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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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Absence of CBO2200-CBO2220 in the UMASS strain. The number above tracks indicates the absence region in the ATCC 3502 genome location and its corresponding Coding Sequence (CDS) location, expressed as CBO number; the middle track is the UMASS strain raw signal intensity; and the bottom track is the ATCC 3502* reference strain raw signal intensity. The top track is normalized log2 ratios of the fluorescence intensity of the reference strain/test strain. UMASS strain genome fragment corresponding to ATCC 3502 genome region from 2351753 (the start of CBO2200) to 2379161 (the end of CBO2220) is absent.
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Figure 1: Absence of CBO2200-CBO2220 in the UMASS strain. The number above tracks indicates the absence region in the ATCC 3502 genome location and its corresponding Coding Sequence (CDS) location, expressed as CBO number; the middle track is the UMASS strain raw signal intensity; and the bottom track is the ATCC 3502* reference strain raw signal intensity. The top track is normalized log2 ratios of the fluorescence intensity of the reference strain/test strain. UMASS strain genome fragment corresponding to ATCC 3502 genome region from 2351753 (the start of CBO2200) to 2379161 (the end of CBO2220) is absent.

Mentions: The comparative genomic hybridization (CGH) microarray featured overlapping probes covering the entire C. botulinum A1 strain ATCC 3502 genome sequence [GenBank: AM412317]. The ATCC 3502* strain was used as reference and the UMASS strain as test strain. The hybridization results indicated the presence of several regions that were different between UMASS strain and Sanger Institute ATCC 3502 strain (Figure 1 and Figure 2), and, in some cases, were even different between ATCC 3502* and Sanger Institute ATCC 3502 strain (Figure 2). The nature of the deleted sequence (27409 bp) in Figure 1 is unclear. The same block sequence was also found in ATCC 19397 genome but not in Hall strain genome, as retrieved through NCBI Blast server.


Analysis of genomic differences among Clostridium botulinum type A1 strains.

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

Absence of CBO2200-CBO2220 in the UMASS strain. The number above tracks indicates the absence region in the ATCC 3502 genome location and its corresponding Coding Sequence (CDS) location, expressed as CBO number; the middle track is the UMASS strain raw signal intensity; and the bottom track is the ATCC 3502* reference strain raw signal intensity. The top track is normalized log2 ratios of the fluorescence intensity of the reference strain/test strain. UMASS strain genome fragment corresponding to ATCC 3502 genome region from 2351753 (the start of CBO2200) to 2379161 (the end of CBO2220) is absent.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: Absence of CBO2200-CBO2220 in the UMASS strain. The number above tracks indicates the absence region in the ATCC 3502 genome location and its corresponding Coding Sequence (CDS) location, expressed as CBO number; the middle track is the UMASS strain raw signal intensity; and the bottom track is the ATCC 3502* reference strain raw signal intensity. The top track is normalized log2 ratios of the fluorescence intensity of the reference strain/test strain. UMASS strain genome fragment corresponding to ATCC 3502 genome region from 2351753 (the start of CBO2200) to 2379161 (the end of CBO2220) is absent.
Mentions: The comparative genomic hybridization (CGH) microarray featured overlapping probes covering the entire C. botulinum A1 strain ATCC 3502 genome sequence [GenBank: AM412317]. The ATCC 3502* strain was used as reference and the UMASS strain as test strain. The hybridization results indicated the presence of several regions that were different between UMASS strain and Sanger Institute ATCC 3502 strain (Figure 1 and Figure 2), and, in some cases, were even different between ATCC 3502* and Sanger Institute ATCC 3502 strain (Figure 2). The nature of the deleted sequence (27409 bp) in Figure 1 is unclear. The same block sequence was also found in ATCC 19397 genome but not in Hall strain genome, as retrieved through NCBI Blast server.

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