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Journal articles on the topic 'CRISPR system'

Author: Grafiati

Published: 13 April 2024

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1

Huescas, C. G. Y., R. I. Pereira, J. Prichula, P. A. Azevedo, J. Frazzon, and A. P. G. Frazzon. "Frequency of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) in non-clinical Enterococcus faecalis and Enterococcus faecium strains." Brazilian Journal of Biology 79, no. 3 (2019): 460–65. http://dx.doi.org/10.1590/1519-6984.183375.

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Abstract The fidelity of the genomes is defended by mechanism known as Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) systems. Three Type II CRISPR systems (CRISPR1- cas, CRISPR2 and CRISPR3-cas) have been identified in enterococci isolates from clinical and environmental samples. The aim of this study was to observe the distribution of CRISPR1-cas, CRISPR2 and CRISPR3-cas in non-clinical strains of Enterococcus faecalis and Enterococcus faecium isolates from food and fecal samples, including wild marine animals. The presence of CRISPRs was evaluated by PCR in 120 enterococ

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2

Serbanescu, M. A., M. Cordova, K. Krastel, et al. "Role of the Streptococcus mutans CRISPR-Cas Systems in Immunity and Cell Physiology." Journal of Bacteriology 197, no. 4 (2014): 749–61. http://dx.doi.org/10.1128/jb.02333-14.

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CRISPR-Cas systems provide adaptive microbial immunity against invading viruses and plasmids. The cariogenic bacteriumStreptococcus mutansUA159 has two CRISPR-Cas systems: CRISPR1 (type II-A) and CRISPR2 (type I-C) with several spacers from both CRISPR cassettes matching sequences of phage M102 or genomic sequences of otherS. mutans. The deletion of thecasgenes of CRISPR1 (ΔC1S), CRISPR2 (ΔC2E), or both CRISPR1+2 (ΔC1SC2E) or the removal of spacers 2 and 3 (ΔCR1SP13E) inS. mutansUA159 did not affect phage sensitivity when challenged with virulent phage M102. Using plasmid transformation experi

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Chapman, Brittany, Jeong Hoon Han, Hong Jo Lee, Isabella Ruud, and Tae Hyun Kim. "Targeted Modulation of Chicken Genes In Vitro Using CRISPRa and CRISPRi Toolkit." Genes 14, no. 4 (2023): 906. http://dx.doi.org/10.3390/genes14040906.

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Engineering of clustered regularly interspaced short palindromic repeats (CRISPR) and the CRISPR-associated protein 9 (Cas9) system has enabled versatile applications of CRISPR beyond targeted DNA cleavage. Combination of nuclease-deactivated Cas9 (dCas9) and transcriptional effector domains allows activation (CRISPRa) or repression (CRISPRi) of target loci. To demonstrate the effectiveness of the CRISPR-mediated transcriptional regulation in chickens, three CRISPRa (VP64, VPR, and p300) and three CRISPRi (dCas9, dCas9-KRAB, and dCas9-KRAB-MeCP2) systems were tested in chicken DF-1 cells. By i

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La Russa, Marie F., and Lei S. Qi. "The New State of the Art: Cas9 for Gene Activation and Repression." Molecular and Cellular Biology 35, no. 22 (2015): 3800–3809. http://dx.doi.org/10.1128/mcb.00512-15.

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CRISPR-Cas9 technology has rapidly changed the landscape for how biologists and bioengineers study and manipulate the genome. Derived from the bacterial adaptive immune system, CRISPR-Cas9 has been coopted and repurposed for a variety of new functions, including the activation or repression of gene expression (termed CRISPRa or CRISPRi, respectively). This represents an exciting alternative to previously used repression or activation technologies such as RNA interference (RNAi) or the use of gene overexpression vectors. We have only just begun exploring the possibilities that CRISPR technology

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Karlson, Chou Khai Soong, Siti Nurfadhlina Mohd-Noor, Nadja Nolte, and Boon Chin Tan. "CRISPR/dCas9-Based Systems: Mechanisms and Applications in Plant Sciences." Plants 10, no. 10 (2021): 2055. http://dx.doi.org/10.3390/plants10102055.

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RNA-guided genomic transcriptional regulation tools, namely clustered regularly interspaced short palindromic repeats interference (CRISPRi) and CRISPR-mediated gene activation (CRISPRa), are a powerful technology for gene functional studies. Deriving from the CRISPR/Cas9 system, both systems consist of a catalytically dead Cas9 (dCas9), a transcriptional effector and a single guide RNA (sgRNA). This type of dCas9 is incapable to cleave DNA but retains its ability to specifically bind to DNA. The binding of the dCas9/sgRNA complex to a target gene results in transcriptional interference. The C

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Yang, Jiayi. "Applications of the CRISPR-Cas9 system in cancer models." Theoretical and Natural Science 21, no. 1 (2023): 28–33. http://dx.doi.org/10.54254/2753-8818/21/20230804.

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Cancer has a high mortality and prevalence rate in the world. CRISPR-Cas9 is one of the novel and most common gene-editing techniques. Compared with the first two generations of gene-editing technologies, CRISPR-Cas9 system has the advantages of easy design, low cost, high efficiency and so on. sgRNA guides Cas9 to the site of the targeted gene, and Cas9 cuts the DNA strand at that site, triggering the NHEJ or HDR mechanism so as to achieve the purpose of deletion or insertion. CRISPR-Cas9 can be combined with other factors for other purposes, such as CRISPRa, CRISPRi, and base editing. The CR

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Shi, Yuqian. "CRISPR/Cas System in Human Genetic Diseases." Highlights in Science, Engineering and Technology 74 (December 29, 2023): 78–85. http://dx.doi.org/10.54097/ztchmw71.

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Clustered regularly interspaced short palindromic repeats/CRISPR-associated CRISPER/Cas system, as the current most popular gene-editing technology, shows great advantages of simple composition, good specificity and high cutting efficiency compared with other gene editing technology. With the rapid development of CRISPR-Cas systems, such as Cas9, Cas12a and Cas12f, can be used to edit the DNA of eukaryotic cells, and then successively found that Cas13a, Cas13b and Cas13d are targeted to the RNA merons. Through various modifications, scientists also developed a new type of the CRISPR-Cas system

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8

Kiro, Ruth, Moran G. Goren, Ido Yosef, and Udi Qimron. "CRISPR adaptation in Escherichia coli subtypeI-E system." Biochemical Society Transactions 41, no. 6 (2013): 1412–15. http://dx.doi.org/10.1042/bst20130109.

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The CRISPRs (clustered regularly interspaced short palindromic repeats) and their associated Cas (CRISPR-associated) proteins are a prokaryotic adaptive defence system against foreign nucleic acids. The CRISPR array comprises short repeats flanking short segments, called ‘spacers’, which are derived from foreign nucleic acids. The process of spacer insertion into the CRISPR array is termed ‘adaptation’. Adaptation allows the system to rapidly evolve against emerging threats. In the present article, we review the most recent studies on the adaptation process, and focus primarily on the subtype

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Heussler, Gary E., Jon L. Miller, Courtney E. Price, Alan J. Collins, and George A. O'Toole. "Requirements for Pseudomonas aeruginosa Type I-F CRISPR-Cas Adaptation Determined Using a Biofilm Enrichment Assay." Journal of Bacteriology 198, no. 22 (2016): 3080–90. http://dx.doi.org/10.1128/jb.00458-16.

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ABSTRACTCRISPR (clustered regularly interspaced short palindromic repeat)-Cas (CRISPR-associated protein) systems are diverse and found in many archaea and bacteria. These systems have mainly been characterized as adaptive immune systems able to protect against invading mobile genetic elements, including viruses. The first step in this protection is acquisition of spacer sequences from the invader DNA and incorporation of those sequences into the CRISPR array, termed CRISPR adaptation. Progress in understanding the mechanisms and requirements of CRISPR adaptation has largely been accomplished

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Sasaki, Shigenori, Hirohito Ogawa, Hirokazu Katoh, and Tomoyuki Honda. "Suppression of Borna Disease Virus Replication during Its Persistent Infection Using the CRISPR/Cas13b System." International Journal of Molecular Sciences 25, no. 6 (2024): 3523. http://dx.doi.org/10.3390/ijms25063523.

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Borna disease virus (BoDV-1) is a bornavirus that infects the central nervous systems of various animal species, including humans, and causes fatal encephalitis. BoDV-1 also establishes persistent infection in neuronal cells and causes neurobehavioral abnormalities. Once neuronal cells or normal neural networks are lost by BoDV-1 infection, it is difficult to regenerate damaged neural networks. Therefore, the development of efficient anti-BoDV-1 treatments is important to improve the outcomes of the infection. Recently, one of the clustered regularly interspaced short palindromic repeats (CRIS

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Ding, Xiao, Lu Yu, Luo Chen, et al. "Recent Progress and Future Prospect of CRISPR/Cas-Derived Transcription Activation (CRISPRa) System in Plants." Cells 11, no. 19 (2022): 3045. http://dx.doi.org/10.3390/cells11193045.

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Genome editing technology has become one of the hottest research areas in recent years. Among diverse genome editing tools, the Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated proteins system (CRISPR/Cas system) has exhibited the obvious advantages of specificity, simplicity, and flexibility over any previous genome editing system. In addition, the emergence of Cas9 mutants, such as dCas9 (dead Cas9), which lost its endonuclease activity but maintains DNA recognition activity with the guide RNA, provides powerful genetic manipulation tools. In particular, combining

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12

Barrangou, Rodolphe, Anne-Claire Coûté-Monvoisin, Buffy Stahl, et al. "Genomic impact of CRISPR immunization against bacteriophages." Biochemical Society Transactions 41, no. 6 (2013): 1383–91. http://dx.doi.org/10.1042/bst20130160.

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CRISPR (clustered regularly interspaced short palindromic repeats) together with cas (CRISPR-associated) genes form the CRISPR–Cas immune system, which provides sequence-specific adaptive immunity against foreign genetic elements in bacteria and archaea. Immunity is acquired by the integration of short stretches of invasive DNA as novel ‘spacers’ into CRISPR loci. Subsequently, these immune markers are transcribed and generate small non-coding interfering RNAs that specifically guide nucleases for sequence-specific cleavage of complementary sequences. Among the four CRISPR–Cas systems present

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Peretolchina, N. P., Yu P. Dzhioev, A. Yu Borisenko, et al. "In silico comparative analysis of crispr-cas system structures of Yersinia pseudotuberculosis causing different clinical manifestations of pseudotuberculosis." Journal Infectology 11, no. 2 (2019): 80–87. http://dx.doi.org/10.22625/2072-6732-2019-11-2-80-87.

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The aim of this research was to analyze and compare CRIPSR loci and cas-proteins of Yersinia pseudotuberculosis strains isolated in different territories from patients with various clinical manifestations of pseudotuberculosis.Materials and Methods. Complete genomes of Y. pseudotuberculosis IP329353 (NC_006155) and IP31758 (NC_009708) were obtained from NCBI Nucleotide Database. Strains were isolated from patients with gastroenteritis and systemic infection respectively. Search, identification, and analysis of CRISPR systems were carried out by onlinetools CRISPROne, CRISPRDetect, and CRISPRTa

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14

Ramachandran, Rajesh. "CRISPR/Cas9 System." Resonance 25, no. 12 (2020): 1669–80. http://dx.doi.org/10.1007/s12045-020-1088-6.

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15

Tong, Yaojun, Christopher M. Whitford, Helene L. Robertsen, et al. "Highly efficient DSB-free base editing for streptomycetes with CRISPR-BEST." Proceedings of the National Academy of Sciences 116, no. 41 (2019): 20366–75. http://dx.doi.org/10.1073/pnas.1913493116.

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Streptomycetes serve as major producers of various pharmacologically and industrially important natural products. Although CRISPR-Cas9 systems have been developed for more robust genetic manipulations, concerns of genome instability caused by the DNA double-strand breaks (DSBs) and the toxicity of Cas9 remain. To overcome these limitations, here we report development of the DSB-free, single-nucleotide–resolution genome editing system CRISPR-BEST (CRISPR-Base Editing SysTem), which comprises a cytidine (CRISPR-cBEST) and an adenosine (CRISPR-aBEST) deaminase-based base editor. Specifically targ

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16

Grüschow, Sabine, Januka S. Athukoralage, Shirley Graham, Tess Hoogeboom, and Malcolm F. White. "Cyclic oligoadenylate signalling mediates Mycobacterium tuberculosis CRISPR defence." Nucleic Acids Research 47, no. 17 (2019): 9259–70. http://dx.doi.org/10.1093/nar/gkz676.

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Abstract The CRISPR system provides adaptive immunity against mobile genetic elements (MGE) in prokaryotes. In type III CRISPR systems, an effector complex programmed by CRISPR RNA detects invading RNA, triggering a multi-layered defence that includes target RNA cleavage, licencing of an HD DNA nuclease domain and synthesis of cyclic oligoadenylate (cOA) molecules. cOA activates the Csx1/Csm6 family of effectors, which degrade RNA non-specifically to enhance immunity. Type III systems are found in diverse archaea and bacteria, including the human pathogen Mycobacterium tuberculosis. Here, we r

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17

Yuan, Bowei, Congcong Yuan, Lulu Li, Miao Long, and Zeliang Chen. "Application of the CRISPR/Cas System in Pathogen Detection: A Review." Molecules 27, no. 20 (2022): 6999. http://dx.doi.org/10.3390/molecules27206999.

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Early and rapid diagnosis of pathogens is important for the prevention and control of epidemic disease. The polymerase chain reaction (PCR) technique requires expensive instrument control, a special test site, complex solution treatment steps and professional operation, which can limit its application in practice. The pathogen detection method based on the clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated protein (CRISPR/Cas) system is characterized by strong specificity, high sensitivity and convenience for detection, which is more suitable for practica

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Shen, Yucong. "CRISPR/Cas system: A powerful tool for de-extinction." Theoretical and Natural Science 20, no. 1 (2023): 227–31. http://dx.doi.org/10.54254/2753-8818/20/20230774.

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The rapid advances in CRISPR technology have opened up new avenues of research and provided hope for a future where extinct species can be brought back to life. De-extinction, the process of resurrecting extinct species by using genetic engineering techniques, is one potential application of CRISPR technology that has gained increasing attention in recent years. The idea is to recover the genetic information of extinct species from preserved tissue samples and recreate them using modern genetic engineering techniques. George Church, a geneticist at Harvard University, is one of the leading sci

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Eitzinger, Simon, Amina Asif, Kyle E. Watters, et al. "Machine learning predicts new anti-CRISPR proteins." Nucleic Acids Research 48, no. 9 (2020): 4698–708. http://dx.doi.org/10.1093/nar/gkaa219.

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Abstract The increasing use of CRISPR–Cas9 in medicine, agriculture, and synthetic biology has accelerated the drive to discover new CRISPR–Cas inhibitors as potential mechanisms of control for gene editing applications. Many anti-CRISPRs have been found that inhibit the CRISPR–Cas adaptive immune system. However, comparing all currently known anti-CRISPRs does not reveal a shared set of properties for facile bioinformatic identification of new anti-CRISPR families. Here, we describe AcRanker, a machine learning based method to aid direct identification of new potential anti-CRISPRs using only

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20

Zhang, Jing, and Malcolm F. White. "Hot and crispy: CRISPR–Cas systems in the hyperthermophile Sulfolobus solfataricus." Biochemical Society Transactions 41, no. 6 (2013): 1422–26. http://dx.doi.org/10.1042/bst20130031.

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The CRISPR (clustered regularly interspaced short palindromic repeats) and Cas (CRISPR-associated) genes are widely spread in bacteria and archaea, representing an intracellular defence system against invading viruses and plasmids. In the system, fragments from foreign DNA are captured and integrated into the host genome at the CRISPR locus. The locus is transcribed and the resulting RNAs are processed by Cas6 into small crRNAs (CRISPR RNAs) that guide a variety of effector complexes to degrade the invading genetic elements. Many bacteria and archaea have one major type of effector complex. Ho

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Borisenko, A. Yu, N. A. Arefieva, Yu P. Dzhioev, et al. "In Silico Analysis of the Structural Diversity of CRISPR-Cas Systems in Genomes of Salmonella enterica and Phage Species Detected by Them." Bulletin of Irkutsk State University. Series Biology. Ecology 45 (2023): 3–20. http://dx.doi.org/10.26516/2073-3372.2023.45.3.

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The problem of resistance of pathogenic bacteria to antibiotics has become global and, therefore, there is renewed interest in the use of bacteriophages. However, bacteria also have phage defense structures, the CRISPR/Cas system. Therefore, the analysis of the structural diversity of CRISPR-Cas systems in the genomes of pathogenic bacteria and phages is an important fundamental and applied direction. The aim. Investigation of the diversity of structures of CRISPR/Cas systems in the genomes of S. enterica strains from the NCBI database using bioinformatics programs and assessment of the possib

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Степаненко, Liliya Stepanenko, Парамонов, et al. "BIoInfoRmatIonal analySIS of YersiniapseudotuberculosisIP32953 CRISPR/CaSSyStem." Бюллетень Восточно-Сибирского научного центра Сибирского отделения Российской академии медицинских наук 1, no. 5 (2016): 64–67. http://dx.doi.org/10.12737/23384.

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The results of this study include Yersinia pseudotuberculosis CRISPR/Cas system structure analysis. CRISPR/Cas system is a specific adaptive protection against heterogeneous genetic elements. The object of research was the complete genome of Y. pseudotuberculosis IP32953 (NC_006155). CRISPR/Cas system screening was performed by program modelling methods MacSyFinder ver. 1.0.2. CRISPR loci screening and analyzing were carried out by program package: CRISPR Recognition tool (CRT), CRISPI: a CRISPR Interactive database, CRISPRFinder, and PilerCR. Spacer sequences were used in order to find protos

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Sunusi, M., Lurwanu, Y., Halidu, J., and Musa, H. "Crispr Cas System in Plant Genome Editing a New Opportunity in Agriculture to Boost Crop Yield." UMYU Journal of Microbiology Research (UJMR) 3, no. 1 (2018): 104–14. http://dx.doi.org/10.47430/ujmr.1831.017.

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Clustered regularly interspaced short palindromic repeats CRISPR/Cas9 technology evolved from a type II bacterial immune system develop in 2013 This system employs RNA-guided nuclease, CRISPR associated (Cas9) to induce double-strand breaks. The Cas9-mediated breaks are repaired by cellular DNA repair mechanisms and mediate gene/genome modifications. The system has the ability to detect specific sequences of letters within the genetic code and to cut DNA at a specific point. Simultaneously with other sequence-specific nucleases, CRISPR/ Cas9 have already breach the boundaries and made genetic

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Mohammadi Ghanbarlou, Mahdi, Shahriyar Abdoli, Hamed Omid, et al. "Delivery of dCas9 Activator System Using Magnetic Nanoparticles Technology as a Vector Delivery Method for Human Skin Fibroblast." Magnetochemistry 9, no. 3 (2023): 71. http://dx.doi.org/10.3390/magnetochemistry9030071.

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The overexpression of stem cell-related genes such as octamer-binding transcription factor 4 (OCT4) and (sex determining region Y)-box 2 (SOX2) has been indicated to play several critical roles in stem cell self-renewal; moreover, the elevation of the self-renewal of cancer cells with stem cell-like properties has been suggested. The clustered and regularly interspaced short palindromic repeats-associated protein 9 (CRISPR/Cas9) protein fused to transactivation domains can be used to activate gene expression in human cells. CRISPR-mediated activation (CRISPRa) systems represent an effective ge

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Selle, Kurt, Todd R. Klaenhammer, and Rodolphe Barrangou. "CRISPR-based screening of genomic island excision events in bacteria." Proceedings of the National Academy of Sciences 112, no. 26 (2015): 8076–81. http://dx.doi.org/10.1073/pnas.1508525112.

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Genomic analysis ofStreptococcus thermophilusrevealed that mobile genetic elements (MGEs) likely contributed to gene acquisition and loss during evolutionary adaptation to milk. Clustered regularly interspaced short palindromic repeats–CRISPR-associated genes (CRISPR-Cas), the adaptive immune system in bacteria, limits genetic diversity by targeting MGEs including bacteriophages, transposons, and plasmids. CRISPR-Cas systems are widespread in streptococci, suggesting that the interplay between CRISPR-Cas systems and MGEs is one of the driving forces governing genome homeostasis in this genus.

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Jwair, Noor A., Mushtak T. S. Al-Ouqaili та Farah Al-Marzooq. "Inverse Association between the Existence of CRISPR/Cas Systems with Antibiotic Resistance, Extended Spectrum β-Lactamase and Carbapenemase Production in Multidrug, Extensive Drug and Pandrug-Resistant Klebsiella pneumoniae". Antibiotics 12, № 6 (2023): 980. http://dx.doi.org/10.3390/antibiotics12060980.

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Antimicrobial resistance, with the production of extended-spectrum β-lactamases (ESBL) and carbapenemases, is common in the opportunistic pathogen, Klebsiella pneumoniae. This organism has a genome that can contain clustered regularly interspaced short palindromic repeats (CRISPRs), which operate as a defense mechanism against external invaders such as plasmids and viruses. This study aims to determine the association of the CRISPR/Cas systems with antibiotic resistance in K. pneumoniae isolates from Iraqi patients. A total of 100 K. pneumoniae isolates were collected and characterized accordi

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Wang, Jiawei, Wei Dai, Jiahui Li, et al. "PaCRISPR: a server for predicting and visualizing anti-CRISPR proteins." Nucleic Acids Research 48, W1 (2020): W348—W357. http://dx.doi.org/10.1093/nar/gkaa432.

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Abstract Anti-CRISPRs are widespread amongst bacteriophage and promote bacteriophage infection by inactivating the bacterial host's CRISPR–Cas defence system. Identifying and characterizing anti-CRISPR proteins opens an avenue to explore and control CRISPR–Cas machineries for the development of new CRISPR–Cas based biotechnological and therapeutic tools. Past studies have identified anti-CRISPRs in several model phage genomes, but a challenge exists to comprehensively screen for anti-CRISPRs accurately and efficiently from genome and metagenome sequence data. Here, we have developed an ensembl

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Akhmetova, E. A., V. M. Golyshev, I. P. Vokhtantcev, M. I. Meschaninova, A. G. Venyaminova, and D. S. Novopashina. "Photoactivatable CRISPR/Cas9 System." Russian Journal of Bioorganic Chemistry 47, no. 2 (2021): 496–504. http://dx.doi.org/10.1134/s1068162021020023.

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Schindele, Patrick, Felix Wolter, and Holger Puchta. "Das CRISPR/Cas-System." Biologie in unserer Zeit 48, no. 2 (2018): 100–105. http://dx.doi.org/10.1002/biuz.201810642.

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Pan, Meichen, Matthew A. Nethery, Claudio Hidalgo-Cantabrana, and Rodolphe Barrangou. "Comprehensive Mining and Characterization of CRISPR-Cas Systems in Bifidobacterium." Microorganisms 8, no. 5 (2020): 720. http://dx.doi.org/10.3390/microorganisms8050720.

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The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas (CRISPR-associated cas) systems constitute the adaptive immune system in prokaryotes, which provides resistance against bacteriophages and invasive genetic elements. The landscape of applications in bacteria and eukaryotes relies on a few Cas effector proteins that have been characterized in detail. However, there is a lack of comprehensive studies on naturally occurring CRISPR-Cas systems in beneficial bacteria, such as human gut commensal Bifidobacterium species. In this study, we mined 954 publicly available Bifidoba

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Gong, Chongzhi, Shengchan Huang, Rentao Song, and Weiwei Qi. "Comparative Study between the CRISPR/Cpf1 (Cas12a) and CRISPR/Cas9 Systems for Multiplex Gene Editing in Maize." Agriculture 11, no. 5 (2021): 429. http://dx.doi.org/10.3390/agriculture11050429.

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Although the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system has been proved to be an efficient multiplex gene editing system in maize, it was still unclear how CRISPR/Cpf1 (Cas12a) system would perform for multiplex gene editing in maize. To this end, this study compared the CRISPR/Cpf1 system and CRISPR/Cas9 system for multiplex gene editing in maize. The bZIP transcription factor Opaque2 (O2) was used as the target gene in both systems. We found that in the T0 and T1 generations, the CRISPR/Cpf1 system showed lower editing efficie

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Maier, Lisa-Katharina, Britta Stoll, Jutta Brendel, et al. "The ring of confidence: a haloarchaeal CRISPR/Cas system." Biochemical Society Transactions 41, no. 1 (2013): 374–78. http://dx.doi.org/10.1042/bst20120263.

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To survive the constant invasions by foreign genetic elements, prokaryotes have evolved various defensive systems. Almost all sequenced archaea, and half of the analysed bacteria use the CRISPR (clustered regularly interspaced short palindromic repeats)/Cas (CRISPR-associated) system, a recently identified prokaryotic immune system that can fend off invading elements in a sequence-specific manner. Few archaeal CRISPR/Cas systems have been analysed so far, and the molecular details of many of the steps involved in adaptation and defence are yet to be understood. In the present paper, we summari

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Osakabe, Keishi, Naoki Wada, Emi Murakami, Naoyuki Miyashita, and Yuriko Osakabe. "Genome editing in mammalian cells using the CRISPR type I-D nuclease." Nucleic Acids Research 49, no. 11 (2021): 6347–63. http://dx.doi.org/10.1093/nar/gkab348.

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Abstract Adoption of CRISPR–Cas systems, such as CRISPR–Cas9 and CRISPR–Cas12a, has revolutionized genome engineering in recent years; however, application of genome editing with CRISPR type I—the most abundant CRISPR system in bacteria—remains less developed. Type I systems, such as type I-E, and I-F, comprise the CRISPR-associated complex for antiviral defense (‘Cascade’: Cas5, Cas6, Cas7, Cas8 and the small subunit) and Cas3, which degrades the target DNA; in contrast, for the sub-type CRISPR–Cas type I-D, which lacks a typical Cas3 nuclease in its CRISPR locus, the mechanism of target DNA

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Westbrook, Adam W., Murray Moo-Young, and C. Perry Chou. "Development of a CRISPR-Cas9 Tool Kit for Comprehensive Engineering of Bacillus subtilis." Applied and Environmental Microbiology 82, no. 16 (2016): 4876–95. http://dx.doi.org/10.1128/aem.01159-16.

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ABSTRACTThe establishment of a clustered regularly interspaced short palindromic repeat (CRISPR)-Cas9 system for strain construction inBacillus subtilisis essential for its progression toward industrial utility. Here we outline the development of a CRISPR-Cas9 tool kit for comprehensive genetic engineering inB. subtilis. In addition to site-specific mutation and gene insertion, our approach enables continuous genome editing and multiplexing and is extended to CRISPR interference (CRISPRi) for transcriptional modulation. Our tool kit employs chromosomal expression of Cas9 and chromosomal transc

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Jing, Yike. "Applications and Prospects of CRISPR-Cas system in Cyanobacteria." BIO Web of Conferences 61 (2023): 01009. http://dx.doi.org/10.1051/bioconf/20236101009.

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Cyanobacteria are prokaryotic microorganisms with capacity to perform photosynthesis and provide valuable platform to produce high-value bioactive compounds in carbon-neutral pathway. However, due to the relative lack of high throughput genetic manipulation tools for cyanobacteria, their usage for complexity chemicals is lagging behind. The gene editing technology based on the CRISPR-Cas system has the advantage of simplicity and efficiency in recent years, making it a new tool for synthetic biology of cyanobacteria. In this review, we first introduced the CRISPR-Cas system and the types of CR

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Aslam, Shakira, Ali Umair, Zaid Aslam, Muhammad Zafar Saleem, and Hamid Bashir. "CRISPR/Cas System: An Effective Tool Against Pathogenic Diseases." Postępy Mikrobiologii - Advancements of Microbiology 62, no. 2 (2023): 87–99. http://dx.doi.org/10.2478/am-2023-0009.

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Abstract Viral pathogens are major concern nowadays. Bacterial CRISPR/Cas systems help in defending the host body against different pathogens including viruses too. This system contains restriction enzymes that introduce dsDNA breaks on target site to make the virus non-functional by damaging its genes. Coronavirus, HIV and Herpes viruses are causing mortality all around the world. To control the spread of disease, early detection and treatment is required. CRISPR system due to its high efficiency provides a platform to restrict the viral entry into host cell, viral genome editing and eliminat

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Haider, Muhammad Zulqarnain, Muhammad Abu Bakr Shabbir, Tahir Yaqub, et al. "CRISPR-Cas System: An Adaptive Immune System’s Association with Antibiotic Resistance in Salmonella enterica Serovar Enteritidis." BioMed Research International 2022 (March 28, 2022): 1–7. http://dx.doi.org/10.1155/2022/9080396.

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Several factors are involved in the emergence of antibiotic-resistant bacteria and pose a serious threat to public health safety. Among them, clustered regularly interspaced short palindromic repeat- (CRISPR-) Cas system, an adaptive immune system, is thought to be involved in the development of antibiotic resistance in bacteria. The current study was aimed at determining not only the presence of antibiotic resistance and CRISPR-Cas system but also their association with each other in Salmonella enteritidis isolated from the commercial poultry. A total of 139 samples were collected from poultr

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Li, Junwei, Yuexia Wang, Bin Wang, et al. "Application of CRISPR/Cas Systems in the Nucleic Acid Detection of Infectious Diseases." Diagnostics 12, no. 10 (2022): 2455. http://dx.doi.org/10.3390/diagnostics12102455.

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The CRISPR/Cas system is a protective adaptive immune system against attacks from foreign mobile genetic elements. Since the discovery of the excellent target-specific sequence recognition ability of the CRISPR/Cas system, the CRISPR/Cas system has shown excellent performance in the development of pathogen nucleic-acid-detection technology. In combination with various biosensing technologies, researchers have made many rapid, convenient, and feasible innovations in pathogen nucleic-acid-detection technology. With an in-depth understanding and development of the CRISPR/Cas system, it is no long

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Lin, Weijia. "Application of CRISPR-Cas System in the Treatment of Human Viral Disease." BIO Web of Conferences 59 (2023): 02003. http://dx.doi.org/10.1051/bioconf/20235902003.

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CRISPR-Cas systems, consisting of clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas), are the latest generation of gene editing technology and have been widely used in molecular biology research. CRISPR-Cas systems also have unlimited potential in the field of medicine, especially in the treatment of human viral diseases, such as blocking virus invasion, interfering with virus replication, and eliminating viral genome and sequelae of virus infection. In this article, the latest research progress of CRISPR-Cas9 system and other CRISPR systems

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McInally, S. G., K. D. Hagen, C. Nosala, et al. "Robust and stable transcriptional repression in Giardia using CRISPRi." Molecular Biology of the Cell 30, no. 1 (2019): 119–30. http://dx.doi.org/10.1091/mbc.e18-09-0605.

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Giardia lamblia is a binucleate protistan parasite causing significant diarrheal disease worldwide. An inability to target Cas9 to both nuclei, combined with the lack of nonhomologous end joining and markers for positive selection, has stalled the adaptation of CRISPR/Cas9-mediated genetic tools for this widespread parasite. CRISPR interference (CRISPRi) is a modification of the CRISPR/Cas9 system that directs catalytically inactive Cas9 (dCas9) to target loci for stable transcriptional repression. Using a Giardia nuclear localization signal to target dCas9 to both nuclei, we developed efficie

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He, Yuxuan, Wei Yan, Likun Long, et al. "The CRISPR/Cas System: A Customizable Toolbox for Molecular Detection." Genes 14, no. 4 (2023): 850. http://dx.doi.org/10.3390/genes14040850.

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Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated proteins (Cas) are promising molecular diagnostic tools for rapidly and precisely elucidating the structure and function of genomes due to their high specificity, programmability, and multi-system compatibility in nucleic acid recognition. Multiple parameters limit the ability of a CRISPR/Cas system to detect DNA or RNA. Consequently, it must be used in conjunction with other nucleic acid amplification techniques or signal detection techniques, and the reaction components and reaction conditions should be m

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Peretolchina, N. P., A. Y. Borisenko, Yu P. Dzhioev, and V. I. Zlobin. "COMPARATIVE ANALYSIS OF CRISPR-CAS SYSTEM STRUCTURES OF YERSINIA PSEUDOTUBERCULOSIS IP32953 AND IP31758." Acta Biomedica Scientifica 3, no. 5 (2018): 54–59. http://dx.doi.org/10.29413/abs.2018-3.5.8.

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Background. Pseudotuberculosis is still relevant problem in medical science and public health of Russia and other countries. Typing of Y. рseudotuberculosis strains by their CRISPR systems is a perspective tool for monitoring of Yersinia populations as was shown in Y. pestis.Aims. Here we describe and compare CRISPR-Cas systems of Yersinia pseudotuberculosis strains IP32953 and IP31758 causing classic pseudotuberculosis and Far-East scarlet-like fever (FESLF) respectively.Materials and methods. Complete genomes of Y. pseudotuberculosis IP329353 and IP31758 (NC_006155 and NC_009708 respectively

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Sorokin, Valery A., Mikhail S. Gelfand, and Irena I. Artamonova. "Evolutionary Dynamics of Clustered Irregularly Interspaced Short Palindromic Repeat Systems in the Ocean Metagenome." Applied and Environmental Microbiology 76, no. 7 (2010): 2136–44. http://dx.doi.org/10.1128/aem.01985-09.

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ABSTRACT Clustered regularly interspaced short palindromic repeats (CRISPRs) form a recently characterized type of prokaryotic antiphage defense system. The phage-host interactions involving CRISPRs have been studied in experiments with selected bacterial or archaeal species and, computationally, in completely sequenced genomes. However, these studies do not allow one to take prokaryotic population diversity and phage-host interaction dynamics into account. This gap can be filled by using metagenomic data: in particular, the largest existing data set, generated from the Sorcerer II Global Ocea

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Pavlova, Yekaterina S., David Paez-Espino, Andrew Yu Morozov, and Ilya S. Belalov. "Searching for fat tails in CRISPR-Cas systems: Data analysis and mathematical modeling." PLOS Computational Biology 17, no. 3 (2021): e1008841. http://dx.doi.org/10.1371/journal.pcbi.1008841.

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Understanding CRISPR-Cas systems—the adaptive defence mechanism that about half of bacterial species and most of archaea use to neutralise viral attacks—is important for explaining the biodiversity observed in the microbial world as well as for editing animal and plant genomes effectively. The CRISPR-Cas system learns from previous viral infections and integrates small pieces from phage genomes called spacers into the microbial genome. The resulting library of spacers collected in CRISPR arrays is then compared with the DNA of potential invaders. One of the most intriguing and least well under

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McBride, Tess M., Shaharn C. Cameron, Peter C. Fineran, and Robert D. Fagerlund. "The biology and type I/III hybrid nature of type I-D CRISPR–Cas systems." Biochemical Journal 480, no. 7 (2023): 471–88. http://dx.doi.org/10.1042/bcj20220073.

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Prokaryotes have adaptive defence mechanisms that protect them from mobile genetic elements and viral infection. One defence mechanism is called CRISPR–Cas (clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins). There are six different types of CRISPR–Cas systems and multiple subtypes that vary in composition and mode of action. Type I and III CRISPR–Cas systems utilise multi-protein complexes, which differ in structure, nucleic acid binding and cleaving preference. The type I-D system is a chimera of type I and III systems. Recently, there has been a burst

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Mimoune, Nora, Oumayma Benadjel, Ratiba Baazizi, and Djamel Kelef. "CRISPR/Cas9 uses." Veterinarska stanica 52, no. 4 (2021): 369–86. http://dx.doi.org/10.46419/vs.52.4.9.

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Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR- associated system (Cas) is a system that provides immunity to most prokaryoticorganisms against viral attacks and other foreign bodies. CRISPR systems consist of a scissor-like protein called Cas9 and a genetic GPS guide “The guide RNA”. However, researchers have reoriented and repurposed the primordial immune system to precisely manipulate genomes in most organisms by introducing DNA double-strand breaks at specific genome locations to introduce specific DNA modifications. More applications of CRISPR have arisen since

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Hegde, Shivanand, Hallie E. Rauch, Grant L. Hughes, and Nikki Shariat. "Identification and characterization of two CRISPR/Cas systems associated with the mosquito microbiome." Access Microbiology 5, no. 8 (2023). http://dx.doi.org/10.1099/acmi.0.000599.v4.

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The microbiome profoundly influences many traits in medically relevant vectors such as mosquitoes, and a greater functional understanding of host–microbe interactions may be exploited for novel microbial-based approaches to control mosquito-borne disease. Here, we characterized two novel clustered regularly interspaced short palindromic repeats (CRISPR)/Cas systems in Serratia sp. Ag1, which was isolated from the gut of an Anopheles gambiae mosquito. Two distinct CRISPR/Cas systems were identified in Serratia Ag1, CRISPR1 and CRISPR2. Based on cas gene composition, CRISPR1 is classified as a t

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Ma, Shuai, Feiyu Wang, Zhang Xuejing, et al. "Repurposing endogenous type II CRISPR‐Cas9 system for genome editing in Streptococcus thermophilus." Biotechnology and Bioengineering, November 23, 2023. http://dx.doi.org/10.1002/bit.28608.

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AbstractStreptococcus thermophilus has been extensively used in industrial milk fermentation. However, lack of efficient genetic manipulation approaches greatly hampered the industrial application of this species. Here, we repurposed the endogenous CRISPR1 and CRISPR3 systems, both belong to type II‐A CRISPR‐Cas9, by delivering a self‐targeting CRISPR array with DNA repair template into S. thermophilus LMD‐9. We achieved 785‐bp deletion in lacZ gene by repurposing CRISPR1 and CRISPR3 systems with efficiencies of 35% and 59%, respectively, when 1‐kb DNA repair template was provided. While provi

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Feng, Qing, Xiaoyu Ning, Lei Qin, Jun Li, and Chun Li. "Quantitative and modularized CRISPR/dCas9-dCpf1 dual function system in Saccharomyces cerevisiae." Frontiers in Bioengineering and Biotechnology 11 (October 18, 2023). http://dx.doi.org/10.3389/fbioe.2023.1218832.

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Introduction: Both CRISPR/dCas9 and CRISPR/dCpf1 genome editing systems have shown exciting promises in modulating yeast cell metabolic pathways. However, each system has its deficiencies to overcome. In this study, to achieve a compensatory effect, we successfully constructed a dual functional CRISPR activation/inhibition (CRISPRa/i) system based on Sp-dCas9 and Fn-dCpf1 proteins, along with their corresponding complementary RNAs.Methods: We validated the high orthogonality and precise quantity targeting of selected yeast promoters. Various activating effector proteins (VP64, p65, Rta, and VP

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Lipatova, Indrė. "Recent doctoral theses (biochemistry, biology, biophysics, ecology and environmental) in Lithuania." Biologija 68, no. 1 (2022). http://dx.doi.org/10.6001/biologija.v68i1.4704.

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The research objective of this work was to investigate and study details of the CRISPR adaptation process in several different CRISPR-Cas systems as well as use genome-wide CRISPR screening to elucidate cell-intermedilysin interactions. The results of this study showed that Cas1-Cas2 complex from S. thermophilus CRISPR4-Cas system forms a complex that integrates prespacers into the CRISPR array. DnaQ domain fused to Cas2 in this system is a 3’–5’ DNA exonuclease. DnaQ domain is dispensable for spacer integration; however, it serves to trim back overextended 3’ overhangs of the prespacer. Cas1,

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