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Epilogue
Published in Paul Pumpens, Single-Stranded RNA Phages, 2020
The examination of bacterial genomes has revealed a class of the CRISPR-associated coding regions with Cas1 fused to a putative reverse transcriptase and raised the possibility of a concerted mechanism of spacer acquisition involving reverse transcription of RNA to DNA: a potentially host-beneficial mechanism for RNA-to-DNA information flow and incorporation of new spacers directly from RNA (Silas et al. 2016, 2017). This finding made it possible to speculate that the CRISPR system goes retro (Marraffini and Sontheimer 2010; Sontheimer and Marraffini 2016). Again, due to limited knowledge on the abundance and distribution of RNA phages and other RNA parasites, with the vast majority restricted to the Escherichia and Pseudomonas genera, the solution of the role of spacers in the reverse transcriptase-associated CRISPR loci among natural populations of bacteria and their environment was left for further massive search for RNA phages (Silas et al. 2016). Up to now, the limited number of known RNA phages appear rather as key actors waiting for their appearance on the stage by the evaluation of the bacterial immune system.
Advances in Genome Editing
Published in Yashwant Pathak, Gene Delivery, 2022
CRISPR–Cas is a bacterial adaptive immune system that cleaves invading nucleic acids. CRISPRs were first discovered in E. coli in 1987 during an examination of genes involved in phosphate metabolism, and later in a variety of other bacterium species (Ishino et al., 2018). CRISPR-Cas systems are classified into two groups (class I and II), based on the structural variation of the Cas genes and the way they are organized. The classes are further subdivided into six types (type I–VI). Class I includes type I, III, and IV, and class II includes type II, V, and VI (Makarova and Koonin, 2015). Class 1 CRISPR–Cas systems have multiprotein effector complexes, whereas class II systems only have a single effector protein. Presently, six subtypes of the Type I system (Type I-A through Type I-F) have been found, each with a different number of Cas genes. All Type I systems, with the exception of cas1, cas2, and cas3, encode a Cascade-like complex. Cascade is the name given to the effector complex of type I systems (CRISPR-associated complex for antiviral defense) (Brouns et al., 2008). Cascade engages crRNA and locates the target, and the majority of variations are also in charge of crRNA processing. In rare circumstances, cascade can also help with spacer acquisition. Cas3 is a component of the Cascade complex in the Type I-A system, a protein with both helicase and DNase domains responsible for degrading the target (Huo et al., 2014; Gong et al., 2014). Cas1 and Cas2, the Cas9 hallmark protein, and occasionally a fourth protein are encoded by Type II CRISPR-Cas systems (Csn2 or Cas4) (Chylinski et al., 2014). Cas9 helps with adaptation, engages in crRNA processing, and cleaves the target DNA with the help of crRNA and tracrRNA (Karvelis et al., 2013). Type II systems are split into subtypes II-A, II-B, and II-C. In Type II-A and Type II-B, respectively, the csn2 and cas4 genes encoding adaptation proteins are present, whereas Type II-C lacks a fourth gene (Rath et al., 2015). The Type III CRISPR-Cas systems contain the hallmark protein Cas10 with unclear function (Dorsey et al., 2019).
A genomic sequence of the type II-A clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated system in Mycoplasma salivarium strain ATCC 29803
Published in Journal of Oral Microbiology, 2022
Harumi Mizuki, Yu Shimoyama, Taichi Ishikawa, Minoru Sasaki
CRISPR/Cas systems containing cas9, tracrRNA, cas1, cas2, and a CRISPR array, in this order, are the most common type found in the complete or draft genomes of Mollicutes [10]. However, inversions have been observed in the sequences of several strains, such as M. dispar ATCC 27140, M. ovipneumoniae NM 2010, M. hyosynoviae 232, M. arginini HAZ 145_1, and Mycoplasma arthritidis 158L3_1 [10]. In M. hyosynoviae 232 and M. arthritidis 158L3_1, the CRISPR arrays are located between the cas9 and csn2 gene loci [10]. No Mycoplasma species have been reported to contain the CRISPR/Cas system components in the same order as that of ATCC 23064 and ATCC 29803; however, the implications of this observation are unclear.
Potential of CRISPR/Cas system in the diagnosis of COVID-19 infection
Published in Expert Review of Molecular Diagnostics, 2021
V. Edwin Hillary, Savarimuthu Ignacimuthu, S. Antony Ceasar
Scientists started to explore modern molecular tools including genome-editing systems, especially the recently invented and noble prize winning clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas) system for rapid diagnosis of SARS-CoV-2 [13,14]. CRISPR/Cas system has become a most popular genome-editing tool. This system uses a programmable protein that is attached to the targeted sequence with the help of guide RNA (gRNA) and creates double-stranded breaks (DSBs) [15]. There are many types of Cas proteins viz. Cas1, Cas2, Cas3, Cas6, Cas9, and Cas10 [16,17]. Among these, Cas9 protein is the efficient genome-editing system to target double-stranded DNA (dsDNA) or single-stranded DNA (ssDNA). Following Cas9 protein, the Cas12, and Cas13 proteins receive more attention in diagnosing viral diseases. Cas12 protein cleaves ssDNA and dsDNA, whereas Cas13 protein cleaves ssRNA; therefore, these proteins play an important role in the diagnosis of CoVs. In this review, we summarize the potential of CRISPR/Cas systems including Cas9, Cas12, and Cas13 proteins utilized for the diagnosis of SARS-CoV-2 infection.
CRISPR/Cas: from adaptive immune system in prokaryotes to therapeutic weapon against immune-related diseases
Published in International Reviews of Immunology, 2020
Juan Esteban Garcia-Robledo, María Claudia Barrera, Gabriel J. Tobón
In the last two decades, the genomic revolution has allowed a more in-depth study of gene sequences, including CRISPR repetitions [27]. The accumulation of gene sequences in genomic libraries from many species has allowed for genomic comparison of CRISPR loci among prokaryotic organisms. Early comparative analyses revealed four highly conserved genes adjacent to these repeated palindromic CRISPR regions encoding the Cas proteins Cas1 − 4. In the intervening years, many additional Cas proteins have been described and categorized into different subtypes. Cas9 is a nuclease used by Type II CRISPR systems for genetic silencing [30, 36, 37]. Comparative genomics studies have also demonstrated that Cas3 and Cas4 are present mainly in bacteria and thermophilic archaea [27, 30, 38] and contain motifs characteristic of superfamily 2 helicases and RecB exonucleases, respectively. These findings further implicated CRISPR/Cas systems in DNA repair and recombination.