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Genomic and physiological variability within Group II (non-proteolytic) Clostridium botulinum.

Stringer SC, Carter AT, Webb MD, Wachnicka E, Crossman LC, Sebaihia M, Peck MW - BMC Genomics (2013)

Bottom Line: These results were compared with characteristics determined from physiological tests.However, these two subsets did not differ strongly in minimum growth temperature or maximum NaCl concentration for growth.No relationship was found between tellurite resistance and toxin type despite all the tested type B and type F strains carrying tehB, while the sequence was absent or diverged in all type E strains.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Food Research (IFR), Norwich Research Park, Colney, Norwich NR4 7UA, UK. sandra.stringer@ifr.ac.uk

ABSTRACT

Background: Clostridium botulinum is a group of four physiologically and phylogenetically distinct bacteria that produce botulinum neurotoxin. While studies have characterised variability between strains of Group I (proteolytic) C. botulinum, the genetic and physiological variability and relationships between strains within Group II (non-proteolytic) C. botulinum are not well understood. In this study the genome of Group II strain C. botulinum Eklund 17B (NRP) was sequenced and used to construct a whole genome DNA microarray. This was used in a comparative genomic indexing study to compare the relatedness of 43 strains of Group II C. botulinum (14 type B, 24 type E and 5 type F). These results were compared with characteristics determined from physiological tests.

Results: Whole genome indexing showed that strains of Group II C. botulinum isolated from a wide variety of environments over more than 75 years clustered together indicating the genetic background of Group II C. botulinum is stable. Further analysis showed that strains forming type B or type F toxin are closely related with only toxin cluster genes targets being unique to either type. Strains producing type E toxin formed a separate subset. Carbohydrate fermentation tests supported the observation that type B and F strains form a separate subset to type E strains. All the type F strains and most of type B strains produced acid from amylopectin, amylose and glycogen whereas type E strains did not. However, these two subsets did not differ strongly in minimum growth temperature or maximum NaCl concentration for growth. No relationship was found between tellurite resistance and toxin type despite all the tested type B and type F strains carrying tehB, while the sequence was absent or diverged in all type E strains.

Conclusions: Although Group II C. botulinum form a tight genetic group, genomic and physiological analysis indicates there are two distinct subsets within this group. All type B strains and type F strains are in one subset and all type E strains in the other.

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Circular figure showing relatedness of the chromosome of sequenced Group II C. botulinum strains. Concentric rings represent the genomes of Eklund 17B (NRP) and three other sequenced strains of Group II C. botulinum. From outermost to innermost ring: 1. Black: DNA coordinates for Eklund 17B (NRP) DNA sequence 2. Black: Forward and reverse frames coding sequences for Eklund 17B (NRP). 3. Green: Orthologous coding sequences for Eklund 17B (JGI) (forward only). 4. Red: Orthologous coding sequences shared with Alaska E43 (forward only). 5. Blue: Orthologous coding sequences shared with Beluga (forward only). 6. Orange: Predicted intact bacteriophage sequences in Eklund 17B (NRP). 7. Black: GC content plot as a percentage for Eklund 17B (NRP). 8. Purple/green: GC skew plot for Eklund 17B (NRP). The figure indicates the rRNA operons as regions containing no coding sequences and also represented by a clear spike in the GC content plot present near the replication origin and termination regions. The GC skew plot shows a positive skew on the leading strand.
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Figure 1: Circular figure showing relatedness of the chromosome of sequenced Group II C. botulinum strains. Concentric rings represent the genomes of Eklund 17B (NRP) and three other sequenced strains of Group II C. botulinum. From outermost to innermost ring: 1. Black: DNA coordinates for Eklund 17B (NRP) DNA sequence 2. Black: Forward and reverse frames coding sequences for Eklund 17B (NRP). 3. Green: Orthologous coding sequences for Eklund 17B (JGI) (forward only). 4. Red: Orthologous coding sequences shared with Alaska E43 (forward only). 5. Blue: Orthologous coding sequences shared with Beluga (forward only). 6. Orange: Predicted intact bacteriophage sequences in Eklund 17B (NRP). 7. Black: GC content plot as a percentage for Eklund 17B (NRP). 8. Purple/green: GC skew plot for Eklund 17B (NRP). The figure indicates the rRNA operons as regions containing no coding sequences and also represented by a clear spike in the GC content plot present near the replication origin and termination regions. The GC skew plot shows a positive skew on the leading strand.

Mentions: CDSs shared between strains Eklund 17B (NRP), Alaska E43 and Beluga were determined by reciprocal best match analysis. The general features of all three genomes are summarised in Table 1 and a circular representation of the genome showing orthologous genes shared between the strains is shown in Figure 1. Figure 1 shows specific regions of variability amongst the strains, which may represent insertions into the backbone DNA of the organism.


Genomic and physiological variability within Group II (non-proteolytic) Clostridium botulinum.

Stringer SC, Carter AT, Webb MD, Wachnicka E, Crossman LC, Sebaihia M, Peck MW - BMC Genomics (2013)

Circular figure showing relatedness of the chromosome of sequenced Group II C. botulinum strains. Concentric rings represent the genomes of Eklund 17B (NRP) and three other sequenced strains of Group II C. botulinum. From outermost to innermost ring: 1. Black: DNA coordinates for Eklund 17B (NRP) DNA sequence 2. Black: Forward and reverse frames coding sequences for Eklund 17B (NRP). 3. Green: Orthologous coding sequences for Eklund 17B (JGI) (forward only). 4. Red: Orthologous coding sequences shared with Alaska E43 (forward only). 5. Blue: Orthologous coding sequences shared with Beluga (forward only). 6. Orange: Predicted intact bacteriophage sequences in Eklund 17B (NRP). 7. Black: GC content plot as a percentage for Eklund 17B (NRP). 8. Purple/green: GC skew plot for Eklund 17B (NRP). The figure indicates the rRNA operons as regions containing no coding sequences and also represented by a clear spike in the GC content plot present near the replication origin and termination regions. The GC skew plot shows a positive skew on the leading strand.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3672017&req=5

Figure 1: Circular figure showing relatedness of the chromosome of sequenced Group II C. botulinum strains. Concentric rings represent the genomes of Eklund 17B (NRP) and three other sequenced strains of Group II C. botulinum. From outermost to innermost ring: 1. Black: DNA coordinates for Eklund 17B (NRP) DNA sequence 2. Black: Forward and reverse frames coding sequences for Eklund 17B (NRP). 3. Green: Orthologous coding sequences for Eklund 17B (JGI) (forward only). 4. Red: Orthologous coding sequences shared with Alaska E43 (forward only). 5. Blue: Orthologous coding sequences shared with Beluga (forward only). 6. Orange: Predicted intact bacteriophage sequences in Eklund 17B (NRP). 7. Black: GC content plot as a percentage for Eklund 17B (NRP). 8. Purple/green: GC skew plot for Eklund 17B (NRP). The figure indicates the rRNA operons as regions containing no coding sequences and also represented by a clear spike in the GC content plot present near the replication origin and termination regions. The GC skew plot shows a positive skew on the leading strand.
Mentions: CDSs shared between strains Eklund 17B (NRP), Alaska E43 and Beluga were determined by reciprocal best match analysis. The general features of all three genomes are summarised in Table 1 and a circular representation of the genome showing orthologous genes shared between the strains is shown in Figure 1. Figure 1 shows specific regions of variability amongst the strains, which may represent insertions into the backbone DNA of the organism.

Bottom Line: These results were compared with characteristics determined from physiological tests.However, these two subsets did not differ strongly in minimum growth temperature or maximum NaCl concentration for growth.No relationship was found between tellurite resistance and toxin type despite all the tested type B and type F strains carrying tehB, while the sequence was absent or diverged in all type E strains.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Food Research (IFR), Norwich Research Park, Colney, Norwich NR4 7UA, UK. sandra.stringer@ifr.ac.uk

ABSTRACT

Background: Clostridium botulinum is a group of four physiologically and phylogenetically distinct bacteria that produce botulinum neurotoxin. While studies have characterised variability between strains of Group I (proteolytic) C. botulinum, the genetic and physiological variability and relationships between strains within Group II (non-proteolytic) C. botulinum are not well understood. In this study the genome of Group II strain C. botulinum Eklund 17B (NRP) was sequenced and used to construct a whole genome DNA microarray. This was used in a comparative genomic indexing study to compare the relatedness of 43 strains of Group II C. botulinum (14 type B, 24 type E and 5 type F). These results were compared with characteristics determined from physiological tests.

Results: Whole genome indexing showed that strains of Group II C. botulinum isolated from a wide variety of environments over more than 75 years clustered together indicating the genetic background of Group II C. botulinum is stable. Further analysis showed that strains forming type B or type F toxin are closely related with only toxin cluster genes targets being unique to either type. Strains producing type E toxin formed a separate subset. Carbohydrate fermentation tests supported the observation that type B and F strains form a separate subset to type E strains. All the type F strains and most of type B strains produced acid from amylopectin, amylose and glycogen whereas type E strains did not. However, these two subsets did not differ strongly in minimum growth temperature or maximum NaCl concentration for growth. No relationship was found between tellurite resistance and toxin type despite all the tested type B and type F strains carrying tehB, while the sequence was absent or diverged in all type E strains.

Conclusions: Although Group II C. botulinum form a tight genetic group, genomic and physiological analysis indicates there are two distinct subsets within this group. All type B strains and type F strains are in one subset and all type E strains in the other.

Show MeSH
Related in: MedlinePlus