scholarly journals CasLocusAnno: a web-based server for annotating Cas loci and their corresponding (sub)types

2018 ◽  
Author(s):  
Chuan Dong ◽  
Zhi Zeng ◽  
Qing-Feng Wen ◽  
Shuo Liu ◽  
Meng-Ze Du ◽  
...  
Keyword(s):  
Protein Sequence ◽  
Adaptive Immune System ◽  
Accessory Proteins ◽  
Web Based ◽  
Adaptive Immune ◽  
Benchmark Data ◽  
Prediction Rate ◽  
Domain Alignment ◽  
Additional Prediction ◽  
Cas Proteins

ABSTRACTCRISPR-Cas systems are prevalent in bacterial and archaeal genomes, and these systems provide a powerful adaptive immune system against predation by phages and other mobile genetic elements (MGEs). They also contribute to other functions, such as gene regulation in prokaryotic organisms. Determining Cas proteins and Cas loci can help mine Cas proteins and facilitate the identification of Cas-associated accessory proteins. Therefore, the purpose of this work is to develop a web-based server, CasLocusAnno, to annotate Cas proteins and Cas loci and to classify them according to (sub)type based on a previous study. CasLocusAnno can annotate Cas proteins and Cas loci and assign their (sub)types within ∽28 seconds for whole protein sequence submissions, with protein sequence numbers ranging from ∽30 to ∽10500. Comparison with Makarova et al.’s benchmark data demonstrates that CasLocusAnno can accurately identify Cas loci and (sub)types. In addition, CasLocusAnno can identify Cas proteins with higher accuracy and a lower additional prediction rate (APR) than two excellent software programs, CRISPRCasFinder and MacSyFinder. The domain alignment of a Cas protein can be easily browsed in the annotation results. Our server can be freely accessed at http://cefg.uestc.edu.cn/CasLocusAnno/.

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.

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-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.

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 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%.

scholarly journals Bioinformatic Identification of CRISPR Leader Motifs

2021 ◽  
Vol 1 (1) ◽  
pp. 14-18
Author(s):  
Pushya Krishna ◽  
Keyword(s):  
Immune System ◽  
Viral Infection ◽  
Adaptive Immune System ◽  
Initial Step ◽  
Bioinformatic Analysis ◽  
Integration Host Factor ◽  
Base Pairs ◽  
Adaptive Immune ◽  
Three Stages ◽  
Cas Proteins

Clustered Regularly Interspersed Short Palindromic Repeats (CRISPR) and CRISPR associated (Cas) proteins serve as a sophisticated adaptive immune system to defend bacteria and archaea from viral infection. CRISPR mediated immunity occurs in three stages which allow the bacteria to adapt and respond to new as well as previously encountered viruses. The initial step of CRISPR adaptation requires the help of the Integration Host Factor (IHF) and a stretch of 200 base pairs known as the CRISPR leader to ensure encounters with new viruses are properly recorded in the host organism’s immunological memory. A bioinformatic analysis of over 15,000 CRISPR leaders reveals that IHF is a prevalent and widespread feature of CRISPR adaptation across several different CRISPR subtypes and host organisms.

Molecular Mechanisms of CRISPR-Cas Immunity in Bacteria

2020 ◽  
Vol 54 (1) ◽  
pp. 93-120 ◽  
Author(s):  
Philip M. Nussenzweig ◽  
Luciano A. Marraffini
Keyword(s):  
Immune Response ◽  
Molecular Mechanisms ◽  
Adaptive Immune System ◽  
Crispr Locus ◽  
Defense Strategies ◽  
Adaptive Immune ◽  
Third Phase ◽  
Short Palindromic Repeat ◽  
The Many ◽  
Cas Proteins

Prokaryotes have developed numerous defense strategies to combat the constant threat posed by the diverse genetic parasites that endanger them. Clustered regularly interspaced short palindromic repeat (CRISPR)-Cas loci guard their hosts with an adaptive immune system against foreign nucleic acids. Protection starts with an immunization phase, in which short pieces of the invader's genome, known as spacers, are captured and integrated into the CRISPR locus after infection. Next, during the targeting phase, spacers are transcribed into CRISPR RNAs (crRNAs) that guide CRISPR-associated (Cas) nucleases to destroy the invader's DNA or RNA. Here we describe the many different molecular mechanisms of CRISPR targeting and how they are interconnected with the immunization phase through a third phase of the CRISPR-Cas immune response: primed spacer acquisition. In this phase, Cas proteins direct the crRNA-guided acquisition of additional spacers to achieve a more rapid and robust immunization of the population.

scholarly journals Cas9-mediated targeting of viral RNA in eukaryotic cells

2015 ◽  
Vol 112 (19) ◽  
pp. 6164-6169 ◽  
Author(s):  
Aryn A. Price ◽  
Timothy R. Sampson ◽  
Hannah K. Ratner ◽  
Arash Grakoui ◽  
David S. Weiss
Keyword(s):  
Adaptive Immune System ◽  
Eukaryotic Cells ◽  
Antiviral Defense ◽  
Francisella Novicida ◽  
Guide Rna ◽  
Adaptive Immune ◽  
Ssrna Virus ◽  
Bacterial Rna ◽  
Rna Targeting ◽  
Cas Proteins

Clustered, regularly interspaced, short palindromic repeats–CRISPR associated (CRISPR-Cas) systems are prokaryotic RNA-directed endonuclease machineries that act as an adaptive immune system against foreign genetic elements. Using small CRISPR RNAs that provide specificity, Cas proteins recognize and degrade nucleic acids. Our previous work demonstrated that the Cas9 endonuclease from Francisella novicida (FnCas9) is capable of targeting endogenous bacterial RNA. Here, we show that FnCas9 can be directed by an engineered RNA-targeting guide RNA to target and inhibit a human +ssRNA virus, hepatitis C virus, within eukaryotic cells. This work reveals a versatile and portable RNA-targeting system that can effectively function in eukaryotic cells and be programmed as an antiviral defense.

scholarly journals Bioinformatic Identification of CRISPR Leader Motifs

2021 ◽  
Vol 1 (1) ◽  
pp. 14-18
Author(s):  
Pushya Krishna ◽  
Keyword(s):  
Immune System ◽  
Viral Infection ◽  
Adaptive Immune System ◽  
Initial Step ◽  
Bioinformatic Analysis ◽  
Integration Host Factor ◽  
Base Pairs ◽  
Adaptive Immune ◽  
Three Stages ◽  
Cas Proteins

Clustered Regularly Interspersed Short Palindromic Repeats (CRISPR) and CRISPR associated (Cas) proteins serve as a sophisticated adaptive immune system to defend bacteria and archaea from viral infection. CRISPR mediated immunity occurs in three stages which allow the bacteria to adapt and respond to new as well as previously encountered viruses. The initial step of CRISPR adaptation requires the help of the Integration Host Factor (IHF) and a stretch of 200 base pairs known as the CRISPR leader to ensure encounters with new viruses are properly recorded in the host organism’s immunological memory. A bioinformatic analysis of over 15,000 CRISPR leaders reveals that IHF is a prevalent and widespread feature of CRISPR adaptation across several different CRISPR subtypes and host organisms.

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