The complete genome sequence ofClostridium botulinumF str. 230613, insertion sites, and recombination of BoNT gene clusters

Genome ◽  
2011 ◽  
Vol 54 (7) ◽  
pp. 546-554 ◽  
Author(s):  
Ren-Mao Tian ◽  
Tao Li ◽  
Xiao-Jun Hou ◽  
Qin Wang ◽  
Kun Cai ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Recombination Event ◽  
Clostridium Botulinum ◽  
Botulinum Neurotoxin ◽  
Gene Clusters ◽  
Pectin Lyase ◽  
Group I ◽  
A Cell ◽  
Insertion Sites ◽  
Lyase Domain

The genomic DNA of Clostridium botulinum F str. 230613 includes a chromosome (3 993 083 bp, 3502 coding sequences (CDs)) and a plasmid (17 531 bp, 25 CDs). The arrangement of the botulinum neurotoxin serotype F (BoNT/F) gene cluster, a 15-kb (or longer) fragment including the bont gene and other relevant genes, and its different insertion sites in C. botulinum A2 and C. botulinum F were formulated. Mobile elements and virulence factors were analysed. We also found a cell adhesion and pectin lyase domain–containing protein, which may function in attaching to the host and as a pectin lyase. The nine BoNT gene clusters of group I C. botulinum strains were located at three sites in the chromosome of C. botulinum F str. 230613. This study showed the inserting inclination of BoNT/A1 tend to have gene clusters inserted at site 3, BoNT/F at site 2, and BoNT/A2 at site 1. Additionally, we found the recombination event between the BoNT gene clusters of sites 2 and 3, a mechanism that contributed to the diversity of the BoNT gene cluster arrangement.

scholarly journals The Distinctive Evolution of orfX Clostridium parabotulinum Strains and Their Botulinum Neurotoxin Type A and F Gene Clusters Is Influenced by Environmental Factors and Gene Interactions via Mobile Genetic Elements

2021 ◽  
Vol 12 ◽  
Author(s):  
Theresa J. Smith ◽  
Charles H. D. Williamson ◽  
Karen K. Hill ◽  
Shannon L. Johnson ◽  
Gary Xie ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Botulinum Neurotoxin ◽  
Genetic Material ◽  
Gene Clusters ◽  
Toxin Gene ◽  
Diverse Range ◽  
Group I ◽  
Extrachromosomal Elements ◽  
Genomic Relationships ◽  
Recent Sequencing

Of the seven currently known botulinum neurotoxin-producing species of Clostridium, C. parabotulinum, or C. botulinum Group I, is the species associated with the majority of human botulism cases worldwide. Phylogenetic analysis of these bacteria reveals a diverse species with multiple genomic clades. The neurotoxins they produce are also diverse, with over 20 subtypes currently represented. The existence of different bont genes within very similar genomes and of the same bont genes/gene clusters within different bacterial variants/species indicates that they have evolved independently. The neurotoxin genes are associated with one of two toxin gene cluster types containing either hemagglutinin (ha) genes or orfX genes. These genes may be located within the chromosome or extrachromosomal elements such as large plasmids. Although BoNT-producing C parabotulinum bacteria are distributed globally, they are more ubiquitous in certain specific geographic regions. Notably, northern hemisphere strains primarily contain ha gene clusters while southern hemisphere strains have a preponderance of orfX gene clusters. OrfX C. parabotulinum strains constitute a subset of this species that contain highly conserved bont gene clusters having a diverse range of bont genes. While much has been written about strains with ha gene clusters, less attention has been devoted to those with orfX gene clusters. The recent sequencing of 28 orfX C. parabotulinum strains and the availability of an additional 91 strains for analysis provides an opportunity to compare genomic relationships and identify unique toxin gene cluster characteristics and locations within this species subset in depth. The mechanisms behind the independent processes of bacteria evolution and generation of toxin diversity are explored through the examination of bacterial relationships relating to source locations and evidence of horizontal transfer of genetic material among different bacterial variants, particularly concerning bont gene clusters. Analysis of the content and locations of the bont gene clusters offers insights into common mechanisms of genetic transfer, chromosomal integration, and development of diversity among these genes.

scholarly journals Looking for the X Factor in Bacterial Pathogenesis: Association of orfX-p47 Gene Clusters with Toxin Genes in Clostridial and Non-Clostridial Bacterial Species

Toxins ◽  
2019 ◽  
Vol 12 (1) ◽  
pp. 19 ◽  
Author(s):  
Maria B. Nowakowska ◽  
François P. Douillard ◽  
Miia Lindström
Keyword(s):  
Gene Cluster ◽  
In Silico ◽  
Botulinum Neurotoxin ◽  
Bacterial Species ◽  
Gene Clusters ◽  
Bacterial Pathogenesis ◽  
Toxin Gene ◽  
Toxin Complex ◽  
Analytical Tools ◽  
Bacillus Isolate

The botulinum neurotoxin (BoNT) has been extensively researched over the years in regard to its structure, mode of action, and applications. Nevertheless, the biological roles of four proteins encoded from a number of BoNT gene clusters, i.e., OrfX1-3 and P47, are unknown. Here, we investigated the diversity of orfX-p47 gene clusters using in silico analytical tools. We show that the orfX-p47 cluster was not only present in the genomes of BoNT-producing bacteria but also in a substantially wider range of bacterial species across the bacterial phylogenetic tree. Remarkably, the orfX-p47 cluster was consistently located in proximity to genes coding for various toxins, suggesting that OrfX1-3 and P47 may have a conserved function related to toxinogenesis and/or pathogenesis, regardless of the toxin produced by the bacterium. Our work also led to the identification of a putative novel BoNT-like toxin gene cluster in a Bacillus isolate. This gene cluster shares striking similarities to the BoNT cluster, encoding a bont/ntnh-like gene and orfX-p47, but also differs from it markedly, displaying additional genes putatively encoding the components of a polymorphic ABC toxin complex. These findings provide novel insights into the biological roles of OrfX1, OrfX2, OrfX3, and P47 in toxinogenesis and pathogenesis of BoNT-producing and non-producing bacteria.

scholarly journals Plasmid-Borne Type E Neurotoxin Gene Clusters in Clostridium botulinum Strains

2013 ◽  
Vol 79 (12) ◽  
pp. 3856-3859 ◽  
Author(s):  
Zhen Zhang ◽  
Hannamari Hintsa ◽  
Ying Chen ◽  
Hannu Korkeala ◽  
Miia Lindström
Keyword(s):  
Gene Cluster ◽  
Gel Electrophoresis ◽  
Clostridium Botulinum ◽  
Southern Hybridization ◽  
Gene Clusters ◽  
Pulsed Field Gel Electrophoresis ◽  
Content Type ◽  
Pulsed Field ◽  
Large Plasmids

ABSTRACTA collection of 36Clostridium botulinumtype E strains was examined by pulsed-field gel electrophoresis (PFGE) and Southern hybridization with probes targeted tobotEandorfX1in the neurotoxin gene cluster. Three strains were found to contain neurotoxin subtype E1 gene clusters in large plasmids of about 146 kb in size.

scholarly journals Novel Structural Elements within the NonproteolyticClostridium botulinumType F Toxin Gene Cluster

2010 ◽  
Vol 77 (5) ◽  
pp. 1904-1906 ◽  
Author(s):  
N. Dover ◽  
J. R. Barash ◽  
K. K. Hill ◽  
J. C. Detter ◽  
S. S. Arnon
Keyword(s):  
Gene Cluster ◽  
Clostridium Botulinum ◽  
Gene Clusters ◽  
Gene Arrangement ◽  
Toxin Gene ◽  
Structural Elements ◽  
Novel Gene ◽  
First Time

ABSTRACTWe sequenced for the first time the complete neurotoxin gene cluster of a nonproteolyticClostridium botulinumtype F. The neurotoxin gene cluster contained a novel gene arrangement that, compared to otherC. botulinumneurotoxin gene clusters, lacked the regulatorybotRgene and contained an intergeniciselement between itsorfX2andorfX3genes.

scholarly journals Sequence Diversity of Genes Encoding Botulinum Neurotoxin Type F

2010 ◽  
Vol 76 (14) ◽  
pp. 4805-4812 ◽  
Author(s):  
Brian H. Raphael ◽  
Mallory J. Choudoir ◽  
Carolina Lúquez ◽  
Rafael Fernández ◽  
Susan E. Maslanka
Keyword(s):  
Clostridium Botulinum ◽  
Botulinum Neurotoxin ◽  
Nucleotide Diversity ◽  
Sequence Variation ◽  
Nucleotide Sequences ◽  
Gene Encoding ◽  
Group I ◽  
Genes Encoding ◽  
Outbreak Investigations ◽  
Result Analysis

ABSTRACT Botulism due to type F botulinum neurotoxin (BoNT/F) is rare (<1% of cases), and only a limited number of clostridial strains producing this toxin type have been isolated. As a result, analysis of the diversity of genes encoding BoNT/F has been challenging. In this study, the entire bont/F nucleotide sequences were determined from 33 type F botulinum toxin-producing clostridial strains isolated from environmental sources and botulism outbreak investigations. We examined proteolytic and nonproteolytic Clostridium botulinum type F strains, bivalent strains, including Bf and Af, and Clostridium baratii type F strains. Phylogenetic analysis revealed that the bont/F genes examined formed 7 subtypes (F1 to F7) and that the nucleotide sequence identities of these subtypes differed by up to 25%. The genes from proteolytic (group I) C. botulinum strains formed subtypes F1 through F5, while the genes from nonproteolytic (group II) C. botulinum strains formed subtype F6. Subtype F7 was composed exclusively of bont/F genes from C. baratii strains. The region of the bont/F5 gene encoding the neurotoxin light chain was found to be highly divergent compared to the other subtypes. Although the bont/F5 nucleotide sequences were found to be identical in strains harboring this gene, the gene located directly upstream (ntnh/F) demonstrated sequence variation among representative strains of this subtype. These results demonstrate that extensive nucleotide diversity exists among genes encoding type F neurotoxins from strains with different phylogenetic backgrounds and from various geographical sources.

scholarly journals Differentiating Botulinum Neurotoxin-Producing Clostridia with a Simple, Multiplex PCR Assay

2017 ◽  
Vol 83 (18) ◽  
Author(s):  
Charles H. D. Williamson ◽  
Adam J. Vazquez ◽  
Karen Hill ◽  
Theresa J. Smith ◽  
Roxanne Nottingham ◽  
...  
Keyword(s):  
Multiplex Pcr ◽  
Gene Cluster ◽  
Botulinum Neurotoxin ◽  
Comparative Genomic ◽  
Pcr Assay ◽  
Content Type ◽  
Multiplex Pcr Assay ◽  
Group I ◽  
Pcr Assays ◽  
Group Ii

ABSTRACT Diverse members of the genus Clostridium produce botulinum neurotoxins (BoNTs), which cause a flaccid paralysis known as botulism. While multiple species of clostridia produce BoNTs, the majority of human botulism cases have been attributed to Clostridium botulinum groups I and II. Recent comparative genomic studies have demonstrated the genomic diversity within these BoNT-producing species. This report introduces a multiplex PCR assay for differentiating members of C. botulinum group I, C. sporogenes, and two major subgroups within C. botulinum group II. Coding region sequences unique to each of the four species/subgroups were identified by in silico analyses of thousands of genome assemblies, and PCR primers were designed to amplify each marker. The resulting multiplex PCR assay correctly assigned 41 tested isolates to the appropriate species or subgroup. A separate PCR assay to determine the presence of the ntnh gene (a gene associated with the botulinum neurotoxin gene cluster) was developed and validated. The ntnh gene PCR assay provides information about the presence or absence of the botulinum neurotoxin gene cluster and the type of gene cluster present (ha positive [ha +] or orfX +). The increased availability of whole-genome sequence data and comparative genomic tools enabled the design of these assays, which provide valuable information for characterizing BoNT-producing clostridia. The PCR assays are rapid, inexpensive tests that can be applied to a variety of sample types to assign isolates to species/subgroups and to detect clostridia with botulinum neurotoxin gene (bont) clusters. IMPORTANCE Diverse clostridia produce the botulinum neurotoxin, one of the most potent known neurotoxins. In this study, a multiplex PCR assay was developed to differentiate clostridia that are most commonly isolated in connection with human botulism cases: C. botulinum group I, C. sporogenes, and two major subgroups within C. botulinum group II. Since BoNT-producing and nontoxigenic isolates can be found in each species, a PCR assay to determine the presence of the ntnh gene, which is a universally present component of bont gene clusters, and to provide information about the type (ha + or orfX +) of bont gene cluster present in a sample was also developed. The PCR assays provide simple, rapid, and inexpensive tools for screening uncharacterized isolates from clinical or environmental samples. The information provided by these assays can inform epidemiological studies, aid with identifying mixtures of isolates and unknown isolates in culture collections, and confirm the presence of bacteria of interest.

Analysis of the Botulinum Neurotoxin Type F Gene Clusters in Proteolytic and Nonproteolytic Clostridium botulinum and Clostridium barati

1998 ◽  
Vol 37 (4) ◽  
pp. 262-268 ◽  
Author(s):  
Alison K. East ◽  
Manju Bhandari ◽  
Sebastian Hielm ◽  
Matthew D. Collins
Keyword(s):  
Clostridium Botulinum ◽  
Botulinum Neurotoxin ◽  
Gene Clusters ◽  
F Gene

scholarly journals Genetic Homogeneity of Clostridium botulinum Type A1 Strains with Unique Toxin Gene Clusters

2008 ◽  
Vol 74 (14) ◽  
pp. 4390-4397 ◽  
Author(s):  
Brian H. Raphael ◽  
Carolina Luquez ◽  
Loretta M. McCroskey ◽  
Lavin A. Joseph ◽  
Mark J. Jacobson ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Clostridium Botulinum ◽  
Variable Region ◽  
Type A ◽  
Gene Clusters ◽  
Comparative Genomic ◽  
Toxin Gene ◽  
Strain Atcc ◽  
Nucleotide Polymorphisms ◽  
Single Strain

ABSTRACT A group of five clonally related Clostridium botulinum type A strains isolated from different sources over a period of nearly 40 years harbored several conserved genetic properties. These strains contained a variant bont/A1 with five nucleotide polymorphisms compared to the gene in C. botulinum strain ATCC 3502. The strains also had a common toxin gene cluster composition (ha−/orfX+) similar to that associated with bont/A in type A strains containing an unexpressed bont/B [termed A(B) strains]. However, bont/B was not identified in the strains examined. Comparative genomic hybridization demonstrated identical genomic content among the strains relative to C. botulinum strain ATCC 3502. In addition, microarray data demonstrated the absence of several genes flanking the toxin gene cluster among the ha−/orfX+ A1 strains, suggesting the presence of genomic rearrangements with respect to this region compared to the C. botulinum ATCC 3502 strain. All five strains were shown to have identical flaA variable region nucleotide sequences. The pulsed-field gel electrophoresis patterns of the strains were indistinguishable when digested with SmaI, and a shift in the size of at least one band was observed in a single strain when digested with XhoI. These results demonstrate surprising genomic homogeneity among a cluster of unique C. botulinum type A strains of diverse origin.

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