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

Unleashing the potential: type I CRISPR-Cas systems in actinomycetes for genome editing

Covering: up to the end of 2023Type I CRISPR-Cas systems are widely distributed, found in over 40% of bacteria and 80% of archaea. Among genome-sequenced actinomycetes (particularly Streptomyces spp.), 45.54% possess type I CRISPR-Cas systems. In comparison to widely used CRISPR systems like Cas9 or Cas12a, these endogenous CRISPR-Cas systems have significant advantages, including better compatibility, wide distribution, and ease of operation (since no exogenous Cas gene delivery is needed). Furthermore, type I CRISPR-Cas systems can simultaneously edit and regulate genes by adjusting the crRNA spacer length. Meanwhile, most actinomycetes are recalcitrant to genetic manipulation, hindering the discovery and engineering of natural products (NPs). The endogenous type I CRISPR-Cas systems in actinomycetes may offer a promising alternative to overcome these barriers. This review summarizes the challenges and recent advances in CRISPR-based genome engineering technologies for actinomycetes. It also presents and discusses how to establish and develop genome editing tools based on type I CRISPR-Cas systems in actinomycetes, with the aim of their future application in gene editing and the discovery of NPs in actinomycetes.

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

Klebsiella variicola, an emerging human pathogen, poses a threat to public health. The horizontal gene transfer (HGT) of plasmids is an important driver of the emergence of multiple antibiotic-resistant K. variicola. Clustered regularly interspersed short palindromic repeats (CRISPR) coupled with CRISPR-associated genes (CRISPR/Cas) constitute an adaptive immune system in bacteria, and can provide acquired immunity against HGT. However, the information about the CRISPR/Cas system in K. variicola is still limited. In this study, 487 genomes of K. variicola obtained from the National Center for Biotechnology Information database were used to analyze the characteristics of CRISPR/Cas systems. Approximately 21.56% of genomes (105/487) harbor at least one confirmed CRISPR array. Three types of CRISPR/Cas systems, namely the type I-E, I-E*, and IV-A systems, were identified among 105 strains. Spacer origin analysis further revealed that approximately one-third of spacers significantly match plasmids or phages, which demonstrates the implication of CRISPR/Cas systems in controlling HGT. Moreover, spacers in K. variicola tend to target mobile genetic elements from K. pneumoniae. This finding provides new evidence of the interaction of K. variicola and K. pneumoniae during their evolution. Collectively, our results provide valuable insights into the role of CRISPR/Cas systems in K. variicola.

Analysis of Probiotic Bacteria Genomes: Comparison of CRISPR/Cas Systems and Spacer Acquisition Diversity

Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) genes constitute an adaptive (acquired) defense system of bacteria and archaea. Here 72 probiotic bacteria genomes were investigated in terms of the presence of CRISPR/Cas systems and phage/plasmid invaders through spacer analysis. 49 CRISPR/Cas systems were detected within probiotic strains, namely,17 type II-A, 10 type I-C, 8 type I-E, 5 Type I-U (I-G), 4 type III-A, 2 type I-B, 1 type I-A, 1 type IV-B, and 1 type II-C. The predicted target of spacers was determined in 25 strains and consequently, three different spacer and target patterns were revealed. The diversity of CRISPR spacers provides insight and understanding to determine strain-specific invaders of probiotic bacteria as well as their relationships between strains. CRISPR systems were clarified in many studies for genomic characterization. However, recently, endogenous genome editing with CRISPR has provided an approach for various genome editing projects. Thus, in the future, producing strain-specific phage-resistant starter cultures or probiotics by endogenous genome editing methods according to phage/plasmid survey can be utilized for industrial and pharmaceutical applications. Therefore, this study intended a comprehensive investigation of CRISPR systems of probiotic bacteria.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12088-021-00971-1.