycine, l-lysine, and l-proline. interestingly, cdss involved in l-lysine and l-proline catabolism were detected outside rgp but showed a codon adaption index below the average. this codon bias could be related to the low expression of these cdss, and might be the consequence of a recent acquisition. an overexpression of these genes by genetic manipulations of n. cyriacigeorgica guh- would be needed to test this hypothesis. low cai was also observed for cdss identified when in vivo activity was assessed. in this case the presence of multiple cds assigned to this function probably allowed a sufficient gene expression level to observe the expected phenotype. a high turnover of rgp appears to occur among n. cyriacigeorgica. n. cyriacigeorgica guh- closest rgp profile among a collection of strains showed the absence of rgp and the conservation of ones. rgp profilings thus suggest a good n. cyriacigeorgica competence towards dna acquisition but the mechanisms involved remain to be determined. rgp-cy appeared to have been recently acquired by n. cyriacigeorgica guh- and was found to harbor all the trademarks of mobile genomic islands. this rgp could be a good candidate for the design of a dna cloning vector. no rgp was found related to prophage-like elements. this is different from the situation observed in corynebacterial and mycobacterial pathogenic genomes, where such prophage-like dna contains virulence genes. a high turnover of is elements was also observed among nocardia. however, while several is were found among the n. cyriacigeorgica and n. farcinica genomes in this work, previous studies had only identified two is among the nocardia: isnfa and is. these low numbers suggested nocardia strains to have a poor propensity at acquiring exogenous dna which are often acting as is shuttles. here, we clearly demonstrate the opposite. the nocardia genomes were found to be rich in is elements and diversity. is of eight families were recorded suggesting a high genomic tolerance towards these elements and a frequent acquisition by these actinobacteria. however, about 45% of the observed is did not show ir and dr. a lack of such sequences could be indicative of a loss of transposition autonomy or of selective pressures leading to their fixation at a particular site because of functional benefits. this would need to be further investigated. is were found involved in the emergence of pathogenic clones by reducing genome size. there are also some reports showing a good match between the presence of a particular is and infra-specific diversifications e.g.. distribution analysis also showed species-specific is elements among the nocardia e.g. isncy and isnfa being restricted to n. cyriacigeorgica and n. farcinica, respectively. furthermore, isncy was restricted to the n. cyriacigeorgica guh- complex, and isnfa of two particular clones of n. farcinica. these data support the hypothesis of a good match between is acquisitions and infra-specific diversifications. interestingly, distribution analysis indicated similar rgp/is repartition profiles among n. cyriacigeorgica strains. these profiles divided n. cyriacigeorgica into two clusters: those with patterns similar to strain guh- and those with patterns similar to the type strain. these similarities in the evolutionary patterns of these elements suggest a strong association. rgp could have been the genetic shuttles for some of these is elements. in fact, even though most is elements were found distributed over the genome without particular insertion site preferences, some e.g. isncy isncy2-b, isncy & isncy1-a were found harbored by rgp. for example, isncy2-b could have been acquired with rgp-cy this is is significantly different from the other isncy2-related copies found in the n. cyriacigeorgica guh- genome, and has dna signatures only detected on the copy found on this rgp. interestingly, a division of n. cyriacigeorgica into two phylogenetic clusters was inferred by mctaggart et al.. however, the strain collection of this latter study was different from the one of this work. it would be interesting to apply mctaggart et al. approach to see if the is/gi sub-groups would match such phylogenetic clusters. these analyses would add further support for the role of is/gi elements in bacterial diversification and speciation. no relation between the habitat nor the geographical origin of the strains used in our study and the observed rgp/is patterns could be inferred. it is noteworthy that isncy was found similar to is of m. tuberculosis and m. bovis, and was not detected in other sequenced bacterial genomes. in order to relate is divergences to the evolution of actinobacteria, the two orthologous is alleles named isnfa and isncy found in n. farcinica and n. cyriacigeorgica, respectively, were used as molecular clocks. these is have 86% identity. using this value, one can consider isncy and is diversification to be more ancient. pcr screenings showed isncy to be broadly distributed among n. cyriacigeorgica whereas it was totally absent from n. farcinica and other nocardia type strains. this would suggest an acquisition by n. cyriacigeorgica at the moment of its differentiation. outdoor-related functional isues although a significant number of virulence genes were identified, with some being harbored by rgp, the main drivers of n. cyriacigeorgica evolution appear to be related to its environmental cycle outside mammalian hosts. nocardioses are without a doubt of environmental origin, and infections are mainly the consequence of exposure to soil or water sources of these opportunistic pathogens. indeed, several characteristics of the n. cyriacigeorgica guh- genome reflect the environmental origin of this species. for instance, n. cyriacigeorgica genome size is in the range of what is expected for saprophytic bacteria. this higher size range is related to the selection of cds likely improving metabolic potentials and regulatory processes, and allowing growth under a wider range of environmental constraints. these observations were further supported by cog analyses which showed nocardia genomes to share a configuration similar to the ones observed among non-pathogenic actinobacteria. interestingly, both nocardia genomes have a higher proportion of k and t cog cds. these cogs encode dna and proteins with regulatory functions, suggesting an ongoing evolution towards regulatory fine tunings of their genetic potentials that likely lead to expression patterns favoring growth under more diverse conditions.  on one hand, primary pathogens are subjected to evolutionary forces driven by the host defense responses which can lead to a specialization for certain hosts and a genome size reduction as observed for b. mallei. on the other hand, opportunistic pathogens are exposed to a multitude of environmental constraints that can favor an increased tolerance towards the acquisition of foreign dna and the selection of novel metabolic properties. the n. cyriacigeorgica guh- genome is a clear reflection of these latter trends. the n. cyriacigeorgica guh- genome shows a great plasticity as shown from its rgp and is patterns, which are strain-specific and appeared to have recently evolved. in fact, this genome appears to be undergoing important genetic rearrangements, and, most surprisingly, to frequently acquire novel dna fragments. so far, nocardia spp. were thought to have a low mating frequency, not acquiring much novel dna from their neighbors. this work shows a completely opposite trend. n. cyriacigeorgica guh- is clearly competent towards dna or sexually active. this property can favor the gain of novel functions, and lead to major changes in niche preference from one strain to another such as differences in the colonization of certain human tisues. 
n. cyriacigeorgica strain guh- genome size is  mb-long, % of its cds have homologs in at least another actinobacterial genome, and % of these are found in n. farcinica. the full genome sequence of n. cyriacigeorgica strain guh- 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. 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. n. cyriacigeorgica guh- genome shows features suggesting a diversification from an ancestral saprophytic state. cog analyses showed this genome to have an organization similar to environmental actinobacteria. 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 and polyketide synthases were identified, with some being likely involved in the synthesis of siderophores and toxins. guh- 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. nocardia cyriacigeorgica is recognized as one of the most prevalent etiological agents of human nocardiosis. nocardia cyriacigeorgicaregions of genomic plasticityinsertion sequencescogevolutionopportunistic pathogen
 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- 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.  n. cyriacigeorgica strain guh- genome size is  mb-long, % of its cds have homologs in at least another actinobacterial genome, and % 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. overall, rgp were identified in this genome, representing % 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 and polyketide synthases 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.  n. cyriacigeorgica guh- genome shows features suggesting a diversification from an ancestral saprophytic state. guh- 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. nocardia cyriacigeorgicaregions of genomic plasticityinsertion sequencescogevolutionopportunistic pathogen 