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Analysis of genomic differences among Clostridium botulinum type A1 strains.

Fang PK, Raphael BH, Maslanka SE, Cai S, Singh BR - BMC Genomics (2010)

Bottom Line: The purpose of this study was to characterize differences among these genomes and compare these differentiating features with two additional unsequenced strains used in previous studies.Several strategies were deployed in this report.Taken together, C. botulinum type A1 strains including Sanger Institute ATCC 3502, ATCC 3502*, ATCC 19397, Hall, Allergan, and UMASS strains demonstrate differences at the level of the neurotoxin gene sequence, in gene content, and in genome arrangement.

View Article: PubMed Central - HTML - PubMed

Affiliation: Botulinum Research Center and Department of Chemistry & Biochemistry, University of Massachusetts Dartmouth, 285 Old Westport Road, North Dartmouth, Massachusetts 02747, USA.

ABSTRACT

Background: Type A1 Clostridium botulinum strains are a group of Gram-positive, spore-forming anaerobic bacteria that produce a genetically, biochemically, and biophysically indistinguishable 150 kD protein that causes botulism. The genomes of three type A1 C. botulinum strains have been sequenced and show a high degree of synteny. The purpose of this study was to characterize differences among these genomes and compare these differentiating features with two additional unsequenced strains used in previous studies.

Results: Several strategies were deployed in this report. First, University of Massachusetts Dartmouth laboratory Hall strain (UMASS strain) neurotoxin gene was amplified by PCR and sequenced; its sequence was aligned with the published ATCC 3502 Sanger Institute Hall strain and Allergan Hall strain neurotoxin gene regions. Sequence alignment showed that there was a synonymous single nucleotide polymorphism (SNP) in the region encoding the heavy chain between Allergan strain and ATCC 3502 and UMASS strains. Second, comparative genomic hybridization (CGH) demonstrated that the UMASS strain and a strain expected to be derived from ATCC 3502 in the Centers for Disease Control and Prevention (CDC) laboratory (ATCC 3502*) differed in gene content compared to the ATCC 3502 genome sequence published by the Sanger Institute. Third, alignment of the three sequenced C. botulinum type A1 strain genomes revealed the presence of four comparable blocks. Strains ATCC 3502 and ATCC 19397 share the same genome organization, while the organization of the blocks in strain Hall were switched. Lastly, PCR was designed to identify UMASS and ATCC 3502* strain genome organizations. The PCR results indicated that UMASS strain belonged to Hall type and ATCC 3502* strain was identical to ATCC 3502 (Sanger Institute) type.

Conclusions: Taken together, C. botulinum type A1 strains including Sanger Institute ATCC 3502, ATCC 3502*, ATCC 19397, Hall, Allergan, and UMASS strains demonstrate differences at the level of the neurotoxin gene sequence, in gene content, and in genome arrangement.

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Schematic representation of sequence elements of strain ATCC3502 genome block 3 and its flanking regions. ATCC3502 genome block 3 spans the region between CBO0525 (the end of block 2) and CBO0543 (the start of block 4) and is 20728 bp in length. The vertical red lines indicate the block boundaries; the boxes in blue indicate annotated coding regions; the boxes in green indicate inverted repeat sequences; and the F1 fragment is indicated by a red box.
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Figure 7: Schematic representation of sequence elements of strain ATCC3502 genome block 3 and its flanking regions. ATCC3502 genome block 3 spans the region between CBO0525 (the end of block 2) and CBO0543 (the start of block 4) and is 20728 bp in length. The vertical red lines indicate the block boundaries; the boxes in blue indicate annotated coding regions; the boxes in green indicate inverted repeat sequences; and the F1 fragment is indicated by a red box.

Mentions: Further analysis of block 3 (20728 bp in strain ATCC 3502) revealed that virtually identical sequences are found in strain ATCC 19397 (20726 identities out of 20728 bp) and strain Hall (20710 identities out of 20714 bp). The GC content (27.3%) of block 3 in strain ATCC 3502 is not significantly different from 28.2% of whole genome GC content for each sequenced subtype A1 strain genome. Within block 3, we identified two 314 bp inverted repeat sequences (93% identities, Figure 7) that are located before the first gene in the block (CBO0526) and after the last gene in the block (CBO0542). Notably, no genes encoding a transposase or a direct repeat sequence (characteristic of transposon mobile element) was found in the region. In addition, the downstream inverted repeat has no overlapping sequence with F1 fragment mentioned above.


Analysis of genomic differences among Clostridium botulinum type A1 strains.

Fang PK, Raphael BH, Maslanka SE, Cai S, Singh BR - BMC Genomics (2010)

Schematic representation of sequence elements of strain ATCC3502 genome block 3 and its flanking regions. ATCC3502 genome block 3 spans the region between CBO0525 (the end of block 2) and CBO0543 (the start of block 4) and is 20728 bp in length. The vertical red lines indicate the block boundaries; the boxes in blue indicate annotated coding regions; the boxes in green indicate inverted repeat sequences; and the F1 fragment is indicated by a red box.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3038992&req=5

Figure 7: Schematic representation of sequence elements of strain ATCC3502 genome block 3 and its flanking regions. ATCC3502 genome block 3 spans the region between CBO0525 (the end of block 2) and CBO0543 (the start of block 4) and is 20728 bp in length. The vertical red lines indicate the block boundaries; the boxes in blue indicate annotated coding regions; the boxes in green indicate inverted repeat sequences; and the F1 fragment is indicated by a red box.
Mentions: Further analysis of block 3 (20728 bp in strain ATCC 3502) revealed that virtually identical sequences are found in strain ATCC 19397 (20726 identities out of 20728 bp) and strain Hall (20710 identities out of 20714 bp). The GC content (27.3%) of block 3 in strain ATCC 3502 is not significantly different from 28.2% of whole genome GC content for each sequenced subtype A1 strain genome. Within block 3, we identified two 314 bp inverted repeat sequences (93% identities, Figure 7) that are located before the first gene in the block (CBO0526) and after the last gene in the block (CBO0542). Notably, no genes encoding a transposase or a direct repeat sequence (characteristic of transposon mobile element) was found in the region. In addition, the downstream inverted repeat has no overlapping sequence with F1 fragment mentioned above.

Bottom Line: The purpose of this study was to characterize differences among these genomes and compare these differentiating features with two additional unsequenced strains used in previous studies.Several strategies were deployed in this report.Taken together, C. botulinum type A1 strains including Sanger Institute ATCC 3502, ATCC 3502*, ATCC 19397, Hall, Allergan, and UMASS strains demonstrate differences at the level of the neurotoxin gene sequence, in gene content, and in genome arrangement.

View Article: PubMed Central - HTML - PubMed

Affiliation: Botulinum Research Center and Department of Chemistry & Biochemistry, University of Massachusetts Dartmouth, 285 Old Westport Road, North Dartmouth, Massachusetts 02747, USA.

ABSTRACT

Background: Type A1 Clostridium botulinum strains are a group of Gram-positive, spore-forming anaerobic bacteria that produce a genetically, biochemically, and biophysically indistinguishable 150 kD protein that causes botulism. The genomes of three type A1 C. botulinum strains have been sequenced and show a high degree of synteny. The purpose of this study was to characterize differences among these genomes and compare these differentiating features with two additional unsequenced strains used in previous studies.

Results: Several strategies were deployed in this report. First, University of Massachusetts Dartmouth laboratory Hall strain (UMASS strain) neurotoxin gene was amplified by PCR and sequenced; its sequence was aligned with the published ATCC 3502 Sanger Institute Hall strain and Allergan Hall strain neurotoxin gene regions. Sequence alignment showed that there was a synonymous single nucleotide polymorphism (SNP) in the region encoding the heavy chain between Allergan strain and ATCC 3502 and UMASS strains. Second, comparative genomic hybridization (CGH) demonstrated that the UMASS strain and a strain expected to be derived from ATCC 3502 in the Centers for Disease Control and Prevention (CDC) laboratory (ATCC 3502*) differed in gene content compared to the ATCC 3502 genome sequence published by the Sanger Institute. Third, alignment of the three sequenced C. botulinum type A1 strain genomes revealed the presence of four comparable blocks. Strains ATCC 3502 and ATCC 19397 share the same genome organization, while the organization of the blocks in strain Hall were switched. Lastly, PCR was designed to identify UMASS and ATCC 3502* strain genome organizations. The PCR results indicated that UMASS strain belonged to Hall type and ATCC 3502* strain was identical to ATCC 3502 (Sanger Institute) type.

Conclusions: Taken together, C. botulinum type A1 strains including Sanger Institute ATCC 3502, ATCC 3502*, ATCC 19397, Hall, Allergan, and UMASS strains demonstrate differences at the level of the neurotoxin gene sequence, in gene content, and in genome arrangement.

Show MeSH
Related in: MedlinePlus