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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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Multiple alignment of Francisella genomes of the Type B lineage identifies conserved sequence regions with rearrangements; pseudogenes are found proximal to predicted breakpoints.A comparison of genome rearrangement patterns between the more ancestral F. tularensis subsp. holarctica FSC022 japonica strain and representative strains of the main holarctica group (F. tularensis subsp. holarctica LVS and F. tularensis subsp. holarctica OSU18) was done using MAUVE (A). MAUVE uses an anchored alignment algorithm that permits reordering of the alignment anchors for identification of rearrangements. Colored Local Collinear Blocks (LCBs) are regions of sequence alignment that are free of rearrangements. Each LCB is defined by the anchor regions or predicted sites of rearrangement. A default LCB cutoff of 175, and a filtering for larger blocks containing 10 Kb or larger was done in Mauve. Sequence inversions are denoted by differential positioning of the LCBs relative to a reference axis. A zoomed-in section of the whole-genome alignment is shown so that the annotated ORFs are visible (black outlined boxes). The small red ORFs are rRNA genes. ORFs proximal to predicted rearrangement breakpoints (red circles) have been color coded and labeled (FWD, INV). A summary of the predicted protein products for these genes is provided in (B). These include genes that have been identified as being either disrupted or absent in the F. tularensis subsp. holarctica subspecies.
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ppat-1000459-g004: Multiple alignment of Francisella genomes of the Type B lineage identifies conserved sequence regions with rearrangements; pseudogenes are found proximal to predicted breakpoints.A comparison of genome rearrangement patterns between the more ancestral F. tularensis subsp. holarctica FSC022 japonica strain and representative strains of the main holarctica group (F. tularensis subsp. holarctica LVS and F. tularensis subsp. holarctica OSU18) was done using MAUVE (A). MAUVE uses an anchored alignment algorithm that permits reordering of the alignment anchors for identification of rearrangements. Colored Local Collinear Blocks (LCBs) are regions of sequence alignment that are free of rearrangements. Each LCB is defined by the anchor regions or predicted sites of rearrangement. A default LCB cutoff of 175, and a filtering for larger blocks containing 10 Kb or larger was done in Mauve. Sequence inversions are denoted by differential positioning of the LCBs relative to a reference axis. A zoomed-in section of the whole-genome alignment is shown so that the annotated ORFs are visible (black outlined boxes). The small red ORFs are rRNA genes. ORFs proximal to predicted rearrangement breakpoints (red circles) have been color coded and labeled (FWD, INV). A summary of the predicted protein products for these genes is provided in (B). These include genes that have been identified as being either disrupted or absent in the F. tularensis subsp. holarctica subspecies.

Mentions: Our finding that there are a significant enrichment of pseudogenes within 1 kb of the FSC022 predicted breakpoints indicate that genome rearrangement events have likely promoted genetic decay in the Type B lineage (Figures 4 and 5). Similarly, we also report the occurrence of rearrangement events when comparing the F. tularensis subsp. mediasiatica FSC147 strain with the other Francisella subspecies strains (Figure S1). Comparative analysis of these newly available strains with highly pathogenic Type A subspecies strains and more distant rare/non-pathogenic novicida and philomiragia strains has provided new insight into how gene decay in different gene functional classes may have contributed to the attenuation of pathogenicity in Francisella.


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)

Multiple alignment of Francisella genomes of the Type B lineage identifies conserved sequence regions with rearrangements; pseudogenes are found proximal to predicted breakpoints.A comparison of genome rearrangement patterns between the more ancestral F. tularensis subsp. holarctica FSC022 japonica strain and representative strains of the main holarctica group (F. tularensis subsp. holarctica LVS and F. tularensis subsp. holarctica OSU18) was done using MAUVE (A). MAUVE uses an anchored alignment algorithm that permits reordering of the alignment anchors for identification of rearrangements. Colored Local Collinear Blocks (LCBs) are regions of sequence alignment that are free of rearrangements. Each LCB is defined by the anchor regions or predicted sites of rearrangement. A default LCB cutoff of 175, and a filtering for larger blocks containing 10 Kb or larger was done in Mauve. Sequence inversions are denoted by differential positioning of the LCBs relative to a reference axis. A zoomed-in section of the whole-genome alignment is shown so that the annotated ORFs are visible (black outlined boxes). The small red ORFs are rRNA genes. ORFs proximal to predicted rearrangement breakpoints (red circles) have been color coded and labeled (FWD, INV). A summary of the predicted protein products for these genes is provided in (B). These include genes that have been identified as being either disrupted or absent in the F. tularensis subsp. holarctica subspecies.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2682660&req=5

ppat-1000459-g004: Multiple alignment of Francisella genomes of the Type B lineage identifies conserved sequence regions with rearrangements; pseudogenes are found proximal to predicted breakpoints.A comparison of genome rearrangement patterns between the more ancestral F. tularensis subsp. holarctica FSC022 japonica strain and representative strains of the main holarctica group (F. tularensis subsp. holarctica LVS and F. tularensis subsp. holarctica OSU18) was done using MAUVE (A). MAUVE uses an anchored alignment algorithm that permits reordering of the alignment anchors for identification of rearrangements. Colored Local Collinear Blocks (LCBs) are regions of sequence alignment that are free of rearrangements. Each LCB is defined by the anchor regions or predicted sites of rearrangement. A default LCB cutoff of 175, and a filtering for larger blocks containing 10 Kb or larger was done in Mauve. Sequence inversions are denoted by differential positioning of the LCBs relative to a reference axis. A zoomed-in section of the whole-genome alignment is shown so that the annotated ORFs are visible (black outlined boxes). The small red ORFs are rRNA genes. ORFs proximal to predicted rearrangement breakpoints (red circles) have been color coded and labeled (FWD, INV). A summary of the predicted protein products for these genes is provided in (B). These include genes that have been identified as being either disrupted or absent in the F. tularensis subsp. holarctica subspecies.
Mentions: Our finding that there are a significant enrichment of pseudogenes within 1 kb of the FSC022 predicted breakpoints indicate that genome rearrangement events have likely promoted genetic decay in the Type B lineage (Figures 4 and 5). Similarly, we also report the occurrence of rearrangement events when comparing the F. tularensis subsp. mediasiatica FSC147 strain with the other Francisella subspecies strains (Figure S1). Comparative analysis of these newly available strains with highly pathogenic Type A subspecies strains and more distant rare/non-pathogenic novicida and philomiragia strains has provided new insight into how gene decay in different gene functional classes may have contributed to the attenuation of pathogenicity in Francisella.

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