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Differential gene repertoire in Mycobacterium ulcerans identifies candidate genes for patho-adaptation.

Käser M, Pluschke G - PLoS Negl Trop Dis (2008)

Bottom Line: Altogether, 229 coding sequences were found to be differentially inactivated, constituting a repertoire of coding sequence variation in the rather monomorphic M. ulcerans.The differential gene inactivation patterns associated with the M. ulcerans haplotypes identified candidate genes that may confer enhanced adaptation upon ablation of expression.Identification of this spectrum of anti-virulence gene candidates expands our understanding of the pathogenicity and ecology of the emerging infectious disease Buruli ulcer.

View Article: PubMed Central - PubMed

Affiliation: Swiss Tropical Institute, Basel, Switzerland. m.kaeser@unibas.ch

ABSTRACT

Background: Based on large genomic sequence polymorphisms, several haplotypes belonging to two major lineages of the human pathogen Mycobacterium ulcerans could be distinguished among patient isolates from various geographic origins. However, the biological relevance of insertional/deletional diversity is not understood.

Methodology: Using comparative genomics, we have investigated the genes located in regions of difference recently identified by DNA microarray based hybridisation analysis. The analysed regions of difference comprise approximately 7% of the entire M. ulcerans genome.

Principal findings: Several different mechanisms leading to loss of functional genes were identified, ranging from pseudogenization, caused by frame shift mutations or mobile genetic element interspersing, to large sequence polymorphisms. Four hot spot regions for genetic instability were unveiled. Altogether, 229 coding sequences were found to be differentially inactivated, constituting a repertoire of coding sequence variation in the rather monomorphic M. ulcerans.

Conclusions/significance: The differential gene inactivation patterns associated with the M. ulcerans haplotypes identified candidate genes that may confer enhanced adaptation upon ablation of expression. A number of gene conversions confined to the classical lineage may contribute to particular virulence of this group comprising isolates from Africa and Australia. Identification of this spectrum of anti-virulence gene candidates expands our understanding of the pathogenicity and ecology of the emerging infectious disease Buruli ulcer.

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Related in: MedlinePlus

Description of RDs1-15 throughout the M. ulcerans haplotypes.Shown are the CDSs of the M. marinum M sequence backbone (which is closest to the entirety of all M. ulcerans haplotypes and thus to an M. ulcerans most recent common ancestor). Variations thereof in M. ulcerans haplotypes are depicted above the M. marinum sequence for members of the ancestral lineage, as indicated, and below for the classical lineage (exemplified by Agy99). Grey areas indicate differences of insertions, deletions, or InDels, as compared to M. marinum. Nomenclature of CDSs is indicated along the M. marinum annotation [40], i.e. 3970 stands for MMAR_3970. Symbol explanations see legend. Note that some genomic loci of Agy99 can neither be aligned directly to M. marinum M nor to M. ulcerans ancestral haplotypes due to major sequence rearrangements and displacements in the classical lineage only (indicated with *). Pseudogenes caused by frame shift mutations, according to the M. ulcerans Agy99 genome annotation, are marked as “x”. Bar = deletion. Blunt ends of bars: breakpoints exactly defined. Blurred ends of bars: breakpoints approximately. MURDs are confined to the M. ulcerans classical lineage but are usually not deleted in the ancestral lineage. Not shown are RDs6 and 7 since they do not reveal deletions relative to M. marinum M. A corresponding and complete list of silenced CDS is supplied in Table S1.
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pntd-0000353-g002: Description of RDs1-15 throughout the M. ulcerans haplotypes.Shown are the CDSs of the M. marinum M sequence backbone (which is closest to the entirety of all M. ulcerans haplotypes and thus to an M. ulcerans most recent common ancestor). Variations thereof in M. ulcerans haplotypes are depicted above the M. marinum sequence for members of the ancestral lineage, as indicated, and below for the classical lineage (exemplified by Agy99). Grey areas indicate differences of insertions, deletions, or InDels, as compared to M. marinum. Nomenclature of CDSs is indicated along the M. marinum annotation [40], i.e. 3970 stands for MMAR_3970. Symbol explanations see legend. Note that some genomic loci of Agy99 can neither be aligned directly to M. marinum M nor to M. ulcerans ancestral haplotypes due to major sequence rearrangements and displacements in the classical lineage only (indicated with *). Pseudogenes caused by frame shift mutations, according to the M. ulcerans Agy99 genome annotation, are marked as “x”. Bar = deletion. Blunt ends of bars: breakpoints exactly defined. Blurred ends of bars: breakpoints approximately. MURDs are confined to the M. ulcerans classical lineage but are usually not deleted in the ancestral lineage. Not shown are RDs6 and 7 since they do not reveal deletions relative to M. marinum M. A corresponding and complete list of silenced CDS is supplied in Table S1.

Mentions: Within the analysed 7% of the entire M. ulcerans genome associated with RDs1 to 15 we observed various genetic mechanisms that led to specific ablation of the expression of sets of proteins across the six haplotypes: i) frameshift mutations resulting in pseudogenization, ii) interspersing of ISEs into CDS that led to their disruption, and iii) physical deletions of sizes between 2 and 53 kbp with replacement by ISEs which made their involvement obvious. Both pseudogenization or functional disruption, leaving the CDSs with scars in the genome, and physical deletion of the CDSs lead to gene silencing. Throughout the RDs, there is a strong bias of the two M. ulcerans lineages in their mechanisms leading to gene loss [9]: in the ancestral lineage deletions of large DNA stretches play a major role, whereas the classical lineage shows preponderance of ISEs interrupting CDSs, often even without concurrent deletions, as shown for RD1 in Fig. 1. Although a sequence of events cannot be deduced for RD1 from Fig. 1, it is clear that the inactivation of MMAR_2766, involved in lipid metabolism, was mediated by independent InDel events in the two lineages. In the ancestral lineage, five additional genes were lost with the 8 kb deletion whereas only in the classical lineage interspersing of an IS2404 element into glnA3 led to its functional disruption (Fig. 1). Thus, independent InDel events have led to a differential gene repertoire between the two lineages. Fig. 2 gives a comprehensive reference overview of all genome variations in the identified RDs1 through 15 and shows a variety of such events. A detailed list of the differentially deleted genes, corresponding to Fig. 2, is provided in the Table S1.


Differential gene repertoire in Mycobacterium ulcerans identifies candidate genes for patho-adaptation.

Käser M, Pluschke G - PLoS Negl Trop Dis (2008)

Description of RDs1-15 throughout the M. ulcerans haplotypes.Shown are the CDSs of the M. marinum M sequence backbone (which is closest to the entirety of all M. ulcerans haplotypes and thus to an M. ulcerans most recent common ancestor). Variations thereof in M. ulcerans haplotypes are depicted above the M. marinum sequence for members of the ancestral lineage, as indicated, and below for the classical lineage (exemplified by Agy99). Grey areas indicate differences of insertions, deletions, or InDels, as compared to M. marinum. Nomenclature of CDSs is indicated along the M. marinum annotation [40], i.e. 3970 stands for MMAR_3970. Symbol explanations see legend. Note that some genomic loci of Agy99 can neither be aligned directly to M. marinum M nor to M. ulcerans ancestral haplotypes due to major sequence rearrangements and displacements in the classical lineage only (indicated with *). Pseudogenes caused by frame shift mutations, according to the M. ulcerans Agy99 genome annotation, are marked as “x”. Bar = deletion. Blunt ends of bars: breakpoints exactly defined. Blurred ends of bars: breakpoints approximately. MURDs are confined to the M. ulcerans classical lineage but are usually not deleted in the ancestral lineage. Not shown are RDs6 and 7 since they do not reveal deletions relative to M. marinum M. A corresponding and complete list of silenced CDS is supplied in Table S1.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2600814&req=5

pntd-0000353-g002: Description of RDs1-15 throughout the M. ulcerans haplotypes.Shown are the CDSs of the M. marinum M sequence backbone (which is closest to the entirety of all M. ulcerans haplotypes and thus to an M. ulcerans most recent common ancestor). Variations thereof in M. ulcerans haplotypes are depicted above the M. marinum sequence for members of the ancestral lineage, as indicated, and below for the classical lineage (exemplified by Agy99). Grey areas indicate differences of insertions, deletions, or InDels, as compared to M. marinum. Nomenclature of CDSs is indicated along the M. marinum annotation [40], i.e. 3970 stands for MMAR_3970. Symbol explanations see legend. Note that some genomic loci of Agy99 can neither be aligned directly to M. marinum M nor to M. ulcerans ancestral haplotypes due to major sequence rearrangements and displacements in the classical lineage only (indicated with *). Pseudogenes caused by frame shift mutations, according to the M. ulcerans Agy99 genome annotation, are marked as “x”. Bar = deletion. Blunt ends of bars: breakpoints exactly defined. Blurred ends of bars: breakpoints approximately. MURDs are confined to the M. ulcerans classical lineage but are usually not deleted in the ancestral lineage. Not shown are RDs6 and 7 since they do not reveal deletions relative to M. marinum M. A corresponding and complete list of silenced CDS is supplied in Table S1.
Mentions: Within the analysed 7% of the entire M. ulcerans genome associated with RDs1 to 15 we observed various genetic mechanisms that led to specific ablation of the expression of sets of proteins across the six haplotypes: i) frameshift mutations resulting in pseudogenization, ii) interspersing of ISEs into CDS that led to their disruption, and iii) physical deletions of sizes between 2 and 53 kbp with replacement by ISEs which made their involvement obvious. Both pseudogenization or functional disruption, leaving the CDSs with scars in the genome, and physical deletion of the CDSs lead to gene silencing. Throughout the RDs, there is a strong bias of the two M. ulcerans lineages in their mechanisms leading to gene loss [9]: in the ancestral lineage deletions of large DNA stretches play a major role, whereas the classical lineage shows preponderance of ISEs interrupting CDSs, often even without concurrent deletions, as shown for RD1 in Fig. 1. Although a sequence of events cannot be deduced for RD1 from Fig. 1, it is clear that the inactivation of MMAR_2766, involved in lipid metabolism, was mediated by independent InDel events in the two lineages. In the ancestral lineage, five additional genes were lost with the 8 kb deletion whereas only in the classical lineage interspersing of an IS2404 element into glnA3 led to its functional disruption (Fig. 1). Thus, independent InDel events have led to a differential gene repertoire between the two lineages. Fig. 2 gives a comprehensive reference overview of all genome variations in the identified RDs1 through 15 and shows a variety of such events. A detailed list of the differentially deleted genes, corresponding to Fig. 2, is provided in the Table S1.

Bottom Line: Altogether, 229 coding sequences were found to be differentially inactivated, constituting a repertoire of coding sequence variation in the rather monomorphic M. ulcerans.The differential gene inactivation patterns associated with the M. ulcerans haplotypes identified candidate genes that may confer enhanced adaptation upon ablation of expression.Identification of this spectrum of anti-virulence gene candidates expands our understanding of the pathogenicity and ecology of the emerging infectious disease Buruli ulcer.

View Article: PubMed Central - PubMed

Affiliation: Swiss Tropical Institute, Basel, Switzerland. m.kaeser@unibas.ch

ABSTRACT

Background: Based on large genomic sequence polymorphisms, several haplotypes belonging to two major lineages of the human pathogen Mycobacterium ulcerans could be distinguished among patient isolates from various geographic origins. However, the biological relevance of insertional/deletional diversity is not understood.

Methodology: Using comparative genomics, we have investigated the genes located in regions of difference recently identified by DNA microarray based hybridisation analysis. The analysed regions of difference comprise approximately 7% of the entire M. ulcerans genome.

Principal findings: Several different mechanisms leading to loss of functional genes were identified, ranging from pseudogenization, caused by frame shift mutations or mobile genetic element interspersing, to large sequence polymorphisms. Four hot spot regions for genetic instability were unveiled. Altogether, 229 coding sequences were found to be differentially inactivated, constituting a repertoire of coding sequence variation in the rather monomorphic M. ulcerans.

Conclusions/significance: The differential gene inactivation patterns associated with the M. ulcerans haplotypes identified candidate genes that may confer enhanced adaptation upon ablation of expression. A number of gene conversions confined to the classical lineage may contribute to particular virulence of this group comprising isolates from Africa and Australia. Identification of this spectrum of anti-virulence gene candidates expands our understanding of the pathogenicity and ecology of the emerging infectious disease Buruli ulcer.

Show MeSH
Related in: MedlinePlus