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Comparative genome sequencing reveals chemotype-specific gene clusters in the toxigenic black mold Stachybotrys.

Semeiks J, Borek D, Otwinowski Z, Grishin NV - BMC Genomics (2014)

Bottom Line: One such satratoxin chemotype-specific cluster is adjacent to the core trichothecene cluster, which has diverged from those of other trichothecene producers to contain a unique polyketide synthase.The results suggest that chemotype-specific gene clusters are likely the genetic basis for the mutually-exclusive toxin chemotypes of Stachybotrys.A unified biochemical model for Stachybotrys toxin production is presented.

View Article: PubMed Central - PubMed

Affiliation: Molecular Biophysics Program and Medical Scientist Training Program, University of Texas Southwestern Medical Center, Dallas, Texas, USA. jeremy@semeiks.com.

ABSTRACT

Background: The fungal genus Stachybotrys produces several diverse toxins that affect human health. Its strains comprise two mutually-exclusive toxin chemotypes, one producing satratoxins, which are a subclass of trichothecenes, and the other producing the less-toxic atranones. To determine the genetic basis for chemotype-specific differences in toxin production, the genomes of four Stachybotrys strains were sequenced and assembled de novo. Two of these strains produce atranones and two produce satratoxins.

Results: Comparative analysis of these four 35-Mbp genomes revealed several chemotype-specific gene clusters that are predicted to make secondary metabolites. The largest, which was named the core atranone cluster, encodes 14 proteins that may suffice to produce all observed atranone compounds via reactions that include an unusual Baeyer-Villiger oxidation. Satratoxins are suggested to be made by products of multiple gene clusters that encode 21 proteins in all, including polyketide synthases, acetyltransferases, and other enzymes expected to modify the trichothecene skeleton. One such satratoxin chemotype-specific cluster is adjacent to the core trichothecene cluster, which has diverged from those of other trichothecene producers to contain a unique polyketide synthase.

Conclusions: The results suggest that chemotype-specific gene clusters are likely the genetic basis for the mutually-exclusive toxin chemotypes of Stachybotrys. A unified biochemical model for Stachybotrys toxin production is presented. Overall, the four genomes described here will be useful for ongoing studies of this mold's diverse toxicity mechanisms.

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Related in: MedlinePlus

Conceptual and ortholog-based maximum likelihood phylogeny ofStachybotrysand other fungi. A. The conceptual phylogeny shows the toxin chemotypes of the four sequenced Stachybotrys strains in relation to other trichothecene-producing fungi of order Hypocreales. S. cerevisiae is only distantly related to Hypocreales and is shown for context. Topology adapted from [18]. B. Phylogeny was constructed from alignment of 2,177 proper protein orthologs identified by OrthoMCL. Scale bar shows number of substitutions per site. All branches have 100% support.
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Fig2: Conceptual and ortholog-based maximum likelihood phylogeny ofStachybotrysand other fungi. A. The conceptual phylogeny shows the toxin chemotypes of the four sequenced Stachybotrys strains in relation to other trichothecene-producing fungi of order Hypocreales. S. cerevisiae is only distantly related to Hypocreales and is shown for context. Topology adapted from [18]. B. Phylogeny was constructed from alignment of 2,177 proper protein orthologs identified by OrthoMCL. Scale bar shows number of substitutions per site. All branches have 100% support.

Mentions: The phylogeny of the four Stachybotrys strains that were sequenced is shown in FigureĀ 2A. The strains include two species, S. chlorohalonata (IBT strain 40285) and S. chartarum (IBT strains 40288, 40293, and 7711), which are distinguishable both by morphology and molecular markers. Strains 40285 and 40288 make atranones, while strains 40293 and 7711 make satratoxins (Figure one; [15]). The genomes of these four strains were obtained by massive parallel sequencing on an Illumina Hiseq 2000. For each strain, a separate 300-bp nominal genomic fragment library was constructed. These libraries were multiplexed in order to combine them all on a single sequencer lane. Sequencing yielded ~70 million 101-bp reads per strain after demultiplexing and error correction. Each genome was then independently assembled with SOAPdenovo [16], followed by protein annotation of each assembly with MAKER [17] using a cross-strain iterative strategy. Ideally these annotations would be supported by RNA data, but the RNA extractable from each of the four strains was too degraded to use for RNA-seq libraries, preventing this additional validation.Figure 2


Comparative genome sequencing reveals chemotype-specific gene clusters in the toxigenic black mold Stachybotrys.

Semeiks J, Borek D, Otwinowski Z, Grishin NV - BMC Genomics (2014)

Conceptual and ortholog-based maximum likelihood phylogeny ofStachybotrysand other fungi. A. The conceptual phylogeny shows the toxin chemotypes of the four sequenced Stachybotrys strains in relation to other trichothecene-producing fungi of order Hypocreales. S. cerevisiae is only distantly related to Hypocreales and is shown for context. Topology adapted from [18]. B. Phylogeny was constructed from alignment of 2,177 proper protein orthologs identified by OrthoMCL. Scale bar shows number of substitutions per site. All branches have 100% support.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4117958&req=5

Fig2: Conceptual and ortholog-based maximum likelihood phylogeny ofStachybotrysand other fungi. A. The conceptual phylogeny shows the toxin chemotypes of the four sequenced Stachybotrys strains in relation to other trichothecene-producing fungi of order Hypocreales. S. cerevisiae is only distantly related to Hypocreales and is shown for context. Topology adapted from [18]. B. Phylogeny was constructed from alignment of 2,177 proper protein orthologs identified by OrthoMCL. Scale bar shows number of substitutions per site. All branches have 100% support.
Mentions: The phylogeny of the four Stachybotrys strains that were sequenced is shown in FigureĀ 2A. The strains include two species, S. chlorohalonata (IBT strain 40285) and S. chartarum (IBT strains 40288, 40293, and 7711), which are distinguishable both by morphology and molecular markers. Strains 40285 and 40288 make atranones, while strains 40293 and 7711 make satratoxins (Figure one; [15]). The genomes of these four strains were obtained by massive parallel sequencing on an Illumina Hiseq 2000. For each strain, a separate 300-bp nominal genomic fragment library was constructed. These libraries were multiplexed in order to combine them all on a single sequencer lane. Sequencing yielded ~70 million 101-bp reads per strain after demultiplexing and error correction. Each genome was then independently assembled with SOAPdenovo [16], followed by protein annotation of each assembly with MAKER [17] using a cross-strain iterative strategy. Ideally these annotations would be supported by RNA data, but the RNA extractable from each of the four strains was too degraded to use for RNA-seq libraries, preventing this additional validation.Figure 2

Bottom Line: One such satratoxin chemotype-specific cluster is adjacent to the core trichothecene cluster, which has diverged from those of other trichothecene producers to contain a unique polyketide synthase.The results suggest that chemotype-specific gene clusters are likely the genetic basis for the mutually-exclusive toxin chemotypes of Stachybotrys.A unified biochemical model for Stachybotrys toxin production is presented.

View Article: PubMed Central - PubMed

Affiliation: Molecular Biophysics Program and Medical Scientist Training Program, University of Texas Southwestern Medical Center, Dallas, Texas, USA. jeremy@semeiks.com.

ABSTRACT

Background: The fungal genus Stachybotrys produces several diverse toxins that affect human health. Its strains comprise two mutually-exclusive toxin chemotypes, one producing satratoxins, which are a subclass of trichothecenes, and the other producing the less-toxic atranones. To determine the genetic basis for chemotype-specific differences in toxin production, the genomes of four Stachybotrys strains were sequenced and assembled de novo. Two of these strains produce atranones and two produce satratoxins.

Results: Comparative analysis of these four 35-Mbp genomes revealed several chemotype-specific gene clusters that are predicted to make secondary metabolites. The largest, which was named the core atranone cluster, encodes 14 proteins that may suffice to produce all observed atranone compounds via reactions that include an unusual Baeyer-Villiger oxidation. Satratoxins are suggested to be made by products of multiple gene clusters that encode 21 proteins in all, including polyketide synthases, acetyltransferases, and other enzymes expected to modify the trichothecene skeleton. One such satratoxin chemotype-specific cluster is adjacent to the core trichothecene cluster, which has diverged from those of other trichothecene producers to contain a unique polyketide synthase.

Conclusions: The results suggest that chemotype-specific gene clusters are likely the genetic basis for the mutually-exclusive toxin chemotypes of Stachybotrys. A unified biochemical model for Stachybotrys toxin production is presented. Overall, the four genomes described here will be useful for ongoing studies of this mold's diverse toxicity mechanisms.

Show MeSH
Related in: MedlinePlus