History and Classification of CRISPR/Cas System

Khan, Zulqurnain; Ali, Zulfiqar; Khan, Asif Ali; Sattar, Tahmina; Zeshan, Ali; Saboor, Tahira; Binyamin, Barkha

doi:10.1007/978-981-16-6305-5_2

Cited by 7 publications

(2 citation statements)

References 147 publications

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“…Clustered regularly interspaced short palindromic repeats/CRISPR-associated system has been divided into 2 classes, 6 types, and 33 subtypes (Koonin et al, 2017). In class 1, including type I, type III, and type IV, interference is carried out with large CRISPR associated complex for Cascade protein complex composed of multiple Cas proteins namely, Cas3 (sometimes fused to Cas2), Cas5-Cas8, Cas10, and Cas11, in different combinations, depending on the type and subtype (Koonin et al, 2017;Makarova et al, 2020;Khan et al, 2022). The mentioned Cas proteins form the interference or effector module, which is involved in target recognition and nucleic acid cleavage in CRISPR-Cas systems (Makarova et al, 2020).…”

Section: Introductionmentioning

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: Introductionmentioning

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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“…The actual function of this unique system remained unclear until the mid-2000s, and later, these sequences were identified in the genomes of other bacteria, including halophilic archaea. These sequences are crucial to a living organism’s evolutionary connection ( Khan et al, 2022 ). The CRISPR system consists of clustered short palindromic repeats with regular spacing and CRISPR-related genes called Cas proteins, which form an adaptive defense system in bacteria and archaea.…”

Section: Introductionmentioning

confidence: 99%

CRISPR-Cas systems feature and targeting phages diversity in Lacticaseibacillus rhamnosus strains

Panahi,

Dehganzad,

Nami

2023

Front. Microbiol.

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One of the most important adaptive immune systems in bacteria against phages is clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (CAS) genes. In this investigation, an approach based on genome mining was employed to characterize the CRISPR-Cas systems of Lacticaseibacillus rhamnosus strains. The analysis involved retrieving complete genome sequences of L. rhamnosus strains, and assessing the diversity, prevalence, and evolution of their CRISPR-Cas systems. Following this, an analysis of homology in spacer sequences from identified CRISPR arrays was carried out to investigate and characterize the range of target phages. The findings revealed that 106 strains possessed valid CRISPR-Cas structures (comprising CRISPR loci and Cas genes), constituting 45% of the examined L. rhamnosus strains. The diversity observed in the CRISPR-Cas systems indicated that all identified systems belonged to subtype II-A. Analyzing the homology of spacer sequences with phage and prophage genomes discovered that strains possessing only CRISPR-Cas subtype II targeted a broader spectrum of foreign phages. In summary, this study suggests that while there is not significant diversity among the CRISPR-Cas systems identified in L. rhamnosus strains, there exists notable variation in subtype II-A systems between L. rhamnosus and other lactobacilli. The diverse nature of these CRISPR-Cas systems underscores their natural activity and importance in adaptive immunity.

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CRISPR/Cas genome editing in plants: mechanisms, applications, and overcoming bottlenecks

Hwarari,

Radani,

et al. 2024

Funct Integr Genomics

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History and Classification of CRISPR/Cas System

Cited by 7 publications

References 147 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

CRISPR-Cas systems feature and targeting phages diversity in Lacticaseibacillus rhamnosus strains

CRISPR/Cas genome editing in plants: mechanisms, applications, and overcoming bottlenecks

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