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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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C. botulinum ATCC 3502, ATCC 19397, and Hall strains genome alignment. The alignment display is organized into one horizontal "panel" per input genome sequence. Each genome's panel contains the name of the genome sequence, a scale showing the sequence coordinates for that genome, and a single black horizontal center line. All the blocks lie above the center line, which indicates that the aligned regions are in the forward orientation relative to the first genome sequence. Colored blocks in the first genome are connected by lines to similarly colored blocks in the second and third genomes. These lines indicate which regions in each genome are homologous and internally free from genomic rearrangement. There are only four blocks (1 to 4) from each genome. ATCC 3502 (top panel) and ATCC 19397 (middle panel) have the same block arrangements, while, in Hall (bottom panel), the positions of blocks 2 and 3 are switched. Inside each block, areas that are completely white were not aligned and contain sequence elements specific to a particular genome. Numbers in white inside the blocks indicate the block numbers.
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Figure 3: C. botulinum ATCC 3502, ATCC 19397, and Hall strains genome alignment. The alignment display is organized into one horizontal "panel" per input genome sequence. Each genome's panel contains the name of the genome sequence, a scale showing the sequence coordinates for that genome, and a single black horizontal center line. All the blocks lie above the center line, which indicates that the aligned regions are in the forward orientation relative to the first genome sequence. Colored blocks in the first genome are connected by lines to similarly colored blocks in the second and third genomes. These lines indicate which regions in each genome are homologous and internally free from genomic rearrangement. There are only four blocks (1 to 4) from each genome. ATCC 3502 (top panel) and ATCC 19397 (middle panel) have the same block arrangements, while, in Hall (bottom panel), the positions of blocks 2 and 3 are switched. Inside each block, areas that are completely white were not aligned and contain sequence elements specific to a particular genome. Numbers in white inside the blocks indicate the block numbers.

Mentions: As mentioned above, three fully sequenced C. botulinum A1 strain genomes are deposited in GenBank: ATCC 3502, ATCC 19397, and Hall. Mauve software [14] was used to compare and analyze the organization of these genomes. At the gross level, based on the ATCC 3502 genome organization, all three genomes were divided into four blocks: blocks 1, 2, 3, and 4, sequentially (Figure 3).


Analysis of genomic differences among Clostridium botulinum type A1 strains.

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

C. botulinum ATCC 3502, ATCC 19397, and Hall strains genome alignment. The alignment display is organized into one horizontal "panel" per input genome sequence. Each genome's panel contains the name of the genome sequence, a scale showing the sequence coordinates for that genome, and a single black horizontal center line. All the blocks lie above the center line, which indicates that the aligned regions are in the forward orientation relative to the first genome sequence. Colored blocks in the first genome are connected by lines to similarly colored blocks in the second and third genomes. These lines indicate which regions in each genome are homologous and internally free from genomic rearrangement. There are only four blocks (1 to 4) from each genome. ATCC 3502 (top panel) and ATCC 19397 (middle panel) have the same block arrangements, while, in Hall (bottom panel), the positions of blocks 2 and 3 are switched. Inside each block, areas that are completely white were not aligned and contain sequence elements specific to a particular genome. Numbers in white inside the blocks indicate the block numbers.
© Copyright Policy - open-access
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3038992&req=5

Figure 3: C. botulinum ATCC 3502, ATCC 19397, and Hall strains genome alignment. The alignment display is organized into one horizontal "panel" per input genome sequence. Each genome's panel contains the name of the genome sequence, a scale showing the sequence coordinates for that genome, and a single black horizontal center line. All the blocks lie above the center line, which indicates that the aligned regions are in the forward orientation relative to the first genome sequence. Colored blocks in the first genome are connected by lines to similarly colored blocks in the second and third genomes. These lines indicate which regions in each genome are homologous and internally free from genomic rearrangement. There are only four blocks (1 to 4) from each genome. ATCC 3502 (top panel) and ATCC 19397 (middle panel) have the same block arrangements, while, in Hall (bottom panel), the positions of blocks 2 and 3 are switched. Inside each block, areas that are completely white were not aligned and contain sequence elements specific to a particular genome. Numbers in white inside the blocks indicate the block numbers.
Mentions: As mentioned above, three fully sequenced C. botulinum A1 strain genomes are deposited in GenBank: ATCC 3502, ATCC 19397, and Hall. Mauve software [14] was used to compare and analyze the organization of these genomes. At the gross level, based on the ATCC 3502 genome organization, all three genomes were divided into four blocks: blocks 1, 2, 3, and 4, sequentially (Figure 3).

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