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 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 Optimal evolutionary decision-making to store immune memory

2020 ◽  
Author(s):  
Oskar H Schnaack ◽  
Armita Nourmohammad
Keyword(s):  
Decision Making ◽  
Immune System ◽  
Cell Fate ◽  
Adaptive Immune System ◽  
Memory Formation ◽  
Immune Memory ◽  
Central Feature ◽  
Cell Fate Decisions ◽  
Adaptive Immune ◽  
Immune Receptors

The adaptive immune system in vertebrates consists of highly diverse immune receptors to mount specific responses against a multitude of pathogens. A central feature of the adaptive immune system is the ability to form a memory to act more efficiently in future encounters with similar pathogens. However, memory formation especially in B-cells is one of the least understood cell fate decisions in the immune system. Here, we present a framework to characterize optimal strategies to store memory in order to maximize the utility of immune response to counter evolving pathogens throughout an organism’s lifetime. To do so, we have incorporated the kinetics and energetics of memory response as ingredients of non-equilibrium decision-making between an adaptive exploration to mount a specific and novel response or exploitation of existing memory that can be activated rapidly yet with a reduced specificity against evolved pathogens. To achieve a long-term benefit for the host, we show that memory generation should be actively regulated and dependent on immune receptors’ affinity, with a preference for cross-reactive receptors with a moderate affinity against pathogens as opposed to high affinity receptors— a recipe that is consistent with recent experimental findings [1, 2]. Moreover, we show that the specificity of memory should depend on the organism’s lifespan, and shorter-lived organisms with fewer pathogenic encounters throughout their lifetime should store more cross-reactive memory. Overall, our framework provides a baseline to gauge the efficacy of immune memory formation in light of an organism’s coevolutionary history with pathogens.

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 Experimental evolution of immunological specificity

2019 ◽  
Vol 116 (41) ◽  
pp. 20598-20604 ◽  
Author(s):  
Kevin Ferro ◽  
Robert Peuß ◽  
Wentao Yang ◽  
Philip Rosenstiel ◽  
Hinrich Schulenburg ◽  
...  
Keyword(s):  
Immune System ◽  
Adaptive Immune System ◽  
High Specificity ◽  
Immune Memory ◽  
Transcriptomic Response ◽  
Immune Priming ◽  
Immune Genes ◽  
Adaptive Immune ◽  
Immunological Specificity ◽  
Invertebrate Model

Memory and specificity are hallmarks of the adaptive immune system. Contrary to prior belief, innate immune systems can also provide forms of immune memory, such as immune priming in invertebrates and trained immunity in vertebrates. Immune priming can even be specific but differs remarkably in cellular and molecular functionality from the well-studied adaptive immune system of vertebrates. To date, it is unknown whether and how the level of specificity in immune priming can adapt during evolution in response to natural selection. We tested the evolution of priming specificity in an invertebrate model, the beetle Tribolium castaneum. Using controlled evolution experiments, we selected beetles for either specific or unspecific immune priming toward the bacteria Pseudomonas fluorescens, Lactococcus lactis, and 4 strains of the entomopathogen Bacillus thuringiensis. After 14 generations of host selection, specificity of priming was not universally higher in the lines selected for specificity, but rather depended on the bacterium used for priming and challenge. The insect pathogen B. thuringiensis induced the strongest priming effect. Differences between the evolved populations were mirrored in the transcriptomic response, revealing involvement of immune, metabolic, and transcription-modifying genes. Finally, we demonstrate that the induction strength of a set of differentially expressed immune genes predicts the survival probability of the evolved lines upon infection. We conclude that high specificity of immune priming can evolve rapidly for certain bacteria, most likely due to changes in the regulation of immune genes.

scholarly journals A scaling law in CRISPR repertoire sizes arises from avoidance of autoimmunity

2021 ◽  
Author(s):  
Hanrong Chen ◽  
Andreas Mayer ◽  
Vijay Balasubramanian
Keyword(s):  
Viral Infections ◽  
Scaling Law ◽  
Adaptive Immune System ◽  
Population Level ◽  
Cross Reactivity ◽  
Immune Memory ◽  
Spacer Length ◽  
Adaptive Immune ◽  
Dna Elements ◽  
Selection Mechanisms

Some bacteria and archaea possess an adaptive immune system that maintains a memory of past viral infections as DNA elements called spacers, stored in the CRISPR loci of their genomes. This memory is used to mount targeted responses against threats. However, cross-reactivity of CRISPR targeting mechanisms suggests that incorporation of foreign spacers can also lead to autoimmunity. We show that balancing antiviral defense against autoimmunity predicts a scaling law relating spacer length and CRISPR repertoire size. By analyzing a database of microbial CRISPR-Cas systems, we find that the predicted scaling law is realized empirically across prokaryotes, and arises through the proportionate use of different CRISPR types by species differing in the size of immune memory. In contrast, strains with nonfunctional CRISPR loci do not show this scaling. We also demonstrate that simple population-level selection mechanisms can generate the scaling, along with observed variations between strains of a given species.

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%.

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.

Adaptive Immune System in Fish

2021 ◽  
Vol 22 (4) ◽  
Author(s):  
Adef Othan Kordon ◽  
Lesya Pinchuk ◽  
Attila Karsi
Keyword(s):  
T Cells ◽  
Immune System ◽  
Immune Responses ◽  
Teleost Fish ◽  
Cytotoxic T Cells ◽  
Adaptive Immune System ◽  
Immune Memory ◽  
Cellular Cytotoxicity ◽  
Th Cells ◽  
Adaptive Immune

The immune system of all jawed vertebrates is composed of two major subsystems, the innate (non-specific) and adaptive (specific) immune system. The innate immune system is the first to respond to infectious agents; however, it does not provide longlasting protection. The adaptive immune system is activated later and responds to pathogens with specificity and memory. The main components of the adaptive immune system, including T cell receptors (TCRs), major histocompatibility complex (MHC), immunoglobulins (Igs), and recombination-activating gene (RAG) arose in the first jawed fish (cartilaginous and teleost fish). This review explores and discusses components of the adaptive immune system in teleost fish and recent developments in comparative immunology. Similar to mammals, the adaptive immune system in teleost fish is divided into two components: cellular-mediated responses and humoralmediated responses. T cells, the principal elements of cellular-mediated adaptive immune responses, differentiate into effector helper T (Th) cells or effector cytotoxic T cells (CTLs). The central elements involved in the differentiation of Th subsets in mammals, cytokines and master transcription factors, have also been identified in teleost fish. In addition, each subset of Th cells, defined with a particular cytokine to control the immune responses, has been described in teleost fish. Similarly, to mammals, CTLs contribute to cellular cytotoxicity in teleost fish. B cells act as a central player in humoral-mediated adaptive immunity by producing opsonizing, neutralizing and complement-binding antibodies and inducing antibody-dependent cellular cytotoxicity (ADCC). Three classes of antibodies named IgM, IgD, and IgT/Z have been characterized in teleost fish. The presence of an adaptive immune system and consequent immune memory in teleost fish allows vaccination, the most appropriate method for disease control in aquaculture. Immunological studies in fish provide a comprehensive assessment of the fish immune system, which is crucial for understanding the evolution of the mammalian immune system.

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