Diversity of the type I-U CRISPR-Cas system in Bifidobacterium

Ou, Lijun; Long, Jinzhao; Teng, Yanli; Yang, Haiyan; Xi, Yang; Duan, Guotao; Chen, Shuaiyin

doi:10.1007/s00203-021-02310-w

Cited by 8 publications

(5 citation statements)

References 53 publications

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“…It is very interesting that relevant protospacers identified in this study were also found in the study of Ou et al 9 , it is the case of LysR family transcriptional regulator, helix-turn-helix domain-containing protein and MFS transporters.…”

Section: Membrane Proteinssupporting

confidence: 79%

“…Another interesting aspect is the recurrent association between CRISPR and aminoacyl-tRNA ligases. For example, Aklujkar & Lovley 21 reported that CRISPR interfered with histidyl-tRNA ligase in Pelobacter carbinolicus and Ou et al 9 found an isoleucine-tRNA ligase gene near the CRISPR locus of several strains of Bifidobacterium.…”

Section: Aminoacyl-trna Synthetasesmentioning

confidence: 99%

“…CC-BY-NC 4.0 International license made available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is Moreover, ABC transporter genes have been found physically linked to CRISPR-Cas locus 9 .…”

Section: Membrane Proteinsmentioning

confidence: 99%

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Self-targeting spacers reveal new functions of CRISPR systems

Cardona¹,

Arboleda-Rivera²

2023

Preprint

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The CRISPR systems enable bacteria and archaea to defend from bacteriophages or mobile genetic elements by inserting portions of the DNA of these elements into its own genome in sequences known as spacers that will later trigger the complementarity-based degradation of invading sequences. The presence of self-targeting spacers is widespread in prokaryotes; however, its functional role is still unclear. In this study, we analyzed self-targeting spacers of CRISPR systems and found a high presence of membrane proteins, aminoacyl-tRNA synthetases and ATP-binding proteins. This is a novel report that supports other research linking CRISPR systems to membrane proteins and could explain the reported relationships between antibiotic resistance and presence of CRISPR systems.

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Section: Membrane Proteinssupporting

confidence: 79%

Section: Aminoacyl-trna Synthetasesmentioning

confidence: 99%

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Self-targeting spacers reveal new functions of CRISPR systems

Cardona¹,

Arboleda-Rivera²

2023

Preprint

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“…However, the conventional Cas9 technology is difficult to manipulate in most prokaryotes, due to its large size and severe toxicity to host cells 19, 20 . The type I CRISPR-Cas system is more prevalent in prokaryote 21 . Type I-E CRISPR Cas system from Escherichia coli includes CRISPR array and the cas genes expressing Cas3 and five different proteins, Cse1, Cse2, Cas7, Cas5, and Cas6e (in 1, 1, 6, 1, and 2 copies, respectively) namely Cascade 22 .…”

Section: Introductionmentioning

confidence: 99%

Engineering probioticEscherichia coliNissle 1917 to block transfer of multiple antibiotic resistance genes by exploiting a type I CRISPR-Cas system

Fang,

Zhang,

Wang

et al. 2024

Preprint

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Many multidrug-resistant (MDR) bacteria evolved through accumulation of antibiotic-resistance genes (ARGs). Although the potential risk of probiotics as reservoirs of ARGs has been recognized, strategies for blocking transfer of ARGs while using probiotics have rarely been explored. The probiotic Escherichia coli Nissle 1917 (EcN) has long been used for treating intestinal diseases. Here, we showed frequent transfer of ARGs into EcN both in vitro and in vivo, raising its potential risk of accumulating antibiotic resistance. Given that no CRISPR-Cas system is found in natural EcN, we integrated the endogenous type I-E CRISPR-Cas system derived from E. coli BW25113 into EcN, and showed that the engineered EcN was able to efficiently cleave multiple ARGs (i.e., mcr-1, blaNDM-1 and tet(X)). By co-incubation of EcN expressing Cas3-Cascade and that expressing Cas9, we showed that the growth of the former strain outcompeted the latter strain, demonstrating better clinical application prospect of EcN expressing the type I-E CRISPR-Cas system. Finally, the engineered EcN exhibited immunity against transfer of targeted ARGs in the intestine of a model animal (i.e. zebrafish). Our work provides a new strategy for restricting transfer of ARGs in EcN, paving the way for safe use of this probiotic and development of probiotics as living therapeutics.

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“…In addition to the adaptive immunity, CRISPR/Cas system performs several other biological roles, including regulating gene expression, and participating in DNA repair and genomic evolution [23][24][25]. Several studies have explored the diversity of CRISPR/Cas systems in multiple species, including Bifidobacterium [26], Escherichia coli [27], and even the relatives toK. variicola, K. pneumoniae [28].…”

mentioning

confidence: 99%

Analysis of the features of 105 confirmed CRISPR loci in 487 Klebsiella variicola

Xi¹,

Zhao²,

Zhang³

et al. 2023

Preprint

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Klebsiella variicola (K. variicola) is an emerging human pathogen, which poses a threat to public health. The horizontal gene transfer (HGT) of plasmids is an important driver for the emergence of multiple antibiotic-resistant K. variicola. The clustered regularly interspersed short palindromic repeats coupled with the CRISPR-associated genes (CRISPR/Cas) constitute an adaptive immune system in bacteria, which provide acquired immunity against HGT. However, the information about CRISPR/Cas system in K. variicola is still limited. In this study, a total of 487 genomes from NCBI database were used to analyze the characterization of CRISPR/Cas systems. 105 of the 487 genomes harbored at least one confirmed CRISPR array. Three types of CRISPR/Cas system, including types I-E, I-E*, and Ⅳ-A systems, were identified among 105 strains. The distribution of type I system was strongly associated with MLST, whereas type IV system was randomly distributed. Approximately one-third of spacer origins were homologous with plasmids or phages, indicating the role of CRISPR/Cas systems in controlling HGT. Moreover, spacers in K. variicola tended to target mobile genetic elements (MGEs) from Klebsiella pneumoniae, which provides new evidence for their interaction during evolution. Collectively, our results provide valuable insights into the role of CRISPR/Cas systems in K. variicola.

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Diversity of the type I-U CRISPR-Cas system in Bifidobacterium

Cited by 8 publications

References 53 publications

Self-targeting spacers reveal new functions of CRISPR systems

Self-targeting spacers reveal new functions of CRISPR systems

Engineering probioticEscherichia coliNissle 1917 to block transfer of multiple antibiotic resistance genes by exploiting a type I CRISPR-Cas system

Analysis of the features of 105 confirmed CRISPR loci in 487 Klebsiella variicola

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