Clustered regularly interspaced short palindromic repeats (CRISPRs): the hallmark of an ingenious antiviral defense mechanism in prokaryotes

2011 ◽  
Vol 392 (4) ◽  
Author(s):  
Sinan Al-Attar ◽  
Edze R. Westra ◽  
John van der Oost ◽  
Stan J.J. Brouns
Keyword(s):  
Dna Sequences ◽  
Defense Mechanism ◽  
Future Research ◽  
Repeated Dna ◽  
Defense System ◽  
Unique Type ◽  
Crispr Array ◽  
Three Stages ◽  
Dna Fragment ◽  
Cas Proteins

AbstractMany prokaryotes contain the recently discovered defense system against mobile genetic elements. This defense system contains a unique type of repetitive DNA stretches, termed Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs). CRISPRs consist of identical repeated DNA sequences (repeats), interspaced by highly variable sequences referred to as spacers. The spacers originate from either phages or plasmids and comprise the prokaryotes' ‘immunological memory’. CRISPR-associated (cas) genes encode conserved proteins that together with CRISPRs make-up the CRISPR/Cas system, responsible for defending the prokaryotic cell against invaders. CRISPR-mediated resistance has been proposed to involve three stages: (i) CRISPR-Adaptation, the invader DNA is encountered by the CRISPR/Cas machinery and an invader-derived short DNA fragment is incorporated in the CRISPR array. (ii) CRISPR-Expression, the CRISPR array is transcribed and the transcript is processed by Cas proteins. (iii) CRISPR-Interference, the invaders' nucleic acid is recognized by complementarity to the crRNA and neutralized. An application of the CRISPR/Cas system is the immunization of industry-relevant prokaryotes (or eukaryotes) against mobile-genetic invasion. In addition, the high variability of the CRISPR spacer content can be exploited for phylogenetic and evolutionary studies. Despite impressive progress during the last couple of years, the elucidation of several fundamental details will be a major challenge in future research.

scholarly journals CRISPR-Cas System: The Powerful Modulator of Accessory Genomes in Prokaryotes

2021 ◽  
pp. 1-16
Author(s):  
Anca Butiuc-Keul ◽  
Anca Farkas ◽  
Rahela Carpa ◽  
Dumitrana Iordache
Keyword(s):  
Nucleic Acids ◽  
Pathogenic Bacteria ◽  
The Novel ◽  
Defense System ◽  
Guide Rnas ◽  
Crispr Array ◽  
Different Types ◽  
Evolutionary Trajectories ◽  
Novel Coronavirus ◽  
Cas Proteins

Being frequently exposed to foreign nucleic acids, bacteria and archaea have developed an ingenious adaptive defense system, called CRISPR-Cas. The system is composed of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) array, together with CRISPR (<i>cas</i>)-associated genes. This system consists of a complex machinery that integrates fragments of foreign nucleic acids from viruses and mobile genetic elements (MGEs), into CRISPR arrays. The inserted segments (spacers) are transcribed and then used by cas proteins as guide RNAs for recognition and inactivation of the targets. Different types and families of CRISPR-Cas systems consist of distinct adaptation and effector modules with evolutionary trajectories, partially independent. The origin of the effector modules and the mechanism of spacer integration/deletion is far less clear. A review of the most recent data regarding the structure, ecology, and evolution of CRISPR-Cas systems and their role in the modulation of accessory genomes in prokaryotes is proposed in this article. The CRISPR-Cas system&apos;s impact on the physiology and ecology of prokaryotes, modulation of horizontal gene transfer events, is also discussed here. This system gained popularity after it was proposed as a tool for plant and animal embryo editing, in cancer therapy, as antimicrobial against pathogenic bacteria, and even for combating the novel coronavirus – SARS-CoV-2; thus, the newest and promising applications are reviewed as well.

Highly repeated DNA sequences in birds: The structure and evolution of an abundant, tandemly repeated 190-bp DNA fragment in parrots

Genomics ◽  
1992 ◽  
Vol 14 (2) ◽  
pp. 462-469 ◽  
Author(s):  
Cort S. Madsen ◽  
Dineke H. de Kloet ◽  
Jean E. Brooks ◽  
Siwo R. de Kloet
Keyword(s):  
Dna Sequences ◽  
Repeated Dna ◽  
Repeated Dna Sequences ◽  
Highly Repeated Dna ◽  
Dna Fragment

scholarly journals Primed CRISPR DNA uptake in Pyrococcus furiosus

2020 ◽  
Vol 48 (11) ◽  
pp. 6120-6135 ◽  
Author(s):  
Sandra Garrett ◽  
Masami Shiimori ◽  
Elizabeth A Watts ◽  
Landon Clark ◽  
Brenton R Graveley ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Pyrococcus Furiosus ◽  
Effector Proteins ◽  
Dna Uptake ◽  
Partial Match ◽  
Immune Systems ◽  
Adaptive Immune ◽  
Crispr Array ◽  
Adaptive Immune Systems ◽  
Cas Proteins

Abstract CRISPR-Cas adaptive immune systems are used by prokaryotes to defend against invaders like viruses and other mobile genetic elements. Immune memories are stored in the form of ‘spacers’ which are short DNA sequences that are captured from invaders and added to the CRISPR array during a process called ‘adaptation’. Spacers are transcribed and the resulting CRISPR (cr)RNAs assemble with different Cas proteins to form effector complexes that recognize matching nucleic acid and destroy it (‘interference’). Adaptation can be ‘naïve’, i.e. independent of any existing spacer matches, or it can be ‘primed’, i.e. spurred by the crRNA-mediated detection of a complete or partial match to an invader sequence. Here we show that primed adaptation occurs in Pyrococcus furiosus. Although P. furiosus has three distinct CRISPR-Cas interference systems (I-B, I-A and III-B), only the I-B system and Cas3 were necessary for priming. Cas4, which is important for selection and processing of new spacers in naïve adaptation, was also essential for priming. Loss of either the I-B effector proteins or Cas3 reduced naïve adaptation. However, when Cas3 and all crRNP genes were deleted, uptake of correctly processed spacers was observed, indicating that none of these interference proteins are necessary for naïve adaptation.

scholarly journals The CRISPR-Cas system: its origin, functions and applications in biotechnology: A Review

2021 ◽  
Vol 13 (2) ◽  
pp. 65-71
Author(s):  
A.M. Tukur
Keyword(s):  
Genome Engineering ◽  
Defense Mechanism ◽  
Genetic Diseases ◽  
Immune Defense ◽  
Ethical Considerations ◽  
Crispr Locus ◽  
Crop Resistance ◽  
A Genome ◽  
Three Stages ◽  
Cas Proteins

The CRISPR-Cas system is a genome editing system seen in prokaryotic immune system. Bacteria and archaea protect itself against invading viruses and plasmid by targeting RNA or DNA of the invading element predominantly using this gene-editing tool. The CRISPR- Cas defense mechanism is carried out in three stages; adaptation stage where the spacers are inserted into the CRISPR locus, the expression stage where crRNA is formed by transcription of the CRISPR loci and the interference stage where the invading element is destroyed by the crRNA and cas proteins. The CRISPR-cas has been involved in many other functions apart from the immune defense they include; DNA repair, regulation of virulence, genome evolution, inhibit biofilm formation etc. The application of CRISPR-Cas system include genome engineering, agriculture to efficiently target and mutate plants, improve crop yield and crop resistance, in medicine to eradicate genetic diseases. However, ethical considerations are a major setback of CRISPR-Cas application especially in medicine. CRISPR-Cas has been used in variety of species including cultured human cell, rice, drosophila and mice.

scholarly journals INDUCTION OF INTRACHROMOSOMAL RECOMBINATION IN YEAST BY INHIBITION OF THYMIDYLATE BIOSYNTHESIS

Genetics ◽  
1986 ◽  
Vol 114 (2) ◽  
pp. 375-392
Author(s):  
B A Kunz ◽  
G R Taylor ◽  
R H Haynes
Keyword(s):  
Gene Conversion ◽  
Dna Sequences ◽  
Dna Hybridization ◽  
Crossing Over ◽  
Repeated Dna ◽  
Yeast Saccharomyces Cerevisiae ◽  
Haploid Strain ◽  
Reciprocal Exchange ◽  
Coli Plasmid ◽  
Antifolate Drugs

ABSTRACT The biosynthesis of thymidylate in the yeast Saccharomyces cerevisiae can be inhibited by antifolate drugs. We have found that antifolate treatment enhances the formation of leucine prototrophs in a haploid strain of yeast carrying, on the same chromosome, two different mutant leu2 alleles separated by Escherichia coli plasmid sequences. That this effect is a consequence of thymine nucleotide depletion was verified by the finding that provision of exogenous thymidylate eliminates the increased production of Leu+ colonies. DNA hybridization analysis revealed that recombination, including reciprocal exchange, gene conversion and unequal sister-chromatid crossing over, between the duplicated genes gave rise to the induced Leu+ segregants. Although gene conversion unaccompanied by crossing over was responsible for the major fraction of leucine prototrophs, events involving reciprocal exchange exhibited the largest increase in frequency. These data show that recombination is induced between directly repeated DNA sequences under conditions of thymine nucleotide depletion. In addition, the results of this and previous studies are consistent with the possibility that inhibition of thymidylate biosynthesis in yeast may create a metabolic condition that provokes all forms of mitotic recombination.

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