Rapid and specific degradation of endogenous proteins in mouse models using auxin-inducible degrons

Auxin-inducible degrons are a chemical genetic tool for targeted protein degradation and are widely used to study protein function in cultured mammalian cells. Here we develop CRISPR-engineered mouse lines that enable rapid and highly specific degradation of tagged endogenous proteins in vivo. Most but not all cell types are competent for degradation. Using mouse genetics, we show that degradation kinetics depend upon the dose of the tagged protein, ligand, and the E3 ligase subunit Tir1. Rapid degradation of condensin I and condensin II, two essential regulators of mitotic chromosome structure, revealed that both complexes are individually required for cell division in precursor lymphocytes, but not in their differentiated peripheral lymphocyte derivatives. This generalisable approach provides unprecedented temporal control over the dose of endogenous proteins in mouse models, with implications for studying essential biological pathways and modelling drug activity in mammalian tissues.

A Foliar Pigment-Based Bioassay for Interrogating Chloroplast Signalling Reveals that Chlorophyll Biosynthesis Requires Carotenoid Isomerisation.

Background: Plastid-derived metabolites can signal control over nuclear gene expression, chloroplast biogenesis, and chlorophyll biosynthesis. Norflurazon (NFZ) inhibition of carotenoid biosynthesis in seedlings can elicit a protoporphyrin retrograde signal that controls chlorophyll and chloroplast biogenesis. Recent evidence reveals that plastid development can be regulated by carotenoid cleavage products called apocarotenoids. The key steps in carotenoid biosynthesis and catabolism that generate apocarotenoid signalling metabolites in foliar tissues remains to be elucidated. Here, we established an Arabidopsis foliar pigment-based bioassay using detached rosettes to differentiate plastid signalling processes in young expanding leaves containing dividing cells with active chloroplast biogenesis, from fully expanded leaves containing mature chloroplasts. Results: We demonstrate that environmental (extended darkness and cold exposure) as well as chemical (norflurazon; NFZ) inhibition of carotenoid biosynthesis can reduce chlorophyll levels in young, but not older leaves following a 24 h of rosette treatment. Mutants that disrupted xanthophyll accumulation, phytohormone biosynthesis (abscisic acid and strigolactone), or enzymatic carotenoid cleavage, did not alter chlorophyll levels in young or old leaves. Perturbations in acyclic cis-carotene biosynthesis revealed that disruption of CAROTENOID ISOMERASE (CRTISO), but not ZETA-CAROTENE ISOMERASE (Z-ISO) activity, reduced chlorophyll levels in young but not older leaves of plants growing under a long photoperiod. NFZ-induced inhibition of PHYTOENE DESATURASE (PDS) activity triggered phytoene accumulation more so in younger relative to older leaves from both WT and the crtiso mutant, indicating a continued substrate supply from the methylerythritol 4-phosphate (MEP) pathway for carotenogenesis. NFZ treatment of WT and crtiso mutant rosettes reveal similar, additive, and opposite effects on individual pigment accumulation.Conclusion: The Arabidopsis foliar pigment-based bioassay was used to differentiate signalling events elicited by environmental, chemical, genetic, and combinations thereof, that control chlorophyll biosynthesis. Genetic perturbations that impaired xanthophyll biosynthesis and/or carotenoid catabolism did not affect chlorophyll biosynthesis. The lack of CAROTENOID ISOMERISATION generated a signal that rate-limited chlorophyll accumulation, but not phytoene biosynthesis in young Arabidopsis leaves exposed to a long photoperiod. Findings generated using this new foliar pigment bioassay implicate that carotenoid isomerisation and NFZ elicit different signalling pathways to control chlorophyll homeostasis in young emerging leaves.

Exploiting diverse chemical collections to uncover novel antifungals

The rise in drug resistance amongst pathogenic fungi, paired with the limited arsenal of antifungals available is an imminent threat to our medical system. To address this, we screened two distinct compound libraries to identify novel strategies to expand the antifungal armamentarium. The first collection wasthe RIKEN Natural Product Depository (NPDepo), which was screened for antifungal activity against four major human fungal pathogens: Candida albicans, Candida glabrata, Candida auris, and Cryptococcus neoformans. Through a prioritization pipeline, one compound, NPD6433, emerged as having broad-spectrum antifungal activity and minimal mammalian cytotoxicity. Chemical-genetic and biochemical assays demonstrated that NPD6433 inhibits the essential fungal enzyme fatty acid synthase 1 (Fas1). Treatment with NPD6433 inhibited various virulence traits in C. neoformans and C. auris, and rescued mammalian cell growth in a co-culture model with C. auris. The second compound library screened was adiversity-oriented collectionfrom Boston University. This chemical screen was focused on identifying novel molecules that enhance the activity of the widely deployed antifungal, fluconazole, against C. auris. Through this endeavour, we discovered a potent compound that enhanced fluconazole efficacy against C. auris through increasing azole intracellular accumulation. This activity was dependent on expression of the multidrug transporter geneCDR1, suggesting that this compound targets efflux mechanisms. Furthermore, this molecule significantly reduced fungal burden alone and in combination with fluconazole in a murine model of C. auris disseminated infection. Overall, this work identifies novel compounds with bioactivity against fungal pathogens, revealing important biology, and paving the way for the critical development of therapeutic strategies.

Using a chemical genetic screen to enhance our understanding of the antimicrobial properties of copper

The competitive toxic and stress inducing nature of copper necessitates systems that sequester and export this metal from the cytoplasm of bacterial cells. Several predicted mechanisms of toxicity include the production of reactive oxygen species, thiol depletion, DNA and iron-sulfur cluster disruption. Accompanying these mechanisms include pathways of homeostasis such as chelation, oxidation, and transport. Still, the mechanisms of copper resistance and sensitivity are not fully understood. Furthermore, studies fail to recognize that the response to copper is likely a result of numerous mechanisms, as in the case for homeostasis, in which proteins and enzymes work as a collective to maintain appropriate copper concentrations. In this study we used the Keio collection, an array of 3985 Escherichia coli mutants, each with a deleted non-essential gene, to gain a better understanding of prolonged copper exposure. In short, we recovered two copper homeostatic gene and genes involved in transporting and assembling to be involved in mediating prolonged copper stress under the conditions assessed. The gene coding for the protein TolC was uncovered as a sensitive hit and we demonstrated that tolC, an outer membrane efflux channel, is key in mitigating copper sensitivity. Additionally, the activity of tRNA processing was enriched and the deletion of several proteins involved in import generated copper tolerance. Lastly, key genes belonging to central carbon metabolism and nicotinamide adenine dinucleotide biosynthesis were uncovered as tolerant hits. Overall, this study shows that copper sensitivity and tolerance are a result of numerous mechanisms acting in combination within the cell.

Chemical Genetics Applied to Elucidate the Physiological Role of Stress-Signaling Molecules on the Wound-Induced Accumulation of Glucosinolates in Broccoli

Wounding stress is an effective strategy to induce glucosinolate (GS) biosynthesis in broccoli. However, there is insufficient knowledge on the physiological and molecular mechanisms underlying this stress response. Herein, a chemical-genetic approach was applied to elucidate the role of jasmonic acid (JA), ethylene (ET), and reactive oxygen species (ROS) on the wound-induced biosynthesis of GS. Broccoli was processed into chops to induce wounding stress. Broccoli chops were treated with phenidone (PHEN) and diphenyleneiodonium chloride (DPI) as inhibitors of JA and ROS biosynthesis, respectively, whereas 1-methylcyclopropene (1-MCP) was applied as an inhibitor of ET action. Wounding stress induced the expression of genes related to the biosynthesis of indolic and aliphatic GS, which was correlated with the accumulation of GS and modulated by the inhibitors of signaling molecules applied. Results of gene expression analysis indicated that JA played a key role in the activation of most genes, followed by ROS. Furthermore, except for the CYP79B2 gene, PHEN and 1-MCP synergistically downregulated the expression of GS biosynthetic genes evaluated, showing that the interaction between JA and ET was fundamental to modulate GS biosynthesis. Results presented herein increased our knowledge of the physiological and molecular mechanisms governing the wound-induced biosynthesis of GS in broccoli.

INFECTION AS A RISK FACTOR FOR GALLBLADDER CANCERLITERATURE REVIEW.

Gallbladder cancer (GBC) is the 6th most common gastrointestinal malignancy and most common hepatobiliary malignancy representing 85-90% worldwide with an annual incident of 2/1,00,000 and marked 1 geographical and ethnic variability and known for late diagnosis and poor outcome. High rates of gallbladder carcinoma are seen in different parts of the world like South America (Chilli, Bolivia, and 2 Ecuador) as well as in some parts of India (specically in north IndiaUP, Bihar, Delhi, West Bengal, Assam, and Madhya Pradesh, mostly in Gangetic belt), Pakistan, Japan, and Korea. In north India, gallbladder cancer is 10 times more common in comparison to south India. R 3 Kanthan et al . (2015) divides the risk factor for GBC into four broad groups: i)Patient demography, ii) GB abnormalities, iii)patient exposure to a specic chemical, genetic and molecular factors, iv) Infection. This study says that not only gallbladder stones but also infection by some microbial agents like salmonella and helicobacter also having contributory risk factors

A chemical-genetic map of the pathways controlling drug potency in Mycobacterium tuberculosis

Mycobacterium tuberculosis infection is notoriously difficult to treat. To define the bacterial determinants that limit treatment efficacy, we developed a CRISPRi chemical genetics platform to titrate the expression of nearly all Mtb genes and quantify bacterial fitness in the presence of different drugs. Mining this dataset, we discovered diverse mechanisms of intrinsic drug resistance, unveiling hundreds of potential targets for synergistic drug combinations. Combining our data with comparative genomics of Mtb clinical isolates, we further identified new mechanisms of acquired drug resistance, one of which is associated with the emergence of a multidrug-resistant tuberculosis (TB) outbreak in South America. Lastly, we make the unexpected discovery of loss-of-function mutations in the intrinsic resistance factor whiB7 in an entire Mtb sublineage endemic to Southeast Asia, presenting an opportunity to repurpose macrolides to treat TB. This chemical-genetic map provides a rich resource to understand drug efficacy and guide future TB drug development and treatment.

Chemical genetic analyses of compounds derived from feijoa fruit

<p>Nature has been a rich source of pharmaceutical compounds, producing 80% of our currently prescribed drugs. The feijoa plant, Acca sellowiana, is classified in the family Myrtaceae, native to South America, and currently grown worldwide to produce feijoa fruit. Compounds with anticancer, anti-inflammatory, antibacterial and antifungal activities have been isolated from feijoa; however, the diversity of these compounds is not known nor is the mechanism of action of any of these compounds. I hypothesized that identifying compounds in novel feijoa cultivars would improve our understanding of the chemical diversity of antifungal compounds in feijoa and determining the antifungal mechanism of action of feijoa compounds would provide insight into the pharmaceutical potential of these compounds. First, GC-MS analyses were used to obtain an unbiased profile of 151 compounds from 16 cultivars of feijoa, of which six were novel cultivars. Multivariate analysis distinguished 18 compounds that were significantly and positively correlated to antifungal activity based on growth inhibition of Saccharomyces cerevisiae, of which seven had not previously been described from feijoa. Two novel cultivars were identified as the most bioactive cultivars, and the compound 4-cyclopentene-1,3-dione found in a couple of cultivars was potently antifungal against human pathogenic isolates of four Candida species. Second, chemical genetic analyses were used to investigate the mechanism of action of estragole, an antifungal compound previously isolated from feijoa. The chemical genetic profile of estragole was distinct from that of other known antifungal compounds, suggesting the mechanism of action of estragole has a novel antifungal mechanism. Third, chemical genetic analyses were used to investigate the mechanism of action of an ethanol adduct of vescalagin (EtOH-vescalagin) isolated from feijoa. We showed EtOH-vescalagin is antifungal against human pathogenic strains. Genome-wide chemical genetic analyses of EtOH-vescalagin indicated antifungal activity is mediated by disruptions of iron homeostasis, zinc homeostasis and retromer recycling through iron chelation. Overall, these results indicate the chemical and biological value of feijoa as a source of antifungal drugs.</p>

Chemical genetic analyses of compounds derived from feijoa fruit

<p>Nature has been a rich source of pharmaceutical compounds, producing 80% of our currently prescribed drugs. The feijoa plant, Acca sellowiana, is classified in the family Myrtaceae, native to South America, and currently grown worldwide to produce feijoa fruit. Compounds with anticancer, anti-inflammatory, antibacterial and antifungal activities have been isolated from feijoa; however, the diversity of these compounds is not known nor is the mechanism of action of any of these compounds. I hypothesized that identifying compounds in novel feijoa cultivars would improve our understanding of the chemical diversity of antifungal compounds in feijoa and determining the antifungal mechanism of action of feijoa compounds would provide insight into the pharmaceutical potential of these compounds. First, GC-MS analyses were used to obtain an unbiased profile of 151 compounds from 16 cultivars of feijoa, of which six were novel cultivars. Multivariate analysis distinguished 18 compounds that were significantly and positively correlated to antifungal activity based on growth inhibition of Saccharomyces cerevisiae, of which seven had not previously been described from feijoa. Two novel cultivars were identified as the most bioactive cultivars, and the compound 4-cyclopentene-1,3-dione found in a couple of cultivars was potently antifungal against human pathogenic isolates of four Candida species. Second, chemical genetic analyses were used to investigate the mechanism of action of estragole, an antifungal compound previously isolated from feijoa. The chemical genetic profile of estragole was distinct from that of other known antifungal compounds, suggesting the mechanism of action of estragole has a novel antifungal mechanism. Third, chemical genetic analyses were used to investigate the mechanism of action of an ethanol adduct of vescalagin (EtOH-vescalagin) isolated from feijoa. We showed EtOH-vescalagin is antifungal against human pathogenic strains. Genome-wide chemical genetic analyses of EtOH-vescalagin indicated antifungal activity is mediated by disruptions of iron homeostasis, zinc homeostasis and retromer recycling through iron chelation. Overall, these results indicate the chemical and biological value of feijoa as a source of antifungal drugs.</p>

Voltage Imaging in Drosophila Using a Hybrid Chemical-Genetic Rhodamine Voltage Reporter

We combine a chemically-synthesized, voltage-sensitive fluorophore with a genetically encoded, self-labeling enzyme to enable voltage imaging in Drosophila melanogaster. Previously, we showed that a rhodamine voltage reporter (RhoVR) combined with the HaloTag self-labeling enzyme could be used to monitor membrane potential changes from mammalian neurons in culture and brain slice. Here, we apply this hybrid RhoVR-Halo approach in vivo to achieve selective neuron labeling in intact fly brains. We generate a Drosophila UAS-HaloTag reporter line in which the HaloTag enzyme is expressed on the surface of cells. We validate the voltage sensitivity of this new construct in cell culture before driving expression of HaloTag in specific brain neurons in flies. We show that selective labeling of synapses, cells, and brain regions can be achieved with RhoVR-Halo in either larval neuromuscular junction (NMJ) or in whole adult brains. Finally, we validate the voltage sensitivity of RhoVR-Halo in fly tissue via dual-electrode/imaging at the NMJ, show the efficacy of this approach for measuring synaptic excitatory post-synaptic potentials (EPSPs) in muscle cells, and perform voltage imaging of carbachol-evoked depolarization and osmolarity-evoked hyperpolarization in projection neurons and in interoceptive subesophageal zone neurons in fly brain explants following in vivo labeling. We envision the turn-on response to depolarizations, fast response kinetics, and two-photon compatibility of chemical indicators, coupled with the cellular and synaptic specificity of genetically-encoded enzymes, will make RhoVR-Halo a powerful complement to neurobiological imaging in Drosophila.