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Genomes, neurotoxins and biology of Clostridium botulinum Group I and Group II.

Carter AT, Peck MW - Res. Microbiol. (2014)

Bottom Line: Recent developments in whole genome sequencing have made a substantial contribution to understanding the genomes, neurotoxins and biology of Clostridium botulinum Group I (proteolytic C. botulinum) and C. botulinum Group II (non-proteolytic C. botulinum).The properties of the different types of neurotoxin formed, and different neurotoxin gene clusters found in C. botulinum Groups I and II are explored.Specific examples of botulinum neurotoxin genes are chosen for an in-depth discussion of neurotoxin gene evolution.

View Article: PubMed Central - PubMed

Affiliation: Institute of Food Research, Norwich Research Park, Colney, Norwich, NR4 7UA, UK.

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Heatmaps and dendrograms generated by two colour microarray analysis of genomic DNA from strains of C. botulinum Group I (panel A) and of C. botulinum Group II (panel B). Microarray probes for the C. botulinum Group I analysis were derived from the genome sequence of ATCC 3502 [61,65] and for the C. botulinum Group II analysis from the genome sequence of Eklund 17B [62]. Competitive hybridisations for the C. botulinum Group I analyses were performed by mixing genomic DNA of strain ATCC 3502 with that of the test strain, each DNA having been labelled with a different fluorescent dye, before adding to the microarray. Similarly, labelled DNA from strain Eklund 17B was used as the hybridisation reference for the C. botulinum Group II experiments. In each heatmap, a yellow colour signals that the test strain genome shares >85% homology with a gene probe on the microarray, generally implying that a very similar gene may be present (with the caveat that due to the small size (60 nt) of each microarray probe, false signals may be generated by small sequence differences, giving a level of background ‘noise’ which has to be normalised during data processing). The bottom, horizontal lane of each heatmap is an internal control experiment, and represents the result of hybridising the reference strain DNA for each Group with itself; any bars which lack a yellow colour in these two lanes indicate the position of microarray probes which for technical reasons have failed to hybridise to their cognate DNA sequence. The Group I clades (panel A) do not respect neurotoxin types formed, while the Group II clades (panel B) do respect neurotoxin types formed; i.e. clade 3 = type E, clade 2 = type B or type F, clade 1 = type B strains most closely related to Eklund 17B (hence the greater proportion of yellow bars in these heatmaps). (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)
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fig3: Heatmaps and dendrograms generated by two colour microarray analysis of genomic DNA from strains of C. botulinum Group I (panel A) and of C. botulinum Group II (panel B). Microarray probes for the C. botulinum Group I analysis were derived from the genome sequence of ATCC 3502 [61,65] and for the C. botulinum Group II analysis from the genome sequence of Eklund 17B [62]. Competitive hybridisations for the C. botulinum Group I analyses were performed by mixing genomic DNA of strain ATCC 3502 with that of the test strain, each DNA having been labelled with a different fluorescent dye, before adding to the microarray. Similarly, labelled DNA from strain Eklund 17B was used as the hybridisation reference for the C. botulinum Group II experiments. In each heatmap, a yellow colour signals that the test strain genome shares >85% homology with a gene probe on the microarray, generally implying that a very similar gene may be present (with the caveat that due to the small size (60 nt) of each microarray probe, false signals may be generated by small sequence differences, giving a level of background ‘noise’ which has to be normalised during data processing). The bottom, horizontal lane of each heatmap is an internal control experiment, and represents the result of hybridising the reference strain DNA for each Group with itself; any bars which lack a yellow colour in these two lanes indicate the position of microarray probes which for technical reasons have failed to hybridise to their cognate DNA sequence. The Group I clades (panel A) do not respect neurotoxin types formed, while the Group II clades (panel B) do respect neurotoxin types formed; i.e. clade 3 = type E, clade 2 = type B or type F, clade 1 = type B strains most closely related to Eklund 17B (hence the greater proportion of yellow bars in these heatmaps). (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

Mentions: DNA microarrays provide an alternative to whole genome sequencing for analysis of whole genomes; they are particularly useful for comparison of many closely related genomes, using a well-characterised, sequenced strain as a hybridisation reference. Fig. 3 displays the main set of results from two different studies, in which a DNA microarray was used to compare sequences representing all predicted genes of the sequenced C. botulinum Group I strain ATCC 3502 with the unknown ones of several strains of the same Group (Fig. 3A), and similarly all predicted genes of the Eklund 17B genome were compared with unknown ones from other members of C. botulinum Group II (Fig. 3B). Strains tested using the C. botulinum Group I microarray included those forming type A, A(B), B, Bf and F neurotoxins, plus several examples of the closely related but non-toxigenic C. sporogenes. Strains tested using the C. botulinum Group II microarray included those forming type B, type E or type F neurotoxin [62,65].


Genomes, neurotoxins and biology of Clostridium botulinum Group I and Group II.

Carter AT, Peck MW - Res. Microbiol. (2014)

Heatmaps and dendrograms generated by two colour microarray analysis of genomic DNA from strains of C. botulinum Group I (panel A) and of C. botulinum Group II (panel B). Microarray probes for the C. botulinum Group I analysis were derived from the genome sequence of ATCC 3502 [61,65] and for the C. botulinum Group II analysis from the genome sequence of Eklund 17B [62]. Competitive hybridisations for the C. botulinum Group I analyses were performed by mixing genomic DNA of strain ATCC 3502 with that of the test strain, each DNA having been labelled with a different fluorescent dye, before adding to the microarray. Similarly, labelled DNA from strain Eklund 17B was used as the hybridisation reference for the C. botulinum Group II experiments. In each heatmap, a yellow colour signals that the test strain genome shares >85% homology with a gene probe on the microarray, generally implying that a very similar gene may be present (with the caveat that due to the small size (60 nt) of each microarray probe, false signals may be generated by small sequence differences, giving a level of background ‘noise’ which has to be normalised during data processing). The bottom, horizontal lane of each heatmap is an internal control experiment, and represents the result of hybridising the reference strain DNA for each Group with itself; any bars which lack a yellow colour in these two lanes indicate the position of microarray probes which for technical reasons have failed to hybridise to their cognate DNA sequence. The Group I clades (panel A) do not respect neurotoxin types formed, while the Group II clades (panel B) do respect neurotoxin types formed; i.e. clade 3 = type E, clade 2 = type B or type F, clade 1 = type B strains most closely related to Eklund 17B (hence the greater proportion of yellow bars in these heatmaps). (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)
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Related In: Results  -  Collection

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fig3: Heatmaps and dendrograms generated by two colour microarray analysis of genomic DNA from strains of C. botulinum Group I (panel A) and of C. botulinum Group II (panel B). Microarray probes for the C. botulinum Group I analysis were derived from the genome sequence of ATCC 3502 [61,65] and for the C. botulinum Group II analysis from the genome sequence of Eklund 17B [62]. Competitive hybridisations for the C. botulinum Group I analyses were performed by mixing genomic DNA of strain ATCC 3502 with that of the test strain, each DNA having been labelled with a different fluorescent dye, before adding to the microarray. Similarly, labelled DNA from strain Eklund 17B was used as the hybridisation reference for the C. botulinum Group II experiments. In each heatmap, a yellow colour signals that the test strain genome shares >85% homology with a gene probe on the microarray, generally implying that a very similar gene may be present (with the caveat that due to the small size (60 nt) of each microarray probe, false signals may be generated by small sequence differences, giving a level of background ‘noise’ which has to be normalised during data processing). The bottom, horizontal lane of each heatmap is an internal control experiment, and represents the result of hybridising the reference strain DNA for each Group with itself; any bars which lack a yellow colour in these two lanes indicate the position of microarray probes which for technical reasons have failed to hybridise to their cognate DNA sequence. The Group I clades (panel A) do not respect neurotoxin types formed, while the Group II clades (panel B) do respect neurotoxin types formed; i.e. clade 3 = type E, clade 2 = type B or type F, clade 1 = type B strains most closely related to Eklund 17B (hence the greater proportion of yellow bars in these heatmaps). (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)
Mentions: DNA microarrays provide an alternative to whole genome sequencing for analysis of whole genomes; they are particularly useful for comparison of many closely related genomes, using a well-characterised, sequenced strain as a hybridisation reference. Fig. 3 displays the main set of results from two different studies, in which a DNA microarray was used to compare sequences representing all predicted genes of the sequenced C. botulinum Group I strain ATCC 3502 with the unknown ones of several strains of the same Group (Fig. 3A), and similarly all predicted genes of the Eklund 17B genome were compared with unknown ones from other members of C. botulinum Group II (Fig. 3B). Strains tested using the C. botulinum Group I microarray included those forming type A, A(B), B, Bf and F neurotoxins, plus several examples of the closely related but non-toxigenic C. sporogenes. Strains tested using the C. botulinum Group II microarray included those forming type B, type E or type F neurotoxin [62,65].

Bottom Line: Recent developments in whole genome sequencing have made a substantial contribution to understanding the genomes, neurotoxins and biology of Clostridium botulinum Group I (proteolytic C. botulinum) and C. botulinum Group II (non-proteolytic C. botulinum).The properties of the different types of neurotoxin formed, and different neurotoxin gene clusters found in C. botulinum Groups I and II are explored.Specific examples of botulinum neurotoxin genes are chosen for an in-depth discussion of neurotoxin gene evolution.

View Article: PubMed Central - PubMed

Affiliation: Institute of Food Research, Norwich Research Park, Colney, Norwich, NR4 7UA, UK.

Show MeSH
Related in: MedlinePlus