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Three classes of plasmid (47-63 kb) carry the type B neurotoxin gene cluster of group II Clostridium botulinum.

Carter AT, Austin JW, Weedmark KA, Corbett C, Peck MW - Genome Biol Evol (2014)

Bottom Line: Unexpectedly, no neurotoxin genes were found on the chromosome.This apparent constraint on neurotoxin gene transfer to the chromosome stands in marked contrast to Group I C. botulinum, in which neurotoxin gene clusters are routinely found in both locations.A plasmid toxin-antitoxin system pemI gene located close to the neurotoxin gene cluster and conserved in each type B4 plasmid class may be important in understanding the mechanism which regulates this unique and unexpected bias toward plasmid-borne neurotoxin genes in Group II C. botulinum type B4.

View Article: PubMed Central - PubMed

Affiliation: Gut Health and Food Safety, Institute of Food Research, Norwich Research Park, Norwich, United Kingdom andrew.carter@ifr.ac.uk.

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ACT modified screen shots showing regions of sequence homology (>90% nt sequence identity) shared between plasmids representing the three classes found in Group II Clostridium botulinum type B4. All classes share the neurotoxin gene cluster, which comprises approximately one-third of each plasmid and is located at the right hand end of each sequence (for example in pCB17B, genes 47–52). (A) Plasmid pIFR 05/025 is represented twice, to demonstrate the separate blocks of sequence that it shares with members of the two other plasmid classes. Plasmid pCB17B is carried by Eklund 17B (NRP). (B and C) Members of the two most common classes of Group II C. botulinum type B4 plasmids share much greater homology, with differences due to insertion/deletion of a small number of genes. The four extra genes carried by pCDC 5900 (when compared with pCDC 3897) are probably all phage-derived (three integrases and a transposase).
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evu164-F2: ACT modified screen shots showing regions of sequence homology (>90% nt sequence identity) shared between plasmids representing the three classes found in Group II Clostridium botulinum type B4. All classes share the neurotoxin gene cluster, which comprises approximately one-third of each plasmid and is located at the right hand end of each sequence (for example in pCB17B, genes 47–52). (A) Plasmid pIFR 05/025 is represented twice, to demonstrate the separate blocks of sequence that it shares with members of the two other plasmid classes. Plasmid pCB17B is carried by Eklund 17B (NRP). (B and C) Members of the two most common classes of Group II C. botulinum type B4 plasmids share much greater homology, with differences due to insertion/deletion of a small number of genes. The four extra genes carried by pCDC 5900 (when compared with pCDC 3897) are probably all phage-derived (three integrases and a transposase).

Mentions: Complete plasmid sequences were compared using ACT (fig. 2). This revealed two different levels of relatedness between the plasmids. Evidence of relatively minor variation was small insertion/deletion events involving up to four CDSs, plus more scattered sequence differences, mostly single nucleotide polymorphisms (data not shown), presumably indicative of genetic drift. The parameters of the ACT analysis depicted in figure 2 are set so that sequence identity of approximately 90% or more appears as a solid red block connecting each pairwise comparison, so at the degree of magnification used in figure 2, the latter form of genetic variation is masked. Allowing for up to 10% sequence differences, the plasmids could be organized into three main classes; class 1, represented by pCB17B of Eklund 17B comprised seven members, each of approximately 48 kb; class 2, represented by pCDC 3875 comprised three members of sizes between approximately 58–63 kb; class 3 is represented by its only member, pIFR 05/025 (60 kb), which appeared to be a hybrid version of the two other classes. Allowing for the genetic drift already discussed, the regions of similarity between each plasmid class are quite marked, being defined by large blocks of sequence rather than by regions of intermittent homology (fig. 2A). Figures 2B and C demonstrate the high degree of relatedness between members within a single class, a fact which facilitated identification of the inserted/deleted CDSs. DNA sequences were used to generate phylogenetic trees; of the complete plasmid (fig. 3A), the neurotoxin gene cluster (fig. 3B) and, together with those also available in GenBank, the type B4 neurotoxin gene (fig. 3C). Three distinct groups of neurotoxin gene cluster and neurotoxin genes were identified (figs. 3B and C). As expected for Group II C. botulinum type B, all neurotoxin genes were of subtype B4; their DNA sequence variation fell within the range for subtype B4 (<48 nt) observed in a previous study of C. botulinum neurotoxin gene diversity (Hill et al. 2007).Fig. 2.—


Three classes of plasmid (47-63 kb) carry the type B neurotoxin gene cluster of group II Clostridium botulinum.

Carter AT, Austin JW, Weedmark KA, Corbett C, Peck MW - Genome Biol Evol (2014)

ACT modified screen shots showing regions of sequence homology (>90% nt sequence identity) shared between plasmids representing the three classes found in Group II Clostridium botulinum type B4. All classes share the neurotoxin gene cluster, which comprises approximately one-third of each plasmid and is located at the right hand end of each sequence (for example in pCB17B, genes 47–52). (A) Plasmid pIFR 05/025 is represented twice, to demonstrate the separate blocks of sequence that it shares with members of the two other plasmid classes. Plasmid pCB17B is carried by Eklund 17B (NRP). (B and C) Members of the two most common classes of Group II C. botulinum type B4 plasmids share much greater homology, with differences due to insertion/deletion of a small number of genes. The four extra genes carried by pCDC 5900 (when compared with pCDC 3897) are probably all phage-derived (three integrases and a transposase).
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Related In: Results  -  Collection

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evu164-F2: ACT modified screen shots showing regions of sequence homology (>90% nt sequence identity) shared between plasmids representing the three classes found in Group II Clostridium botulinum type B4. All classes share the neurotoxin gene cluster, which comprises approximately one-third of each plasmid and is located at the right hand end of each sequence (for example in pCB17B, genes 47–52). (A) Plasmid pIFR 05/025 is represented twice, to demonstrate the separate blocks of sequence that it shares with members of the two other plasmid classes. Plasmid pCB17B is carried by Eklund 17B (NRP). (B and C) Members of the two most common classes of Group II C. botulinum type B4 plasmids share much greater homology, with differences due to insertion/deletion of a small number of genes. The four extra genes carried by pCDC 5900 (when compared with pCDC 3897) are probably all phage-derived (three integrases and a transposase).
Mentions: Complete plasmid sequences were compared using ACT (fig. 2). This revealed two different levels of relatedness between the plasmids. Evidence of relatively minor variation was small insertion/deletion events involving up to four CDSs, plus more scattered sequence differences, mostly single nucleotide polymorphisms (data not shown), presumably indicative of genetic drift. The parameters of the ACT analysis depicted in figure 2 are set so that sequence identity of approximately 90% or more appears as a solid red block connecting each pairwise comparison, so at the degree of magnification used in figure 2, the latter form of genetic variation is masked. Allowing for up to 10% sequence differences, the plasmids could be organized into three main classes; class 1, represented by pCB17B of Eklund 17B comprised seven members, each of approximately 48 kb; class 2, represented by pCDC 3875 comprised three members of sizes between approximately 58–63 kb; class 3 is represented by its only member, pIFR 05/025 (60 kb), which appeared to be a hybrid version of the two other classes. Allowing for the genetic drift already discussed, the regions of similarity between each plasmid class are quite marked, being defined by large blocks of sequence rather than by regions of intermittent homology (fig. 2A). Figures 2B and C demonstrate the high degree of relatedness between members within a single class, a fact which facilitated identification of the inserted/deleted CDSs. DNA sequences were used to generate phylogenetic trees; of the complete plasmid (fig. 3A), the neurotoxin gene cluster (fig. 3B) and, together with those also available in GenBank, the type B4 neurotoxin gene (fig. 3C). Three distinct groups of neurotoxin gene cluster and neurotoxin genes were identified (figs. 3B and C). As expected for Group II C. botulinum type B, all neurotoxin genes were of subtype B4; their DNA sequence variation fell within the range for subtype B4 (<48 nt) observed in a previous study of C. botulinum neurotoxin gene diversity (Hill et al. 2007).Fig. 2.—

Bottom Line: Unexpectedly, no neurotoxin genes were found on the chromosome.This apparent constraint on neurotoxin gene transfer to the chromosome stands in marked contrast to Group I C. botulinum, in which neurotoxin gene clusters are routinely found in both locations.A plasmid toxin-antitoxin system pemI gene located close to the neurotoxin gene cluster and conserved in each type B4 plasmid class may be important in understanding the mechanism which regulates this unique and unexpected bias toward plasmid-borne neurotoxin genes in Group II C. botulinum type B4.

View Article: PubMed Central - PubMed

Affiliation: Gut Health and Food Safety, Institute of Food Research, Norwich Research Park, Norwich, United Kingdom andrew.carter@ifr.ac.uk.

Show MeSH
Related in: MedlinePlus