Diversity of CRISPR/Cas system in Clostridium perfringens

Long, Jinzhao; Xu, Yake; Ou, Lijun; Yang, Haiyan; Xi, Yang; Chen, Shuaiyin; Duan, Guotao

doi:10.1007/s00438-019-01579-3

Cited by 14 publications

(11 citation statements)

References 58 publications

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“…Turning now to the evidence on size and rate of occurrence of subtype II-A, we thought that this subtype is the most active loci in L. brevis genome. The present findings seem to be inconsistent with other research which hypothesized that subtype I-E CRISPR-Cas in Bifidobacterium and L. casei (Briner et al, 2015;Yang et al, 2020) and I-B/Tneap subtype in Clostridium perfringens (Long et al, 2019) are the most active systems against foreign DNA and phages.…”

Section: Lactobacillus Brevis Strainscontrasting

confidence: 99%

Genome Mining Approach Reveals the Occurrence and Diversity Pattern of Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-Associated Systems in Lactobacillus brevis Strains

2022

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Clustered regularly interspaced short palindromic repeats (CRISPR) together with their CRISPR-associated (Cas) genes are widely distributed in prokaryotes that provide an adaptive defense mechanism against foreign invasive DNA. There is relatively little knowledge about the CRISPR-Cas diversity and evolution in Lactobacillus brevis strains. Therefore, in this study, a genome-mining approach was employed to investigate the diversity and occurrence of the CRISPR-Cas system in 83 L. brevis strains. Moreover, trans-activating CRISPR RNA (tracrRNA) and protospacer adjacent motif (PAM) as pivotal elements for the successful targeting and inference of phages by the subtype II CRISPR-Cas systems were surveyed. Finally, evolutionary paths of L. brevis strains under selective pressure from foreign invasive DNA such as plasmids and phages of studied strains were surveyed using acquisition and deletion events analysis of spacers. A total of 127 confirmed CRISPRs were identified, which were distributed in 69 strains. Among strains with confirmed CRISPRs, 35 strains only contained one CRISPR locus, 23 strains contained two CRISPR loci, and 12 strains contained three to six CRISPR loci. L. brevis strains frequently harbor more than one CRISPR system. Analysis of confirmed CRISPR arrays showed that 31 out of 127 confirmed CRISPRs included Cas genes which were categorized as one of the II-A, II-C, and I-E subtypes. Analysis of subtype II-A spacers reflected divergent evolution for 18 strains into 16 unique groups. Additional analysis of spacer sequences also confirmed the implication of characterizing CRISPR-Cas systems in targeting of phages and plasmids. The current study highlighted the potential of utilizing CRISPR spacer polymorphism in genotyping lactobacillus strains. Moreover, it provides deep insights into the occurrence, diversity, and functional impacts of the CRISPR-Cas system in L. brevis strains.

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Section: Lactobacillus Brevis Strainscontrasting

confidence: 99%

Genome Mining Approach Reveals the Occurrence and Diversity Pattern of Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-Associated Systems in Lactobacillus brevis Strains

2022

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“…Among the spacers whose origin was identified, plasmids and phages were found in equivalent proportions (respectively 51.2 and 48.8% of all MGEs), as already previously reported in C. botulinum group I, II, and III ( Negahdaripour et al, 2017 ). This distribution is different from what is commonly reported in prokaryotes, where 85% of spacers usually map to phages ( Mcginn and Marraffini, 2019 ), including in other clostridia species such as C. perfringens ( Long et al, 2019 ). In addition, some MGEs of Clostridium novyi sensu lato contain proteins characteristic of phages as well as plasmids (e.g., p1_BKT015925, p1_Cst, p4_BKT015925, and p6_Cst), resulting in misleading annotations in public databases, which may have artificially inflated the proportion of spacers from plasmids.…”

Section: Discussioncontrasting

confidence: 92%

“…Accordingly, a CRISPR prevalence of 80% was detected in C. botulinum strains, in a study including only eight Clostridium novyi sensu lato genomes (Negahdaripour et al, 2017). This prevalence is much higher than the rate of 46% reported for bacteria (Grissa et al, 2007) or other clostridia species such as C. perfringens, which showed a CRISPR prevalence of 53.15% (Long et al, 2019). The location of some CRISPR-Cas systems on MGEs may play a role in this high prevalence.…”

Section: Clostridium Novyi Sensu Lato Species Harbor a Range Of Crispr-cas Systemsmentioning

confidence: 86%

“…Type I-B seems to be typical of clostridia. It has indeed been detected in C. perfringens ( Long et al, 2019 ) as well as in C. chauvoei ( Thomas et al, 2017 ), C. tetani ( Cohen et al, 2017 ), and in all C. difficile genomes ( Hargreaves et al, 2014 ; Andersen et al, 2016 ). Here, several type I-B CRISPR arrays were also located on MGEs such as the BoNT phages and the plasmid p2_BKT015925.…”

Section: Discussionmentioning

confidence: 96%

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Exploration of the Diversity of Clustered Regularly Interspaced Short Palindromic Repeats-Cas Systems in Clostridium novyi sensu lato

et al. 2021

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Classified as the genospecies Clostridium novyi sensu lato and distributed into four lineages (I–IV), Clostridium botulinum (group III), Clostridium novyi, and Clostridium haemolyticum are clostridial pathogens that cause animal diseases. Clostridium novyi sensu lato contains a large mobilome consisting of plasmids and circular bacteriophages. Here, we explored clustered regularly interspaced short palindromic repeats (CRISPR) arrays and their associated proteins (Cas) to shed light on the link between evolution of CRISPR-Cas systems and the plasmid and phage composition in a study of 58 Clostridium novyi sensu lato genomes. In 55 of these genomes, types I-B (complete or partial), I-D, II-C, III-B, III-D, or V-U CRISPR-Cas systems were detected in chromosomes as well as in mobile genetic elements (MGEs). Type I-B predominated (67.2%) and was the only CRISPR type detected in the Ia, III, and IV genomic lineages. Putative type V-U CRISPR Cas14a genes were detected in two different cases: next to partial type-IB CRISPR loci on the phage encoding the botulinum neurotoxin (BoNT) in lineage Ia and in 12 lineage II genomes, as part of a putative integrative element related to a phage-inducible chromosomal island (PICI). In the putative PICI, Cas14a was associated with CRISPR arrays and restriction modification (RM) systems as part of an accessory locus. This is the first time a PICI containing such locus has been detected in C. botulinum. Mobilome composition and dynamics were also investigated based on the contents of the CRISPR arrays and the study of spacers. A large proportion of identified protospacers (20.2%) originated from Clostridium novyi sensu lato (p1_Cst, p4_BKT015925, p6_Cst, CWou-2020a, p1_BKT015925, and p2_BKT015925), confirming active exchanges within this genospecies and the key importance of specific MGEs in Clostridium novyi sensu lato.

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“…septicum had CRISPR elements present in all genomes. This was similar to C. chauvoei, but different to C. perfringens, where studies showed the absence of CRISPR regions in many strains (Long et al, 2019). The CRISPR repeat arrays were interrupted by two mobile elements in strain DSM 7534 T , which was also found in C. chavuoei (Rychener et al, 2017).…”

Section: Discussionsupporting

confidence: 59%

First Comparative Analysis of Clostridium septicum Genomes Provides Insights Into the Taxonomy, Species Genetic Diversity, and Virulence Related to Gas Gangrene

et al. 2021

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Clostridium septicum is a Gram-positive, toxin-producing, and spore-forming bacterium that is recognized, together with C. perfringens, as the most important etiologic agent of progressive gas gangrene. Clostridium septicum infections are almost always fatal in humans and animals. Despite its clinical and agricultural relevance, there is currently limited knowledge of the diversity and genome structure of C. septicum. This study presents the complete genome sequence of C. septicum DSM 7534T type strain as well as the first comparative analysis of five C. septicum genomes. The taxonomy of C. septicum, as revealed by 16S rRNA analysis as well as by genomic wide indices such as protein-based phylogeny, average nucleotide identity, and digital DNA–DNA hybridization indicates a stable clade. The composition and presence of prophages, CRISPR elements and accessory genetic material was variable in the investigated genomes. This is in contrast to the limited genetic variability described for the phylogenetically and phenotypically related species Clostridium chauvoei. The restriction-modification (RM) systems between two C. septicum genomes were heterogeneous for the RM types they encoded. C. septicum has an open pangenome with 2,311 genes representing the core genes and 1,429 accessory genes. The core genome SNP divergence between genome pairs varied up to 4,886 pairwise SNPs. A vast arsenal of potential virulence genes was detected in the genomes studied. Sequence analysis of these genes revealed that sialidase, hemolysin, and collagenase genes are conserved compared to the α-toxin and hyaluronidase genes. In addition, a conserved gene found in all C. septicum genomes was predicted to encode a leucocidin homolog (beta-channel forming cytolysin) similar (71.10% protein identity) to Clostridium chauvoei toxin A (CctA), which is a potent toxin. In conclusion, our results provide first, valuable insights into strain relatedness and genomic plasticity of C. septicum and contribute to our understanding of the virulence mechanisms of this important human and animal pathogen.

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Diversity of CRISPR/Cas system in Clostridium perfringens

Cited by 14 publications

References 58 publications

Genome Mining Approach Reveals the Occurrence and Diversity Pattern of Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-Associated Systems in Lactobacillus brevis Strains

Genome Mining Approach Reveals the Occurrence and Diversity Pattern of Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-Associated Systems in Lactobacillus brevis Strains

Exploration of the Diversity of Clustered Regularly Interspaced Short Palindromic Repeats-Cas Systems in Clostridium novyi sensu lato

First Comparative Analysis of Clostridium septicum Genomes Provides Insights Into the Taxonomy, Species Genetic Diversity, and Virulence Related to Gas Gangrene

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