scholarly journals Optimizing Systems for Cas9 Expression in Toxoplasma gondii

mSphere ◽  
2019 ◽  
Vol 4 (3) ◽  
Author(s):  
Benedikt M. Markus ◽  
George W. Bell ◽  
Hernan A. Lorenzi ◽  
Sebastian Lourido
Keyword(s):  
Toxoplasma Gondii ◽  
Genome Engineering ◽  
Childhood Mortality ◽  
Loss Of Function ◽  
Content Type ◽  
Guide Rna ◽  
Severe Diarrhea ◽  
Biological Studies ◽  
Recent Developments ◽  
Improved Stability

ABSTRACT CRISPR-Cas9 technologies have enabled genome engineering in an unprecedented array of species, accelerating biological studies in both model and nonmodel systems. However, Cas9 can be inherently toxic, which has limited its use in some organisms. We previously described the serendipitous discovery of a single guide RNA (sgRNA) that helped overcome Cas9 toxicity in the apicomplexan parasite Toxoplasma gondii, enabling the first genome-wide loss-of-function screens in any apicomplexan. Even in the presence of the buffering sgRNA, low-level Cas9 toxicity persists and results in frequent loss of Cas9 expression, which can affect the outcome of these screens. Similar Cas9-mediated toxicity has also been described in other organisms. We therefore sought to define the requirements for stable Cas9 expression, comparing different expression constructs and characterizing the role of the buffering sgRNA to understand the basis of Cas9 toxicity. We find that viral 2A peptides can substantially improve the selection and stability of Cas9 expression. We also demonstrate that the sgRNA has two functions: primarily facilitating integration of the Cas9-expression construct following initial genome targeting and secondarily improving long-term parasite fitness by alleviating Cas9 toxicity. We define a set of guidelines for the expression of Cas9 with improved stability and selection stringency, which are directly applicable to a variety of genetic approaches in diverse organisms. Our work also emphasizes the need for further characterizing the effects of Cas9 expression. IMPORTANCE Toxoplasma gondii is an intracellular parasite that causes life-threatening disease in immunocompromised patients and affects the developing fetus when contracted during pregnancy. Closely related species cause malaria and severe diarrhea, thereby constituting leading causes for childhood mortality. Despite their importance to global health, this family of parasites has remained enigmatic. Given its remarkable experimental tractability, T. gondii has emerged as a model also for the study of related parasites. Genetic approaches are important tools for studying the biology of organisms, including T. gondii. As such, the recent developments of CRISPR-Cas9-based techniques for genome editing have vastly expanded our ability to study the biology of numerous species. In some organisms, however, CRISPR-Cas9 has been difficult to implement due to its inherent toxicity. Our research characterizes the basis of the observed toxicity, using T. gondii as a model, allowing us to develop approaches to aid the use of CRISPR-Cas9 in diverse species.

scholarly journals Loss of the Conserved Alveolate Kinase MAPK2 Decouples Toxoplasma Cell Growth from Cell Division

mBio ◽  
2020 ◽  
Vol 11 (6) ◽  
Author(s):  
Xiaoyu Hu ◽  
William J. O’Shaughnessy ◽  
Tsebaot G. Beraki ◽  
Michael L. Reese
Keyword(s):  
Toxoplasma Gondii ◽  
Protein Kinases ◽  
Daughter Cell ◽  
Protozoan Parasite ◽  
Productive Infection ◽  
Centrosome Duplication ◽  
Loss Of Function ◽  
Content Type ◽  
Mitogen Activated Protein ◽  
Parasite Replication

ABSTRACT Mitogen-activated protein kinases (MAPKs) are a conserved family of protein kinases that regulate signal transduction, proliferation, and development throughout eukaryotes. The apicomplexan parasite Toxoplasma gondii expresses three MAPKs. Two of these, extracellular signal-regulated kinase 7 (ERK7) and MAPKL1, have been implicated in the regulation of conoid biogenesis and centrosome duplication, respectively. The third kinase, MAPK2, is specific to and conserved throughout the Alveolata, although its function is unknown. We used the auxin-inducible degron system to determine phenotypes associated with MAPK2 loss of function in Toxoplasma. We observed that parasites lacking MAPK2 failed to duplicate their centrosomes and therefore did not initiate daughter cell budding, which ultimately led to parasite death. MAPK2-deficient parasites initiated but did not complete DNA replication and arrested prior to mitosis. Surprisingly, the parasites continued to grow and replicate their Golgi apparatus, mitochondria, and apicoplasts. We found that the failure in centrosome duplication is distinct from the phenotype caused by the depletion of MAPKL1. As we did not observe MAPK2 localization at the centrosome at any point in the cell cycle, our data suggest that MAPK2 regulates a process at a distal site that is required for the completion of centrosome duplication and the initiation of parasite mitosis. IMPORTANCE Toxoplasma gondii is a ubiquitous intracellular protozoan parasite that can cause severe and fatal disease in immunocompromised patients and the developing fetus. Rapid parasite replication is critical for establishing a productive infection. Here, we demonstrate that a Toxoplasma protein kinase called MAPK2 is conserved throughout the Alveolata and essential for parasite replication. We found that parasites lacking MAPK2 protein were defective in the initiation of daughter cell budding and were rendered inviable. Specifically, T. gondii MAPK2 (TgMAPK2) appears to be required for centrosome replication at the basal end of the nucleus, and its loss causes arrest early in parasite division. MAPK2 is unique to the Alveolata and not found in metazoa and likely is a critical component of an essential parasite-specific signaling network.

scholarly journals New CRISPR Mutagenesis Strategies Reveal Variation in Repair Mechanisms among Fungi

mSphere ◽  
2018 ◽  
Vol 3 (2) ◽  
Author(s):  
Valmik K. Vyas ◽  
G. Guy Bushkin ◽  
Douglas A. Bernstein ◽  
Matthew A. Getz ◽  
Magdalena Sewastianik ◽  
...  
Keyword(s):  
Fungal Pathogens ◽  
Genome Engineering ◽  
High Efficiency ◽  
Selection Marker ◽  
Important Species ◽  
Content Type ◽  
Guide Rna ◽  
Wide Range ◽  
Repair Mechanisms ◽  
The Creation

ABSTRACT We have created new vectors for clustered regularly interspaced short palindromic repeat (CRISPR) mutagenesis in Candida albicans , Saccharomyces cerevisiae , Candida glabrata , and Naumovozyma castellii . These new vectors permit a comparison of the requirements for CRISPR mutagenesis in each of these species and reveal different dependencies for repair of the Cas9 double-stranded break. Both C. albicans and S. cerevisiae rely heavily on homology-directed repair, whereas C. glabrata and N. castellii use both homology-directed and nonhomologous end-joining pathways. The high efficiency of these vectors permits the creation of unmarked deletions in each of these species and the recycling of the dominant selection marker for serial mutagenesis in prototrophs. A further refinement, represented by the "Unified" Solo vectors, incorporates Cas9, guide RNA, and repair template into a single vector, thus enabling the creation of vector libraries for pooled screens. To facilitate the design of such libraries, we have identified guide sequences for each of these species with updated guide selection algorithms. IMPORTANCE CRISPR-mediated genome engineering technologies have revolutionized genetic studies in a wide range of organisms. Here we describe new vectors and guide sequences for CRISPR mutagenesis in the important human fungal pathogens C. albicans and C. glabrata , as well as in the related yeasts S. cerevisiae and N. castellii . The design of these vectors enables efficient serial mutagenesis in each of these species by leaving few, if any, exogenous sequences in the genome. In addition, we describe strategies for the creation of unmarked deletions in each of these species and vector designs that permit the creation of vector libraries for pooled screens. These tools and strategies promise to advance genetic engineering of these medically and industrially important species.

scholarly journals mSphere of Influence: Ushering in the CRISPR Revolution to Toxoplasma Biology

mSphere ◽  
2019 ◽  
Vol 4 (4) ◽  
Author(s):  
Alfredo J. Guerra
Keyword(s):  
Toxoplasma Gondii ◽  
Structural Biology ◽  
Gene Disruption ◽  
Gene Editing ◽  
Genome Engineering ◽  
Content Type ◽  
Efficient Gene ◽  
Implementing Strategies ◽  
Molecular Parasitology

ABSTRACT Alfredo J. Guerra works in the field of molecular parasitology and structural biology. In this mSphere of Influence article, he reflects on how “Efficient Gene Disruption in Diverse Strains of Toxoplasma gondii Using CRISPR/CAS9” by Bang Shen et al. (mBio 5:e01114-14, 2014, https://doi.org/10.1128/mBio.01114-14) and “Efficient Genome Engineering of Toxoplasma gondii using CRISPR/CAS9” by Saima M. Sidik et al. (PLoS One 9:e100450, 2014, https://doi.org/10.1371/journal.pone.0100450) made an impact on him by successfully implementing strategies to genetically manipulate T. gondii using CRISPR/CAS9 gene editing technology.

scholarly journals An optimized CRISPR/Cas toolbox for efficient germline and somatic genome engineering in Drosophila

2014 ◽  
Author(s):  
Fillip Port ◽  
Hui-Min Chen ◽  
Tzumin Lee ◽  
Simon L Bullock
Keyword(s):  
Genome Engineering ◽  
High Efficiency ◽  
Systematic Evaluation ◽  
Loss Of Function ◽  
Potent Effect ◽  
Single Nucleotide ◽  
Guide Rna ◽  
U6 Snrna ◽  
Somatic Genome ◽  
Mutant Phenotypes

The type II CRISPR/Cas system has recently emerged as a powerful method to manipulate the genomes of various organisms. Here, we report a novel toolbox for high efficiency genome engineering of Drosophila melanogaster consisting of transgenic Cas9 lines and versatile guide RNA (gRNA) expression plasmids. Systematic evaluation reveals Cas9 lines with ubiquitous or germline restricted patterns of activity. We also demonstrate differential activity of the same gRNA expressed from different U6 snRNA promoters, with the previously untested U6:3 promoter giving the most potent effect. Choosing an appropriate combination of Cas9 and gRNA allows targeting of essential and non-essential genes with transmission rates ranging from 25% - 100%. We also provide evidence that our optimized CRISPR/Cas tools can be used for offset nicking-based mutagenesis and, in combination with oligonucleotide donors, to precisely edit the genome by homologous recombination with efficiencies that do not require the use of visible markers. Lastly, we demonstrate a novel application of CRISPR/Cas-mediated technology in revealing loss-of-function phenotypes in somatic cells following efficient biallelic targeting by Cas9 expressed in a ubiquitous or tissue-restricted manner. In summary, our CRISPR/Cas tools will facilitate the rapid evaluation of mutant phenotypes of specific genes and the precise modification of the genome with single nucleotide precision. Our results also pave the way for high throughput genetic screening with CRISPR/Cas.

scholarly journals Efficient multiplexed genome engineering with a polycistronic tRNA and CRISPR guide-RNA reveals an important role of detonator in reproduction of Drosophila melanogaster

PLoS ONE ◽  
2021 ◽  
Vol 16 (1) ◽  
pp. e0245454
Author(s):  
Cristin Chon ◽  
Grace Chon ◽  
Yurika Matsui ◽  
Huiqing Zeng ◽  
Zhi-Chun Lai ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Genome Engineering ◽  
Transmembrane Protein ◽  
Association Studies ◽  
Fruit Fly ◽  
Loss Of Function ◽  
Guide Rna ◽  
Genome Association

Genome association studies in human and genetic studies in mouse implicated members of the transmembrane protein 132 (TMEM132) family in multiple conditions including panic disorder, hearing loss, limb and kidney malformation. However, the presence of five TMEM132 paralogs in mammalian genomes makes it extremely challenging to reveal the full requirement for these proteins in vivo. In contrast, there is only one TMEM132 homolog, detonator (dtn), in the genome of fruit fly Drosophila melanogaster, enabling straightforward research into its in vivo function. In the current study, we generate multiple loss-of-function dtn mutant fly strains through a polycistronic tRNA-gRNA approach, and show that most embryos lacking both maternal and paternal dtn fail to hatch into larvae, indicating an essential role of dtn in Drosophila reproduction.

scholarly journals Evaluation and rational design of guide RNAs for efficient CRISPR/Cas9-mediated mutagenesis in Ciona

2016 ◽  
Author(s):  
Shashank Gandhi ◽  
Maximilian Haeussler ◽  
Florian Razy-Krajka ◽  
Lionel Christiaen ◽  
Alberto Stolfi
Keyword(s):  
High Throughput ◽  
Rational Design ◽  
Genome Engineering ◽  
High Throughput Sequencing ◽  
Loss Of Function ◽  
Tissue Specific ◽  
Guide Rna ◽  
Guide Rnas ◽  
Highly Active

AbstractThe CRISPR/Cas9 system has emerged as an important tool for various genome engineering applications. A current obstacle to high throughput applications of CRISPR/Cas9 is the imprecise prediction of highly active single guide. RNAs (sgRNAs). We previously implemented the CRISPR/Cas9 system to induce tissue-specific mutations in the tunicate Ciona. In the present study, we designed and tested 83 single guide RNA (sgRNA) vectors targeting 23 genes expressed in the cardiopharyngeal progenitors and surrounding tissues of Ciona embryo. Using high-throughput sequencing of mutagenized alleles, we identified guide sequences that correlate with sgRNA mutagenesis activity and used this information for the rational design of all possible sgRNAs targeting the Ciona transcriptome. We also describe a one-step cloning-free protocol for the assembly of sgRNA expression cassettes. These cassettes can be directly electroporated as unpurified PCR products into Ciona embryos for sgRNA expression in vivo, resulting in high frequency of CRISPR/Cas9-mediated mutagenesis in somatic cells of electroporated embryos.We found a strong correlation between the frequency of an Ebf loss-of-function phenotype and the mutagenesis efficacies of individual Ebf-targeting sgRNAs tested using this method. We anticipate that our approach can be scaled up to systematically design and deliver highly efficient sgRNAs for the tissue-specific investigation of gene functions in Ciona.

Recent Developments on Synthesis of Indole Derivatives Through Green Approaches and Their Pharmaceutical Applications

2020 ◽  
Vol 24 (22) ◽  
pp. 2665-2693
Author(s):  
Dipayan Mondal ◽  
Pankaj Lal Kalar ◽  
Shivam Kori ◽  
Shovanlal Gayen ◽  
Kalpataru Das
Keyword(s):  
Biological Activities ◽  
Synthetic Methods ◽  
Pharmaceutical Chemistry ◽  
Indole Derivatives ◽  
Biological Studies ◽  
Recent Developments ◽  
Pharmaceutical Industries ◽  
Green Methodology ◽  
Conventional Methods ◽  
High Yields

Indole moiety is often found in different classes of pharmaceutically active molecules having various biological activities including anticancer, anti-viral, anti-psychotic, antihypertensive, anti-migraine, anti-arthritis and analgesic activities. Due to enormous applications of indole derivatives in pharmaceutical chemistry, a number of conventional synthetic methods as well as green methodology have been developed for their synthesis. Green methodology has many advantages including high yields, short reaction time, and inexpensive reagents, highly efficient and environmentally benign over conventional methods. Currently, the researchers in academia as well as in pharmaceutical industries have been developing various methods for the chemical synthesis of indole based compounds via green approaches to overcome the drawbacks of conventional methods. This review reflects the last ten years developments of the various greener methods for the synthesis of indole derivatives by using microwave, ionic liquids, water, ultrasound, nanocatalyst, green catalyst, multicomponent reaction and solvent-free reactions etc. (please see the scheme below). Furthermore, the applications of green chemistry towards developments of indole containing pharmaceuticals and their biological studies have been represented in this review.

scholarly journals Mutations in fbiD (Rv2983) as a Novel Determinant of Resistance to Pretomanid and Delamanid in Mycobacterium tuberculosis

2020 ◽  
Vol 65 (1) ◽  
pp. e01948-20
Author(s):  
Dalin Rifat ◽  
Si-Yang Li ◽  
Thomas Ioerger ◽  
Keshav Shah ◽  
Jean-Philippe Lanoix ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Clinical Evidence ◽  
Clinical Samples ◽  
Loss Of Function ◽  
Wild Type ◽  
Content Type ◽  
Solid Media ◽  
High Level ◽  
Level Resistance

ABSTRACTThe nitroimidazole prodrugs delamanid and pretomanid comprise one of only two new antimicrobial classes approved to treat tuberculosis (TB) in 50 years. Prior in vitro studies suggest a relatively low barrier to nitroimidazole resistance in Mycobacterium tuberculosis, but clinical evidence is limited to date. We selected pretomanid-resistant M. tuberculosis mutants in two mouse models of TB using a range of pretomanid doses. The frequency of spontaneous resistance was approximately 10−5 CFU. Whole-genome sequencing of 161 resistant isolates from 47 mice revealed 99 unique mutations, of which 91% occurred in 1 of 5 genes previously associated with nitroimidazole activation and resistance, namely, fbiC (56%), fbiA (15%), ddn (12%), fgd (4%), and fbiB (4%). Nearly all mutations were unique to a single mouse and not previously identified. The remaining 9% of resistant mutants harbored mutations in Rv2983 (fbiD), a gene not previously associated with nitroimidazole resistance but recently shown to be a guanylyltransferase necessary for cofactor F420 synthesis. Most mutants exhibited high-level resistance to pretomanid and delamanid, although Rv2983 and fbiB mutants exhibited high-level pretomanid resistance but relatively small changes in delamanid susceptibility. Complementing an Rv2983 mutant with wild-type Rv2983 restored susceptibility to pretomanid and delamanid. By quantifying intracellular F420 and its precursor Fo in overexpressing and loss-of-function mutants, we provide further evidence that Rv2983 is necessary for F420 biosynthesis. Finally, Rv2983 mutants and other F420H2-deficient mutants displayed hypersusceptibility to some antibiotics and to concentrations of malachite green found in solid media used to isolate and propagate mycobacteria from clinical samples.

Recent developments in China’s biopharmaceutical industry (2012-2017)

2019 ◽  
Vol 10 (3) ◽  
pp. 686-707
Author(s):  
Marcus Conlé
Keyword(s):  
Product Innovation ◽  
Academic Research ◽  
Domestic Market ◽  
Growth Strategy ◽  
Future Research ◽  
Biopharmaceutical Industry ◽  
Content Type ◽  
Drug Regulator ◽  
Recent Developments ◽  
Product Portfolios

Purpose The paper aims to take stock of China’s recent biopharmaceutical industry development by analyzing product innovation and changes in the firms’ product portfolios during the five-year period between 2012 and 2017. Design/methodology/approach The paper introduces a classification of biopharmaceutical products. By applying the classification to the product data of China’s drug regulator, the CFDA, it becomes possible to trace the developments within the sector by looking at changes in the number of firms within each subgroup and changes in the number of subgroups in which each firm is involved. The classification allows an evaluation of the latest product innovation achievements. Findings The paper demonstrates a mild shakeout of firms in the relatively long-existing domestic market segments, a trend toward more specialized product portfolios and an enduring prevalence of innovation strategies aimed at exploiting relatively unpopulated domestic market niches instead of pioneering entirely new products. Especially the capability of upgrading to second-generation protein therapeutics has become a key criterion for separating the wheat and the chaff in China’s domestic sector. The paper moreover points out the relevance of acquisitions as a corporate growth strategy. Research limitations/implications The research does not consider complementary indicators, product pipelines in particular. Future research should compare patterns across emerging economies. Originality/value The paper is unique in using the CFDA database for systematic academic research on (bio)pharmaceutical innovation and in introducing a biopharmaceutical product classification to trace innovative activities and changes in corporate product portfolios over time.

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