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Comparative genomic characterization of Francisella tularensis strains belonging to low and high virulence subspecies.

Champion MD, Zeng Q, Nix EB, Nano FE, Keim P, Kodira CD, Borowsky M, Young S, Koehrsen M, Engels R, Pearson M, Howarth C, Larson L, White J, Alvarado L, Forsman M, Bearden SW, Sjöstedt A, Titball R, Michell SL, Birren B, Galagan J - PLoS Pathog. (2009)

Bottom Line: We have also identified genes exhibiting sequence similarity to effectors of the Type III (T3SS) and components of the Type IV secretion systems (T4SS).One of the genes, msrA2 (FTT1797c), is disrupted in F. tularensis subsp. mediasiatica and has recently been shown to mediate bacterial pathogen survival in host organisms.Our findings suggest that in addition to the duplication of the Francisella Pathogenicity Island, and acquisition of individual loci, adaptation by gene loss in the more recently emerged tularensis, holarctica, and mediasiatica subspecies occurred and was distinct from evolutionary events that differentiated these subspecies, and the novicida subspecies, from a common ancestor.

View Article: PubMed Central - PubMed

Affiliation: Microbial Analysis Group, Broad Institute of MIT and Harvard, Cambridge, MA, USA. champion@broad.mit.edu

ABSTRACT
Tularemia is a geographically widespread, severely debilitating, and occasionally lethal disease in humans. It is caused by infection by a gram-negative bacterium, Francisella tularensis. In order to better understand its potency as an etiological agent as well as its potential as a biological weapon, we have completed draft assemblies and report the first complete genomic characterization of five strains belonging to the following different Francisella subspecies (subsp.): the F. tularensis subsp. tularensis FSC033, F. tularensis subsp. holarctica FSC257 and FSC022, and F. tularensis subsp. novicida GA99-3548 and GA99-3549 strains. Here, we report the sequencing of these strains and comparative genomic analysis with recently available public Francisella sequences, including the rare F. tularensis subsp. mediasiatica FSC147 strain isolate from the Central Asian Region. We report evidence for the occurrence of large-scale rearrangement events in strains of the holarctica subspecies, supporting previous proposals that further phylogenetic subdivisions of the Type B clade are likely. We also find a significant enrichment of disrupted or absent ORFs proximal to predicted breakpoints in the FSC022 strain, including a genetic component of the Type I restriction-modification defense system. Many of the pseudogenes identified are also disrupted in the closely related rarely human pathogenic F. tularensis subsp. mediasiatica FSC147 strain, including modulator of drug activity B (mdaB) (FTT0961), which encodes a known NADPH quinone reductase involved in oxidative stress resistance. We have also identified genes exhibiting sequence similarity to effectors of the Type III (T3SS) and components of the Type IV secretion systems (T4SS). One of the genes, msrA2 (FTT1797c), is disrupted in F. tularensis subsp. mediasiatica and has recently been shown to mediate bacterial pathogen survival in host organisms. Our findings suggest that in addition to the duplication of the Francisella Pathogenicity Island, and acquisition of individual loci, adaptation by gene loss in the more recently emerged tularensis, holarctica, and mediasiatica subspecies occurred and was distinct from evolutionary events that differentiated these subspecies, and the novicida subspecies, from a common ancestor. Our findings are applicable to future studies focused on variations in Francisella subspecies pathogenesis, and of broader interest to studies of genomic pathoadaptation in bacteria.

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Pairwise alignments between five new Francisella genome sequences and a reference genome exhibit >95% sequence conservation.Genome comparative maps were constructed using CGview software to map pairwise blastn alignments between several Francisella genomes (minimum percent identity = 95 and expected threshold = 1e-5). Specifically, five newly sequenced Francisella genomes (F. tularensis subsp. holarctica FSC257 and FSC022; F. tularensis subsp. tularensis FSC033; and F. tularensis subsp. novicida GA99-3548, and GA99-3549 strains) were aligned to the F. tularensis subsp. holarctica OSU18 reference sequence (outside blue track of genome map). A high degree of similarity between the genomes (>95%) is evident from the continuous blocks of synteny (colored regions).
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ppat-1000459-g001: Pairwise alignments between five new Francisella genome sequences and a reference genome exhibit >95% sequence conservation.Genome comparative maps were constructed using CGview software to map pairwise blastn alignments between several Francisella genomes (minimum percent identity = 95 and expected threshold = 1e-5). Specifically, five newly sequenced Francisella genomes (F. tularensis subsp. holarctica FSC257 and FSC022; F. tularensis subsp. tularensis FSC033; and F. tularensis subsp. novicida GA99-3548, and GA99-3549 strains) were aligned to the F. tularensis subsp. holarctica OSU18 reference sequence (outside blue track of genome map). A high degree of similarity between the genomes (>95%) is evident from the continuous blocks of synteny (colored regions).

Mentions: The draft genomic sequences of F. tularemia subsp. tularensis strain FSC033, F. tularemia subsp. holarctica strains: FSC022, and FSC257, and F. tularemia subsp. novicida strains: GA99-3548 and GA99-3549 have been annotated and deposited in GenBank (Materials and Methods). Genome and assembly statistics for each strain are summarized in Table 1. All of the genomes consist of a single circular chromosome and are approximately 2 Mb in size. Although the five strains represent different subspecies of Francisella, the overall features of the genomes are quite similar (Table 1). The average GC content and distribution is consistent with previous studies reporting the lower G+C content in Francisella [9]. The average number of genes is 1,730, with a mean of 1,574 total protein-coding genes. The genomes of the novicida subspecies carry the highest percentage of intact ORFs (97%) and conversely, the F. tularensis subsp. holarctica FSC257 strain sequence carries the lowest percentage (84%) in comparison to the other five genomes. Pairwise alignment using blastn (1e-5, 95%) of the draft genomes with the F.tularemia subsp. holarctica OSU18 reference genome shows the high level of overall similarity between genomes across subspecies (>95%) (Figure 1). The average gene length does vary across the different strains of Francisella and is correlated with the abundance of pseudogenes (Table 1). We also report a significantly larger number of total transposable elements present in the Type A and Type B strains in comparison to the novicida strains, which is consistent with previous studies [17]. It is worth noting that the highest numbers are present in Type B strains, even though rearrangement events have not been characterized by previous comparisons between these genomes.


Comparative genomic characterization of Francisella tularensis strains belonging to low and high virulence subspecies.

Champion MD, Zeng Q, Nix EB, Nano FE, Keim P, Kodira CD, Borowsky M, Young S, Koehrsen M, Engels R, Pearson M, Howarth C, Larson L, White J, Alvarado L, Forsman M, Bearden SW, Sjöstedt A, Titball R, Michell SL, Birren B, Galagan J - PLoS Pathog. (2009)

Pairwise alignments between five new Francisella genome sequences and a reference genome exhibit >95% sequence conservation.Genome comparative maps were constructed using CGview software to map pairwise blastn alignments between several Francisella genomes (minimum percent identity = 95 and expected threshold = 1e-5). Specifically, five newly sequenced Francisella genomes (F. tularensis subsp. holarctica FSC257 and FSC022; F. tularensis subsp. tularensis FSC033; and F. tularensis subsp. novicida GA99-3548, and GA99-3549 strains) were aligned to the F. tularensis subsp. holarctica OSU18 reference sequence (outside blue track of genome map). A high degree of similarity between the genomes (>95%) is evident from the continuous blocks of synteny (colored regions).
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2682660&req=5

ppat-1000459-g001: Pairwise alignments between five new Francisella genome sequences and a reference genome exhibit >95% sequence conservation.Genome comparative maps were constructed using CGview software to map pairwise blastn alignments between several Francisella genomes (minimum percent identity = 95 and expected threshold = 1e-5). Specifically, five newly sequenced Francisella genomes (F. tularensis subsp. holarctica FSC257 and FSC022; F. tularensis subsp. tularensis FSC033; and F. tularensis subsp. novicida GA99-3548, and GA99-3549 strains) were aligned to the F. tularensis subsp. holarctica OSU18 reference sequence (outside blue track of genome map). A high degree of similarity between the genomes (>95%) is evident from the continuous blocks of synteny (colored regions).
Mentions: The draft genomic sequences of F. tularemia subsp. tularensis strain FSC033, F. tularemia subsp. holarctica strains: FSC022, and FSC257, and F. tularemia subsp. novicida strains: GA99-3548 and GA99-3549 have been annotated and deposited in GenBank (Materials and Methods). Genome and assembly statistics for each strain are summarized in Table 1. All of the genomes consist of a single circular chromosome and are approximately 2 Mb in size. Although the five strains represent different subspecies of Francisella, the overall features of the genomes are quite similar (Table 1). The average GC content and distribution is consistent with previous studies reporting the lower G+C content in Francisella [9]. The average number of genes is 1,730, with a mean of 1,574 total protein-coding genes. The genomes of the novicida subspecies carry the highest percentage of intact ORFs (97%) and conversely, the F. tularensis subsp. holarctica FSC257 strain sequence carries the lowest percentage (84%) in comparison to the other five genomes. Pairwise alignment using blastn (1e-5, 95%) of the draft genomes with the F.tularemia subsp. holarctica OSU18 reference genome shows the high level of overall similarity between genomes across subspecies (>95%) (Figure 1). The average gene length does vary across the different strains of Francisella and is correlated with the abundance of pseudogenes (Table 1). We also report a significantly larger number of total transposable elements present in the Type A and Type B strains in comparison to the novicida strains, which is consistent with previous studies [17]. It is worth noting that the highest numbers are present in Type B strains, even though rearrangement events have not been characterized by previous comparisons between these genomes.

Bottom Line: We have also identified genes exhibiting sequence similarity to effectors of the Type III (T3SS) and components of the Type IV secretion systems (T4SS).One of the genes, msrA2 (FTT1797c), is disrupted in F. tularensis subsp. mediasiatica and has recently been shown to mediate bacterial pathogen survival in host organisms.Our findings suggest that in addition to the duplication of the Francisella Pathogenicity Island, and acquisition of individual loci, adaptation by gene loss in the more recently emerged tularensis, holarctica, and mediasiatica subspecies occurred and was distinct from evolutionary events that differentiated these subspecies, and the novicida subspecies, from a common ancestor.

View Article: PubMed Central - PubMed

Affiliation: Microbial Analysis Group, Broad Institute of MIT and Harvard, Cambridge, MA, USA. champion@broad.mit.edu

ABSTRACT
Tularemia is a geographically widespread, severely debilitating, and occasionally lethal disease in humans. It is caused by infection by a gram-negative bacterium, Francisella tularensis. In order to better understand its potency as an etiological agent as well as its potential as a biological weapon, we have completed draft assemblies and report the first complete genomic characterization of five strains belonging to the following different Francisella subspecies (subsp.): the F. tularensis subsp. tularensis FSC033, F. tularensis subsp. holarctica FSC257 and FSC022, and F. tularensis subsp. novicida GA99-3548 and GA99-3549 strains. Here, we report the sequencing of these strains and comparative genomic analysis with recently available public Francisella sequences, including the rare F. tularensis subsp. mediasiatica FSC147 strain isolate from the Central Asian Region. We report evidence for the occurrence of large-scale rearrangement events in strains of the holarctica subspecies, supporting previous proposals that further phylogenetic subdivisions of the Type B clade are likely. We also find a significant enrichment of disrupted or absent ORFs proximal to predicted breakpoints in the FSC022 strain, including a genetic component of the Type I restriction-modification defense system. Many of the pseudogenes identified are also disrupted in the closely related rarely human pathogenic F. tularensis subsp. mediasiatica FSC147 strain, including modulator of drug activity B (mdaB) (FTT0961), which encodes a known NADPH quinone reductase involved in oxidative stress resistance. We have also identified genes exhibiting sequence similarity to effectors of the Type III (T3SS) and components of the Type IV secretion systems (T4SS). One of the genes, msrA2 (FTT1797c), is disrupted in F. tularensis subsp. mediasiatica and has recently been shown to mediate bacterial pathogen survival in host organisms. Our findings suggest that in addition to the duplication of the Francisella Pathogenicity Island, and acquisition of individual loci, adaptation by gene loss in the more recently emerged tularensis, holarctica, and mediasiatica subspecies occurred and was distinct from evolutionary events that differentiated these subspecies, and the novicida subspecies, from a common ancestor. Our findings are applicable to future studies focused on variations in Francisella subspecies pathogenesis, and of broader interest to studies of genomic pathoadaptation in bacteria.

Show MeSH
Related in: MedlinePlus