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.

Optimization of Process Conditions for Effective Degradation of Azo Blue Dye by Streptomyces sp. DJP15: A Secondary Modelling Approac

The well function of aquatic and soil organisms including terrestrial, as well as those of all other living things, can be jeopardized if dyes aren't properly treated, as their degradation might lead to carcinogenic chemicals. Complete mineralization of dye is the only option, and this can be done using microorganisms. The azo blue dye inhibitory effect to its biodegradation by Streptomyces DJP15 was modelled using several inhibition kinetic models such as Haldane, Monod, Luong, Aiba, Teissier-Edwards, Han-Levenspiel and Yano. The result shows that only the Luong model failed to fit the data. The rest of the models visually ft the data although data fitting is problematic with datapoints of less than 10, which the result in this work demonstrates where it is not easy to choose the best model where nearly all of the models fit the data in a similar manner. Resorting to statistical discriminatory function, the best model was Monod with the smallest RMSE and AICc values and the highest adjR2 values and values for AF and BF close to unity. However, Monod has only two parameters and is the most robust. The Monod’s parameters were maximum specific degradation rate of 0.431 (1/h) (95% confidence interval from 0.391 to 0.456) and concentration of substrate giving half maximal rate or Ks value of 0.0001 (mg/L) (95% C.I. from -0.01 to 12.12). The confidence interval value for the Ks value was very large indicating poor data quality. This should be an important consideration in future works where the data point number can be increased to improve model fitting exercise.

Water Erosion in the Moulouya Watershed and its Impact on Dams' Siltation (Eastern Morocco)

The Moulouya watershed presents high risks of water erosion. The dams built on this river lose each year, by siltation, a volume of water of about 10 M m3 (Lahlou, 1994). This worrying rate shows that water erosion can hinder the socio-economic development of the basin if soil protection and siltation measures are not taken. This study defines the areas most threatened by water erosion to protect them as a priority. Using a GIS and the Universal Earth Loss Equation (USLE), we mapped soil losses. The adopted model determines soil loss from erosivity of rainfall, soil erodibility, inclination and slope length, soil cover, and erosion control practices. The possible origins of the deposits alluviating the dams are related to the products of alteration of the Secondary's carbonate formations and the Tertiary and Quaternary formations. The modalities of the transport of deposits of banks of the network of Moulouya are mainly by a suspension. The specific degradation in the Moulouya watershed is estimated at 214 t/km2/year. Precipitation intensity, steep slopes and deforestation are responsible for these losses.

DAF-2/insulin IGF-1 receptor regulates mobility during ageing by integrating opposite inputs from muscle and neuronal tissues

During ageing, preservation of locomotion is generally considered an indicator of sustained good health, in elderlies and in animal models. In C. elegans, mutants of the insulin receptor DAF-2 represent a paradigm of healthy ageing, as their increased lifespan is accompanied by a delay in age-related loss of mobility. However, these animals are less mobile than wild-type animals in early adulthood. Here we investigated the DAF-2-dependent relationship between longevity and mobility using an auxin-inducible degron to trigger tissue-specific degradation of endogenous DAF-2. As previously reported, inactivation of DAF-2 in neurons or intestine was sufficient to extend the lifespan of worms, whereas depletion in epidermis, germline or muscle was not. However, neither intestinal nor neuronal depletion of DAF-2 prevented the age-related loss of mobility. In 1-day-old adults, DAF-2 depletion in neurons reduced mobility, while muscle depletion had no effect. By contrast, DAF-2 depletion in the muscle of middle-age animals improved their mobility. The combination of neuronal and muscle effects thus mimics the global locomotor phenotype of daf-2 mutants. Yet, we observed that neuronal or muscle DAF-2 depletion both preserved the mitochondria network in ageing muscle. Overall, these results show that the mobility pattern of daf-2 mutants is determined by the sequential and opposing impact of neurons and muscle tissues and can be dissociated from the regulation of the lifespan. This work also provides the characterization of a versatile tool to analyze the tissue-specific contribution of insulin-like signaling in integrated phenotypes at the whole organism level.

NudCL2 is an autophagy receptor that mediates selective autophagic degradation of CP110 at mother centrioles to promote ciliogenesis

Primary cilia extending from mother centrioles are essential for vertebrate development and homeostasis maintenance. Centriolar coiled-coil protein 110 (CP110) has been reported to suppress ciliogenesis initiation by capping the distal ends of mother centrioles. However, the mechanism underlying the specific degradation of mother centriole-capping CP110 to promote cilia initiation remains unknown. Here, we find that autophagy is crucial for CP110 degradation at mother centrioles after serum starvation in MEF cells. We further identify NudC-like protein 2 (NudCL2) as a novel selective autophagy receptor at mother centrioles, which contains an LC3-interacting region (LIR) motif mediating the association of CP110 and the autophagosome marker LC3. Knockout of NudCL2 induces defects in the removal of CP110 from mother centrioles and ciliogenesis, which are rescued by wild-type NudCL2 but not its LIR motif mutant. Knockdown of CP110 significantly attenuates ciliogenesis defects in NudCL2-deficient cells. In addition, NudCL2 morphants exhibit ciliation-related phenotypes in zebrafish, which are reversed by wild-type NudCL2, but not its LIR motif mutant. Importantly, CP110 depletion significantly reverses these ciliary phenotypes in NudCL2 morphants. Taken together, our data suggest that NudCL2 functions as an autophagy receptor mediating the selective degradation of mother centriole-capping CP110 to promote ciliogenesis, which is indispensable for embryo development in vertebrates.

Novel Mechanism and Kinetics of Tetramethrin Degradation Using an Indigenous Gordonia cholesterolivorans A16

Tetramethrin is a pyrethroid insecticide that is commonly used worldwide. The toxicity of this insecticide into the living system is an important concern. In this study, a novel tetramethrin-degrading bacterial strain named A16 was isolated from the activated sludge and identified as Gordonia cholesterolivorans. Strain A16 exhibited superior tetramethrin degradation activity, and utilized tetramethrin as the sole carbon source for growth in a mineral salt medium (MSM). High-performance liquid chromatography (HPLC) analysis revealed that the A16 strain was able to completely degrade 25 mg·L−1 of tetramethrin after 9 days of incubation. Strain A16 effectively degraded tetramethrin at temperature 20–40 °C, pH 5–9, and initial tetramethrin 25–800 mg·L−1. The maximum specific degradation rate (qmax), half-saturation constant (Ks), and inhibition constant (Ki) were determined to be 0.4561 day−1, 7.3 mg·L−1, and 75.2 mg·L−1, respectively. The Box–Behnken design was used to optimize degradation conditions, and maximum degradation was observed at pH 8.5 and a temperature of 38 °C. Five intermediate metabolites were identified after analyzing the degradation products through gas chromatography–mass spectrometry (GC-MS), which suggested that tetramethrin could be degraded first by cleavage of its carboxylester bond, followed by degradation of the five-carbon ring and its subsequent metabolism. This is the first report of a metabolic pathway of tetramethrin in a microorganism. Furthermore, bioaugmentation of tetramethrin-contaminated soils (50 mg·kg−1) with strain A16 (1.0 × 107 cells g−1 of soil) significantly accelerated the degradation rate of tetramethrin, and 74.1% and 82.9% of tetramethrin was removed from sterile and non-sterile soils within 11 days, respectively. The strain A16 was also capable of efficiently degrading a broad spectrum of synthetic pyrethroids including D-cyphenothrin, chlorempenthrin, prallethrin, and allethrin, with a degradation efficiency of 68.3%, 60.7%, 91.6%, and 94.7%, respectively, after being cultured under the same conditions for 11 days. The results of the present study confirmed the bioremediation potential of strain A16 from a contaminated environment.

Fusarium graminearum DICER-like-dependent sRNAs are required for the suppression of host immune genes and full virulence

In filamentous fungi, gene silencing by RNA interference (RNAi) shapes many biological processes, including pathogenicity. Recently, fungal small RNAs (sRNAs) have been shown to act as effectors that disrupt gene activity in interacting plant hosts, thereby undermining their defence responses. We show here that the devastating mycotoxin-producing ascomycete Fusarium graminearum (Fg) utilizes DICER-like (DCL)-dependent sRNAs to target defence genes in two Poaceae hosts, barley (Hordeum vulgare, Hv) and Brachypodium distachyon (Bd). We identified 104 Fg-sRNAs with sequence homology to host genes that were repressed during interactions of Fg and Hv, while they accumulated in plants infected by the DCL double knock-out (dKO) mutant PH1-dcl1/2. The strength of target gene expression correlated with the abundance of the corresponding Fg-sRNA. Specifically, the abundance of three tRNA-derived fragments (tRFs) targeting immunity-related Ethylene overproducer 1-like 1 (HvEOL1) and three Poaceae orthologues of Arabidopsis thaliana BRI1-associated receptor kinase 1 (HvBAK1, HvSERK2 and BdSERK2) was dependent on fungal DCL. Additionally, RNA-ligase-mediated Rapid Amplification of cDNA Ends (RLM-RACE) identified infection-specific degradation products for the three barley gene transcripts, consistent with the possibility that tRFs contribute to fungal virulence via targeted gene silencing.

Root engineering in maize by increasing cytokinin degradation causes enhanced root growth and leaf mineral enrichment

Key message Root-specific expression of a cytokinin-degrading CKX gene in maize roots causes formation of a larger root system leading to higher element content in shoot organs. Abstract The size and architecture of the root system is functionally relevant for the access to water and soil nutrients. A great number of mostly unknown genes are involved in regulating root architecture complicating targeted breeding of plants with a larger root system. Here, we have explored whether root-specific degradation of the hormone cytokinin, which is a negative regulator of root growth, can be used to genetically engineer maize (Zea mays L.) plants with a larger root system. Root-specific expression of a CYTOKININ OXIDASE/DEHYDROGENASE (CKX) gene of Arabidopsis caused the formation of up to 46% more root dry weight while shoot growth of these transgenic lines was similar as in non-transgenic control plants. The concentration of several elements, in particular of those with low soil mobility (K, P, Mo, Zn), was increased in leaves of transgenic lines. In kernels, the changes in concentration of most elements were less pronounced, but the concentrations of Cu, Mn and Zn were significantly increased in at least one of the three independent lines. Our data illustrate the potential of an increased root system as part of efforts towards achieving biofortification. Taken together, this work has shown that root-specific expression of a CKX gene can be used to engineer the root system of maize and alter shoot element composition.