scholarly journals CASPredict: a web service for identifying Cas proteins

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11887
Author(s):  
Shanshan Yang ◽  
Jian Huang ◽  
Bifang He
Keyword(s):  
Web Service ◽  
Genome Editing ◽  
Search Algorithm ◽  
Adaptive Immune System ◽  
Support Vector ◽  
Adaptive Immune ◽  
Complementary Role ◽  
Fold Cross Validation ◽  
Eukaryotic Genomes ◽  
Cas Proteins

Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated (Cas) proteins constitute the CRISPR-Cas systems, which play a key role in prokaryote adaptive immune system against invasive foreign elements. In recent years, the CRISPR-Cas systems have also been designed to facilitate target gene editing in eukaryotic genomes. As one of the important components of the CRISPR-Cas system, Cas protein plays an irreplaceable role. The effector module composed of Cas proteins is used to distinguish the type of CRISPR-Cas systems. Effective prediction and identification of Cas proteins can help biologists further infer the type of CRISPR-Cas systems. Moreover, the class 2 CRISPR-Cas systems are gradually applied in the field of genome editing. The discovery of Cas protein will help provide more candidates for genome editing. In this paper, we described a web service named CASPredict (http://i.uestc.edu.cn/caspredict/cgi-bin/CASPredict.pl) for identifying Cas proteins. CASPredict first predicts Cas proteins based on support vector machine (SVM) by using the optimal dipeptide composition and then annotates the function of Cas proteins based on the hmmscan search algorithm. The ten-fold cross-validation results showed that the 84.84% of Cas proteins were correctly classified. CASPredict will be a useful tool for the identification of Cas proteins, or at least can play a complementary role to the existing methods in this area.

scholarly journals Programming Native CRISPR Arrays for the Generation of Targeted Immunity

mBio ◽  
2016 ◽  
Vol 7 (3) ◽  
Author(s):  
Alexander P. Hynes ◽  
Simon J. Labrie ◽  
Sylvain Moineau
Keyword(s):  
Immune System ◽  
Nucleic Acid ◽  
Genome Editing ◽  
Dna Sequence ◽  
Adaptive Immune System ◽  
Natural Process ◽  
The Public ◽  
Adaptive Immune ◽  
Public Consciousness ◽  
Industrial Settings

ABSTRACT The adaptive immune system of prokaryotes, called CRISPR-Cas (clustered regularly interspaced short palindromic repeats and CRISPR-associated genes), results in specific cleavage of invading nucleic acid sequences recognized by the cell’s “memory” of past encounters. Here, we exploited the properties of native CRISPR-Cas systems to program the natural “memorization” process, efficiently generating immunity not only to a bacteriophage or plasmid but to any specifically chosen DNA sequence. IMPORTANCE CRISPR-Cas systems have entered the public consciousness as genome editing tools due to their readily programmable nature. In industrial settings, natural CRISPR-Cas immunity is already exploited to generate strains resistant to potentially disruptive viruses. However, the natural process by which bacteria acquire new target specificities (adaptation) is difficult to study and manipulate. The target against which immunity is conferred is selected stochastically. By biasing the immunization process, we offer a means to generate customized immunity, as well as provide a new tool to study adaptation.

scholarly journals CRISPR-Cas Biology and Its Application to Infectious Diseases

2018 ◽  
Vol 57 (4) ◽  
Author(s):  
Jeffrey R. Strich ◽  
Daniel S. Chertow
Keyword(s):  
Infectious Diseases ◽  
Adaptive Immune System ◽  
Biomedical Science ◽  
Adaptive Immune ◽  
Disease Outcomes ◽  
Excess Morbidity ◽  
Efficient Gene ◽  
Global Threat ◽  
Human Infections ◽  
Cas Proteins

ABSTRACT Infectious diseases remain a global threat contributing to excess morbidity and death annually, with the persistent potential for destabilizing pandemics. Improved understanding of the pathogenesis of bacteria, viruses, fungi, and parasites, along with rapid diagnosis and treatment of human infections, is essential for improving infectious disease outcomes worldwide. Genomic loci in bacteria and archaea, termed clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins, function as an adaptive immune system for prokaryotes, protecting them against foreign invaders. CRISPR-Cas9 technology is now routinely applied for efficient gene editing, contributing to advances in biomedical science. In the past decade, improved understanding of other diverse CRISPR-Cas systems has expanded CRISPR applications, including in the field of infectious diseases. In this review, we summarize the biology of CRISPR-Cas systems and discuss existing and emerging applications to evaluate mechanisms of host-pathogen interactions, to develop accurate and portable diagnostic tests, and to advance the prevention and treatment of infectious diseases.

Repurposing CRISPR-Cas Systems as Genetic Tools for the Enterobacteriales

EcoSal Plus ◽  
2021 ◽  
Author(s):  
Nicholas Backes ◽  
Gregory J. Phillips
Keyword(s):  
Gene Regulation ◽  
Immune System ◽  
Gene Editing ◽  
Defense Mechanism ◽  
Adaptive Immune System ◽  
Plasmid Curing ◽  
Genetic Tools ◽  
Adaptive Immune ◽  
Domains Of Life ◽  
Eukaryotic Genomes

Over the last decade, the study of CRISPR-Cas systems has progressed from a newly discovered bacterial defense mechanism to a diverse suite of genetic tools that have been applied across all domains of life. While the initial applications of CRISPR-Cas technology fulfilled a need to more precisely edit eukaryotic genomes, creative “repurposing” of this adaptive immune system has led to new approaches for genetic analysis of microorganisms, including improved gene editing, conditional gene regulation, plasmid curing and manipulation, and other novel uses.

scholarly journals Costs of CRISPR-Cas-mediated resistance in Streptococcus thermophilus

2015 ◽  
Vol 282 (1812) ◽  
pp. 20151270 ◽  
Author(s):  
Pedro F. Vale ◽  
Guillaume Lafforgue ◽  
Francois Gatchitch ◽  
Rozenn Gardan ◽  
Sylvain Moineau ◽  
...  
Keyword(s):  
Protein Expression ◽  
Adaptive Immune System ◽  
Streptococcus Thermophilus ◽  
Immune Memory ◽  
Fitness Costs ◽  
Viral Pathogens ◽  
Adaptive Immune ◽  
Fitness Measures ◽  
The Cost ◽  
Cas Proteins

CRISPR-Cas is a form of adaptive sequence-specific immunity in microbes. This system offers unique opportunities for the study of coevolution between bacteria and their viral pathogens, bacteriophages. A full understanding of the coevolutionary dynamics of CRISPR-Cas requires knowing the magnitude of the cost of resisting infection. Here, using the gram-positive bacterium Streptococcus thermophilus and its associated virulent phage 2972, a well-established model system harbouring at least two type II functional CRISPR-Cas systems, we obtained different fitness measures based on growth assays in isolation or in pairwise competition. We measured the fitness cost associated with different components of this adaptive immune system: the cost of Cas protein expression, the constitutive cost of increasing immune memory through additional spacers, and the conditional costs of immunity during phage exposure. We found that Cas protein expression is particularly costly, as Cas-deficient mutants achieved higher competitive abilities than the wild-type strain with functional Cas proteins. Increasing immune memory by acquiring up to four phage-derived spacers was not associated with fitness costs. In addition, the activation of the CRISPR-Cas system during phage exposure induces significant but small fitness costs. Together these results suggest that the costs of the CRISPR-Cas system arise mainly due to the maintenance of the defence system. We discuss the implications of these results for the evolution of CRISPR-Cas-mediated immunity.

scholarly journals CRISPR Cas9 Tip of an Iceberg: It’s Potential in Genome Editing and Many More

2021 ◽  
Author(s):  
Jalal Ahmad ◽  
Nayyer Siddique
Keyword(s):  
Genome Editing ◽  
Genetic Diseases ◽  
Adaptive Immune System ◽  
Biological Research ◽  
Adaptive Immune ◽  
Scientific World ◽  
A Genome ◽  
Foreign Dna ◽  
Immense Potential ◽  
Potential Use

Clustered regularly interspaced short palindromic repeats or CRISPR, one of the major technological tools from nature's toolbox, has revolutionized the scientific world with its potential use in humans and plants. CRISPR Cas9 was first known as an adaptive immune system of bacteria. It is a system that cleaves foreign DNA. It has been exploited to be used as a genome editing tool for correcting genetic diseases in humans, for plants to create stress-resistant plants, and for a variety of different purposes. This review provides a basic overview of its applications in different areas of biological research. It has immense potential for a variety of researches, but it's still a mystery for science. It feels like scientists just know a tip of an iceberg.

scholarly journals CRISPR-Cas Controls Cryptic Prophages

2021 ◽  
Author(s):  
Sooyeon Song ◽  
Thomas K Wood
Keyword(s):  
Escherichia Coli ◽  
Cell Death ◽  
Adaptive Immune System ◽  
The Novel ◽  
E Coli ◽  
Adaptive Immune ◽  
Persister Cell ◽  
Key Genes ◽  
K 12 ◽  
Cas Proteins

The bacterial archetypal adaptive immune system, CRISPR-Cas, is thought to be non-functional in the best-studied bacterium, Escherichia coli K-12. Instead, we demonstrate here that the E. coli CRISPR-Cas system is active and inhibits its nine defective (i.e., cryptic) prophages. Specifically, deactivation of CRISPR-Cas via deletion of cas2, which encodes one of the two conserved CRISPR-Cas proteins, reduces growth by 40%, increases cell death by 700%, and prevents persister cell resuscitation; hence, CRISPR-Cas serves to inhibit the remaining deleterious effects of these cryptic prophages. Consistently, seven of the 13 E. coli spacers contain matches to the cryptic prophages, and, after excision, CRISPR-Cas cleaves cryptic prophage CP4-57 and DLP-12 DNA. Moreover, we determine that the key genes in these cryptic prophages that CRISPR-Cas represses by cleaving the excised DNA include lysis protein YdfD of Qin and lysis protein RzoD of DLP-12. Therefore, we report the novel results that (i) CRISPR-Cas is active in E. coli and (ii) CRISPR-Cas is used to tame cryptic prophages; i.e., unlike with active lysogens, CRISPR-Cas and cryptic prophages may stably exist.

CRISPR/Cas-Systems: characteristics and possibilities of use for editing bacterial genomes

Bacteriology ◽  
2020 ◽  
Vol 5 (2) ◽  
pp. 38-48
Author(s):  
I.A. Blatov ◽  
◽  
A.S. Shchurova ◽  
D.Yu. Guschin ◽  
S.D. Zvereva ◽  
...  
Keyword(s):  
Immune System ◽  
Genome Editing ◽  
Bacterial Species ◽  
Adaptive Immune System ◽  
Bacterial Genomes ◽  
Modern Biology ◽  
Adaptive Immune ◽  
History Of ◽  
Genomic Editing ◽  
Classification Structure

CRISPR-Cas is the adaptive immune system of bacteria and archaea. Since 2012, when the first opportunity to use the CRISPR/Cas system for genome editing was realized, the number of studies in this area has been growing rapidly. Today, genomic editing to modify specific regions of the genomes of various organisms is considered one of the key methodologies of modern biology. This review is devoted to the history of discovery, classification, structure, operational mechanisms of CRISPRCas systems and strategies for editing the genomes of various bacterial species using this technology. Key words: genome editing, genome, CRISPR-Cas system, bacteria

scholarly journals Editor's cut: DNA cleavage by CRISPR RNA-guided nucleases Cas9 and Cas12a

2019 ◽  
Vol 48 (1) ◽  
pp. 207-219 ◽  
Author(s):  
Thomas Swartjes ◽  
Raymond H.J. Staals ◽  
John van der Oost
Keyword(s):  
Immune System ◽  
Genome Editing ◽  
Dna Cleavage ◽  
Adaptive Immune System ◽  
New Developments ◽  
Biochemical Characteristics ◽  
Base Editing ◽  
Dna Cleaving ◽  
Adaptive Immune ◽  
General Method

Discovered as an adaptive immune system of prokaryotes, CRISPR–Cas provides many promising applications. DNA-cleaving Cas enzymes like Cas9 and Cas12a, are of great interest for genome editing. The specificity of these DNA nucleases is determined by RNA guides, providing great targeting adaptability. Besides this general method of programmable DNA cleavage, these nucleases have different biochemical characteristics, that can be exploited for different applications. Although Cas nucleases are highly promising, some room for improvement remains. New developments and discoveries like base editing, prime editing, and CRISPR-associated transposons might address some of these challenges.

scholarly journals CRISPR-Cas: biology, mechanisms and relevance

2016 ◽  
Vol 371 (1707) ◽  
pp. 20150496 ◽  
Author(s):  
Frank Hille ◽  
Emmanuelle Charpentier
Keyword(s):  
Dna Sequences ◽  
Adaptive Immune System ◽  
Crispr Locus ◽  
Biochemical Processes ◽  
Adaptive Immune ◽  
Physiological Properties ◽  
Target Dna ◽  
Associated Proteins ◽  
Cas Proteins

Prokaryotes have evolved several defence mechanisms to protect themselves from viral predators. Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated proteins (Cas) display a prokaryotic adaptive immune system that memorizes previous infections by integrating short sequences of invading genomes—termed spacers—into the CRISPR locus. The spacers interspaced with repeats are expressed as small guide CRISPR RNAs (crRNAs) that are employed by Cas proteins to target invaders sequence-specifically upon a reoccurring infection. The ability of the minimal CRISPR-Cas9 system to target DNA sequences using programmable RNAs has opened new avenues in genome editing in a broad range of cells and organisms with high potential in therapeutical applications. While numerous scientific studies have shed light on the biochemical processes behind CRISPR-Cas systems, several aspects of the immunity steps, however, still lack sufficient understanding. This review summarizes major discoveries in the CRISPR-Cas field, discusses the role of CRISPR-Cas in prokaryotic immunity and other physiological properties, and describes applications of the system as a DNA editing technology and antimicrobial agent. This article is part of the themed issue ‘The new bacteriology’.

scholarly journals Crystallization and preliminary X-ray diffraction analysis of the CRISPR–Cas RNA-silencing Cmr complex

2015 ◽  
Vol 71 (6) ◽  
pp. 735-740 ◽  
Author(s):  
Takuo Osawa ◽  
Hideko Inanaga ◽  
Tomoyuki Numata
Keyword(s):  
Pyrococcus Furiosus ◽  
Adaptive Immune System ◽  
Diffusion Method ◽  
X Ray Diffraction ◽  
Triclinic Space Group ◽  
Cell Parameters ◽  
Adaptive Immune ◽  
Guide Sequence ◽  
Short Palindromic Repeat ◽  
Cas Proteins

Clustered regularly interspaced short palindromic repeat (CRISPR)-derived RNA (crRNA) and CRISPR-associated (Cas) proteins constitute a prokaryotic adaptive immune system (CRISPR–Cas system) that targets and degrades invading genetic elements. The type III-B CRISPR–Cas Cmr complex, composed of the six Cas proteins (Cmr1–Cmr6) and a crRNA, captures and cleaves RNA complementary to the crRNA guide sequence. Here, a Cmr1-deficient functional Cmr (CmrΔ1) complex composed ofPyrococcus furiosusCmr2–Cmr3,Archaeoglobus fulgidusCmr4–Cmr5–Cmr6 and the 39-merP. furiosus7.01-crRNA was prepared. The CmrΔ1 complex was cocrystallized with single-stranded DNA (ssDNA) complementary to the crRNA guide by the vapour-diffusion method. The crystals diffracted to 2.1 Å resolution using synchrotron radiation at the Photon Factory. The crystals belonged to the triclinic space groupP1, with unit-cell parametersa= 75.5,b= 76.2,c= 139.2 Å, α = 90.3, β = 104.8, γ = 118.6°. The asymmetric unit of the crystals is expected to contain one CmrΔ1–ssDNA complex, with a Matthews coefficient of 2.03 Å3 Da−1and a solvent content of 39.5%.

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