scholarly journals Predicted highly derived class 1 CRISPR-Cas system in Haloarchaea containing diverged Cas5 and Cas7 homologs but no CRISPR array

2019 ◽  
Vol 366 (7) ◽  
Author(s):  
Kira S Makarova ◽  
Svetlana Karamycheva ◽  
Shiraz A Shah ◽  
Gisle Vestergaard ◽  
Roger A Garrett ◽  
...  
Keyword(s):  
Adaptive Immunity ◽  
Defense Mechanism ◽  
Crispr Array ◽  
Class 1

ABSTRACT Screening of genomic and metagenomic databases for new variants of CRISPR-Cas systems increasingly results in the discovery of derived variants that do not seem to possess the interference capacity and are implicated in functions distinct from adaptive immunity. We describe an extremely derived putative class 1 CRISPR-Cas system that is present in many Halobacteria and consists of distant homologs of the Cas5 and Cas7 protein along with an uncharacterized conserved protein and various nucleases. We hypothesize that, although this system lacks typical CRISPR effectors or a CRISPR array, it functions as a RNA-dependent defense mechanism that, unlike other derived CRISPR-Cas, utilizes alternative nucleases to cleave invader genomes.

scholarly journals Optimal number of spacers in CRISPR arrays

2017 ◽  
Author(s):  
Alexander Martynov ◽  
Konstantin Severinov ◽  
Yaroslav Ispolatov
Keyword(s):  
Adaptive Immunity ◽  
Mutation Rate ◽  
Bacterial Genome ◽  
Molecular Machines ◽  
Optimal Number ◽  
Evolutionary Models ◽  
Bacterial Survival ◽  
Crispr Array ◽  
Viral Mutation ◽  
Huge Variety

AbstractWe estimate the number of spacers in a CRISPR array of a bacterium which maximizes its protection against a viral attack. The optimality follows from a competition between two trends: too few distinct spacers make the bacteria vulnerable to an attack by a virus with mutated corresponding protospacers, while an excessive variety of spacers dilutes the number of the CRISPR complexes armed with the most recent and thus most effective spacers. We first evaluate the optimal number of spacers in a simple scenario of an infection by a single viral species and later consider a more general case of multiple viral species. We find that depending on such parameters as the concentration of CRISPR-CAS interference complexes and its preference to arm with more recently acquired spacers, the rate of viral mutation, and the number of viral species, the predicted optimal array length lies within a range quite reasonable from the viewpoint of recent experiments.Author summaryCRISPR-Cas system is an adaptive immunity defense in bacteria and archaea against viruses. It works by accumulating in bacterial genome an array of spacers, or fragments of virus DNA from previous attacks. By matching spacers to corresponding parts of virus DNA called protospacers, CRISPR-Cas system identifies and destroys intruder DNA. Here we theoretically estimate the number of spacers that maximizes bacterial survival. This optimum emerges from a competition between two trends: More spacers allow a bacterium to hedge against mutations in viral protospacers. However, keeping too many spacers makes the older ones inefficient because of accumulation of mutations in corresponding protospacers in viruses. Thus, fewer CRISPR-Cas molecular machines are left armed with more efficient young spacers. We have shown that a higher efficiency of CRISPR-Cas system allows a bacterium to utilize more spacers, increasing the optimal array length. On contrary, a higher viral mutation rate makes older spacers useless and favors shorter arrays. A higher diversity in viral species reduces the efficiency of CRISPR-Cas but does not necessary lead to longer arrays. We think that our study provides a new viewpoint at a huge variety in the observed array lengths and adds relevance to evolutionary models of bacterial-phage coexistence.

scholarly journals TOP the Transcription Orientation Pipeline and its use to investigate the transcription of non-coding regions: assessment with CRISPR direct repeats and intergenic sequences

2020 ◽  
Author(s):  
Kimberley Houenoussi ◽  
Roudaina Boukheloua ◽  
Jean-Philippe Vernadet ◽  
Daniel Gautheret ◽  
Gilles Vergnaud ◽  
...  
Keyword(s):  
Defense Mechanism ◽  
Statistical Tests ◽  
Cell Metabolism ◽  
Rna Seq ◽  
Direct Repeats ◽  
Coding Regions ◽  
Repeat Sequences ◽  
Crispr Array ◽  
Intergenic Sequences ◽  
Non Coding Rnas

AbstractA large proportion of non-coding sequences in prokaryotes are transcribed, playing an important role in the cell metabolism and defense against exogenous elements. This is the case of small RNAs and of clustered regularly interspaced short palindromic repeats “CRISPR” arrays. The CRISPR-Cas system is a defense mechanism that protects bacterial and archaeal genomes against invasions by mobile genetic elements such as viruses and plasmids. The CRISPR array, made of repeats separated by unique sequences called spacers, is transcribed but the nature of the promoter and of the transcription regulation is not well known. We describe the Transcription Orientation Pipeline (TOP) which makes use of transcriptome sequence reads to recover those corresponding to a selected sequence, and determine the direction of the transcription. CRISPR repeat sequences extracted from CRISPRCasdb were used to test the performances of the program. Statistical tests show that CRISPR elements can be reliably oriented with as little as 100 mapped reads. TOP was applied to all the available RNA-Seq Illumina sequencing archives from species possessing a CRISPR array, allowing comparisons with programs dedicated to the orientation of CRISPR repeats. In addition TOP was used to analyze small non-coding RNAs in Staphylococcus aureus, demonstrating that it is a valuable and convenient tool to investigate the transcription orientation of any sequence of interest.Availability and implementationTOPs is implemented in Python and is freely available via the I2BC github repository at https://github.com/i2bc/TOP.

scholarly journals CRISPR-Cas: a brief overview

KIDNEYS ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 2-3
Author(s):  
Yusuf Ercin Sonmez
Keyword(s):  
Adaptive Immunity ◽  
Congenital Abnormalities ◽  
Congenital Diseases ◽  
Crispr Array ◽  
The Future ◽  
Cas A

CRISPR-Cas is an adaptive immunity in prokaryotes against infections by viruses and plasmids. CRISPR array recognizes foreign sequences of the invaders and Cas destroys them. Using this system seems possible to find the unwanted sequences in the genome and to destroy or to change them with the suitable ones. This system might not only protect ourselves from the future infections but also correct congenital abnormalities which may predispose to carcinogenesis or some congenital diseases.

scholarly journals A transferrable and integrative type I-F Cascade for heterologous genome editing and transcription modulation

2021 ◽  
Author(s):  
Zeling Xu ◽  
Yanran Li ◽  
Huiluo Cao ◽  
Meiru Si ◽  
Guangming Zhang ◽  
...  
Keyword(s):  
Genome Editing ◽  
Sequence Information ◽  
Type I ◽  
Cascade System ◽  
Highly Active ◽  
Crispr Array ◽  
Class 1 ◽  
Transcription Modulation ◽  
One Step ◽  
Generic Genome

ABSTRACTThe Class 1 type I CRISPR-Cas systems represent the most abundant and diverse CRISPR systems in nature. However, their applications for generic genome editing have been hindered by difficulties of introducing the class-specific, multi-component effectors in heterologous hosts for functioning. Here we established a transferrable Cascade system that enables stable integration and expression of a complete and highly active I-F Cascade in the notoriously recalcitrant and diverse P. aeruginosa genomes by conjugation. The transferred Cascade displayed substantially higher DNA interference activity and greater editing capacity than the Cas9 system in diverse genetic backgrounds, including removal of the large (21-kb) integrated cassette with efficiency and simplicity. An advanced λred-I-F system enabled editing in genotypes with poor homologous recombination capacity, clinical isolates lacking sequence information, and cells containing anti-CRISPR elements Acrs. Lastly, an ‘all-in-one’ I-F Cascade-mediated CRISPRi platform was developed for transcription modulation by simultaneous introduction of the Cascade and the mini-CRISPR array expressing desired crRNA in one-step. This study provides a framework for expanding the diverse type I Cascades for widespread, heterologous genome editing and establishment of editing techniques in non-model isolates of pathogens.

scholarly journals CRISPRStudio: A User-Friendly Software for Rapid CRISPR Array Visualization

Viruses ◽  
2018 ◽  
Vol 10 (11) ◽  
pp. 602 ◽  
Author(s):  
Moïra Dion ◽  
Simon Labrie ◽  
Shiraz Shah ◽  
Sylvain Moineau
Keyword(s):  
Large Scale ◽  
Defense Mechanism ◽  
Sequence Similarity ◽  
Viral Origin ◽  
Crispr Locus ◽  
Sequence Identity ◽  
Crispr Array ◽  
Command Line Tool ◽  
Computational Resources ◽  
User Friendly

The CRISPR-Cas system biologically serves as an adaptive defense mechanism against phages. However, there is growing interest in exploiting the hypervariable nature of the CRISPR locus, often of viral origin, for microbial typing and tracking. Moreover, the spacer content of any given strain provides a phage resistance profile. Large-scale CRISPR typing studies require an efficient method for showcasing CRISPR array similarities across multiple isolates. Historically, CRISPR arrays found in microbes have been represented by colored shapes based on nucleotide sequence identity and, while this approach is now routinely used, only scarce computational resources are available to automate the process, making it very time-consuming for large datasets. To alleviate this tedious task, we introduce CRISPRStudio, a command-line tool developed to accelerate CRISPR analysis and standardize the preparation of CRISPR array figures. It first compares nucleotide spacer sequences present in a dataset and then clusters them based on sequence similarity to assign a meaningful representative color. CRISPRStudio offers versatility to suit different biological contexts by including options such as automatic sorting of CRISPR loci and highlighting of shared spacers, while remaining fast and user-friendly.

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 Genome Maintenance Proteins Modulate Autoimmunity Mediated Primed Adaptation by the Escherichia coli Type I-E CRISPR-Cas System

Genes ◽  
2019 ◽  
Vol 10 (11) ◽  
pp. 872
Author(s):  
Elena Kurilovich ◽  
Anna Shiriaeva ◽  
Anastasia Metlitskaya ◽  
Natalia Morozova ◽  
Ivana Ivancic-Bace ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Adaptive Immunity ◽  
Genome Stability ◽  
Chromosomal Rearrangements ◽  
Type I ◽  
Cell Selection ◽  
Genome Maintenance ◽  
Crispr Array ◽  
Negative Cell

Bacteria and archaea use CRISPR-Cas adaptive immunity systems to interfere with viruses, plasmids, and other mobile genetic elements. During the process of adaptation, CRISPR-Cas systems acquire immunity by incorporating short fragments of invaders’ genomes into CRISPR arrays. The acquisition of fragments of host genomes leads to autoimmunity and may drive chromosomal rearrangements, negative cell selection, and influence bacterial evolution. In this study, we investigated the role of proteins involved in genome stability maintenance in spacer acquisition by the Escherichia coli type I-E CRISPR-Cas system targeting its own genome. We show here, that the deletion of recJ decreases adaptation efficiency and affects accuracy of spacers incorporation into CRISPR array. Primed adaptation efficiency is also dramatically inhibited in double mutants lacking recB and sbcD but not in single mutants suggesting independent involvement and redundancy of RecBCD and SbcCD pathways in spacer acquisition. While the presence of at least one of two complexes is crucial for efficient primed adaptation, RecBCD and SbcCD affect the pattern of acquired spacers. Overall, our data suggest distinct roles of the RecBCD and SbcCD complexes and of RecJ in spacer precursor selection and insertion into CRISPR array and highlight the functional interplay between CRISPR-Cas systems and host genome maintenance mechanisms.

Nonspecific Chronic Back Pain: Sixth Edition Approaches

2019 ◽  
Vol 24 (5) ◽  
pp. 14-15
Author(s):  
Jay Blaisdell ◽  
James B. Talmage
Keyword(s):  
Back Pain ◽  
Chronic Back Pain ◽  
Intervertebral Disk ◽  
Key Factors ◽  
Sixth Edition ◽  
Whole Person ◽  
Class 1 ◽  
A Cell ◽  
Intervertebral Disk Herniation ◽  
The Individual

Abstract Ratings for “non-specific chronic, or chronic reoccurring, back pain” are based on the diagnosis-based impairment method whereby an impairment class, usually representing a range of impairment values within a cell of a grid, is selected by diagnosis and “specific criteria” (key factors). Within the impairment class, the default impairment value then can be modified using non-key factors or “grade modifiers” such as functional history, physical examination, and clinical studies using the net adjustment formula. The diagnosis of “nonspecific chronic, or chronic reoccurring, back pain” can be rated in class 0 and 1; the former has a default value of 0%, and the latter has a default value of 2% before any modifications. The key concept here is that the physician believes that the patient is experiencing pain, yet there are no related objective findings, most notably radiculopathy as distinguished from “nonverifiable radicular complaints.” If the individual is found not to have radiculopathy and the medical record shows that the patient has never had clinically verifiable radiculopathy, then the diagnosis of “intervertebral disk herniation and/or AOMSI [alteration of motion segment integrity] cannot be used.” If the patient is asymptomatic at maximum medical improvement, then impairment Class 0 should be chosen, not Class 1; a final whole person impairment rating of 1% indicates incorrect use of the methodology.

The Use of the Defense Mechanism Test to Aid in Understanding the Personality of Senior Executives and the Implications for Their Careers

2009 ◽  
Vol 30 (1) ◽  
pp. 73-96 ◽  
Author(s):  
Olya Khaleelee
Keyword(s):  
Crisis Intervention ◽  
Defense Mechanisms ◽  
Defense Mechanism ◽  
Senior Executives ◽  
Ideal Types ◽  
The Individual ◽  
Test Profiles ◽  
Real Test

This paper describes the use of the Defense Mechanism Test as an aid in helping to assess senior executives in four areas: for selection, development, career strategy, and crisis intervention. The origins of this test, developed to measure the defense mechanisms used to protect the individual from stress, are described. The paper shows how it was used to predict the capacity of trainee fighter pilots to withstand stress and its later application to other stressful occupations. Finally, some ideal types of the test are shown followed by four real test profiles, two of them with their associated histories.

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