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 In Vivo Genome Editing as a Therapeutic Approach

2018 ◽  
Vol 19 (9) ◽  
pp. 2721 ◽  
Author(s):  
Beatrice Ho ◽  
Sharon Loh ◽  
Woon Chan ◽  
Boon Soh
Keyword(s):  
Genome Editing ◽  
Genome Engineering ◽  
Genetic Diseases ◽  
Gene Mutations ◽  
Genetic Mutation ◽  
Zinc Finger Nucleases ◽  
Transcription Activator ◽  
Therapeutic Benefits ◽  
A Genome

Genome editing has been well established as a genome engineering tool that enables researchers to establish causal linkages between genetic mutation and biological phenotypes, providing further understanding of the genetic manifestation of many debilitating diseases. More recently, the paradigm of genome editing technologies has evolved to include the correction of mutations that cause diseases via the use of nucleases such as zinc-finger nucleases (ZFN), transcription activator-like effector nucleases (TALENs), and more recently, Cas9 nuclease. With the aim of reversing disease phenotypes, which arise from somatic gene mutations, current research focuses on the clinical translatability of correcting human genetic diseases in vivo, to provide long-term therapeutic benefits and potentially circumvent the limitations of in vivo cell replacement therapy. In this review, in addition to providing an overview of the various genome editing techniques available, we have also summarized several in vivo genome engineering strategies that have successfully demonstrated disease correction via in vivo genome editing. The various benefits and challenges faced in applying in vivo genome editing in humans will also be discussed.

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 A multiplex guide RNA expression system and its efficacy for plant genome engineering

2020 ◽  
Author(s):  
Youngbin Oh ◽  
Hyeonjin Kim ◽  
Bora Lee ◽  
Sang-Gyu Kim
Keyword(s):  
Genome Engineering ◽  
Binary Vector ◽  
Expression System ◽  
Plant Genome ◽  
Nicotiana Attenuata ◽  
Specific Sequence ◽  
Editing Efficiency ◽  
Guide Rna ◽  
Assembly Method ◽  
A Genome

Abstract BackgroundThe Streptococcus pyogenes CRISPR system is composed of a Cas9 endonuclease (SpCas9) and a single-stranded guide RNA (gRNA) harboring a target-specific sequence. Theoretically, SpCas9 proteins could cleave as many targeted loci as gRNAs bind in a genome.ResultsWe introduce a PCR-free multiple gRNA cloning system for editing plant genomes. This method consists of two steps: (1) cloning annealed products of two oligonucleotides harboring target-binding sequence between tRNA and gRNA scaffold sequences in a pGRNA vector; and (2) assembling tRNA-gRNA units from several pGRNA vectors with a plant binary vector containing a SpCas9 expression cassette using the Golden Gate assembly method. We validated the editing efficiency and patterns of the multiplex gRNA expression system in wild tobacco (Nicotiana attenuata) protoplasts and in transformed plants by performing targeted deep sequencing. Two proximal cleavages by SpCas9-gRNA largely increased the editing efficiency and induced large deletions between two cleavage sites.ConclusionsThis multiplex gRNA expression system enables high-throughput production of a single binary vector and increases the efficiency of plant genome editing.

scholarly journals Building a genome engineering toolbox in nonmodel prokaryotic microbes

2018 ◽  
Vol 115 (9) ◽  
pp. 2120-2138 ◽  
Author(s):  
Emily Freed ◽  
Jacob Fenster ◽  
Sharon L. Smolinski ◽  
Julie Walker ◽  
Calvin A. Henard ◽  
...  
Keyword(s):  
Genome Engineering ◽  
A Genome

scholarly journals Cnidarian Interaction with Microbial Communities: From Aid to Animal’s Health to Rejection Responses

Marine Drugs ◽  
2018 ◽  
Vol 16 (9) ◽  
pp. 296 ◽  
Author(s):  
Loredana Stabili ◽  
Maria Parisi ◽  
Daniela Parrinello ◽  
Matteo Cammarata
Keyword(s):  
Microbial Communities ◽  
Environmental Changes ◽  
Defense Mechanism ◽  
Immune Defense ◽  
Innate Immune ◽  
Animal Disease ◽  
Normal Microbiota ◽  
Essential Components ◽  
Pathogenic Agents ◽  
And Behavior

The phylum Cnidaria is an ancient branch in the tree of metazoans. Several species exert a remarkable longevity, suggesting the existence of a developed and consistent defense mechanism of the innate immunity capable to overcome the potential repeated exposure to microbial pathogenic agents. Increasing evidence indicates that the innate immune system in Cnidarians is not only involved in the disruption of harmful microorganisms, but also is crucial in structuring tissue-associated microbial communities that are essential components of the Cnidarian holobiont and useful to the animal’s health for several functions, including metabolism, immune defense, development, and behavior. Sometimes, the shifts in the normal microbiota may be used as “early” bio-indicators of both environmental changes and/or animal disease. Here the Cnidarians relationships with microbial communities and the potential biotechnological applications are summarized and discussed.

CRISPR/Cas9: a historical and chemical biology perspective of targeted genome engineering

2016 ◽  
Vol 45 (24) ◽  
pp. 6666-6684 ◽  
Author(s):  
Amrita Singh ◽  
Debojyoti Chakraborty ◽  
Souvik Maiti
Keyword(s):  
Genome Editing ◽  
Chemical Biology ◽  
Genome Engineering ◽  
A Genome

The development and adaptation of CRISPR–Cas9 as a genome editing tool and chemical biology approaches for modulating its activity.

scholarly journals The Lipid Virulence Factors of Mycobacterium tuberculosis Exert Multilayered Control over Autophagy-Related Pathways in Infected Human Macrophages

Cells ◽  
2020 ◽  
Vol 9 (3) ◽  
pp. 666 ◽  
Author(s):  
Aïcha Bah ◽  
Merlin Sanicas ◽  
Jérôme Nigou ◽  
Christophe Guilhot ◽  
Catherine Astarie-Dequeker ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Virulence Factors ◽  
Defense Mechanism ◽  
Immune Defense ◽  
Knock Out ◽  
Human Macrophages ◽  
Type Vii Secretion ◽  
Type Vii Secretion System ◽  
Phagosomal Membrane ◽  
Phthiocerol Dimycocerosates

Autophagy is an important innate immune defense mechanism that controls Mycobacterium tuberculosis (Mtb) growth inside macrophages. Autophagy machinery targets Mtb-containing phagosomes via xenophagy after damage to the phagosomal membrane due to the Type VII secretion system Esx-1 or via LC3-associated phagocytosis without phagosomal damage. Conversely, Mtb restricts autophagy-related pathways via the production of various bacterial protein factors. Although bacterial lipids are known to play strategic functions in Mtb pathogenesis, their role in autophagy manipulation remains largely unexplored. Here, we report that the lipid virulence factors sulfoglycolipids (SLs) and phthiocerol dimycocerosates (DIMs) control autophagy-related pathways through distinct mechanisms in human macrophages. Using knock-out and knock-in mutants of Mtb and Mycobacterium bovis BCG (Bacille Calmette Guerin) and purified lipids, we found that (i) Mtb mutants with DIM and SL deficiencies promoted functional autophagy via an MyD88-dependent and phagosomal damage-independent pathway in human macrophages; (ii) SLs limited this pathway by acting as TLR2 antagonists; (iii) DIMs prevented phagosomal damage-independent autophagy while promoting Esx-1-dependent xenophagy; (iv) and DIMs, but not SLs, limited the acidification of LC3-positive Mtb compartments. In total, our study reveals an unexpected and intricate role for Mtb lipid virulence factors in controlling autophagy-related pathways in human macrophages, thus providing further insight into the autophagy manipulation tactics deployed by intracellular bacterial pathogens.

scholarly journals The Genetic Basis of Natural Variation in Drosophila melanogaster Immune Defense against Enterococcus faecalis

Genes ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 234 ◽  
Author(s):  
Joanne R Chapman ◽  
Maureen A Dowell ◽  
Rosanna Chan ◽  
Robert L Unckless
Keyword(s):  
Drosophila Melanogaster ◽  
Enterococcus Faecalis ◽  
Natural Variation ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Association Studies ◽  
Immune Defense ◽  
Nucleotide Polymorphisms ◽  
Disease Response ◽  
A Genome

Dissecting the genetic basis of natural variation in disease response in hosts provides insights into the coevolutionary dynamics of host-pathogen interactions. Here, a genome-wide association study of Drosophila melanogaster survival after infection with the Gram-positive entomopathogenic bacterium Enterococcus faecalis is reported. There was considerable variation in defense against E. faecalis infection among inbred lines of the Drosophila Genetics Reference Panel. We identified single nucleotide polymorphisms associated with six genes with a significant (p < 10−08, corresponding to a false discovery rate of 2.4%) association with survival, none of which were canonical immune genes. To validate the role of these genes in immune defense, their expression was knocked-down using RNAi and survival of infected hosts was followed, which confirmed a role for the genes krishah and S6k in immune defense. We further identified a putative role for the Bomanin gene BomBc1 (also known as IM23), in E. faecalis infection response. This study adds to the growing set of association studies for infection in Drosophila melanogaster and suggests that the genetic causes of variation in immune defense differ for different pathogens.

scholarly journals PP2Ac Modulates AMPK-Mediated Induction of Autophagy in Mycobacterium bovis—Infected Macrophages

2019 ◽  
Vol 20 (23) ◽  
pp. 6030
Author(s):  
Hussain ◽  
Zhao ◽  
Shah ◽  
Sabir ◽  
Wang ◽  
...  
Keyword(s):  
Mycobacterium Bovis ◽  
Defense Mechanism ◽  
Kinase Inhibitor ◽  
Inhibitory Effect ◽  
Immune Defense ◽  
Host Cells ◽  
Human Beings ◽  
Ampk Signaling ◽  
Autophagy Induction ◽  
Wide Range

Mycobacterium bovis (M. bovis) is the causative agent of bovine tuberculosis in cattle population across the world. Human beings are at equal risk of developing tuberculosis beside a wide range of M. bovis infections in animal species. Autophagic sequestration and degradation of intracellular pathogens is a major innate immune defense mechanism adopted by host cells for the control of intracellular infections. It has been reported previously that the catalytic subunit of protein phosphatase 2A (PP2Ac) is crucial for regulating AMP-activated protein kinase (AMPK)-mediated autophagic signaling pathways, yet its role in tuberculosis is still unclear. Here, we demonstrated that M. bovis infection increased PP2Ac expression in murine macrophages, while nilotinib a tyrosine kinase inhibitor (TKI) significantly suppressed PP2Ac expression. In addition, we observed that TKI-induced AMPK activation was dependent on PP2Ac regulation, indicating the contributory role of PP2Ac towards autophagy induction. Furthermore, we found that the activation of AMPK signaling is vital for the regulating autophagy during M. bovis infection. Finally, the transient inhibition of PP2Ac expression enhanced the inhibitory effect of TKI-nilotinib on intracellular survival and multiplication of M. bovis in macrophages by regulating the host’s immune responses. Based on these observations, we suggest that PP2Ac should be exploited as a promising molecular target to intervene in host–pathogen interactions for the development of new therapeutic strategies towards the control of M. bovis infections in humans and animals.

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