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WebIn both laboratory and field studies, engineering translational control of immune mediator production in Arabidopsis and rice confers disease resistance, without compromising plant fitness. Programming plant immunity It is well established that plants elicit immune responses by reprogramming their transcriptional response. Controlling this for agricultural purposes without reducing the plant's fitness has been a challenge. Xinnian Dong and colleagues have engineered translational control into Arabidopsis and rice to promote production of immune mediators and show, in laboratory and field studies, that this confers disease resistance without compromising plant fitness. This was achieved using insights from a related paper published in this issue, in which Xinnian Dong and colleagues uncover new regulators of plant immune responses. Through global translatome analysis, they observe that plants modify their translational output independently of the changes in the transcriptional output to establish pathogen-triggered immunity. Controlling plant disease has been a struggle for humankind since the advent of agriculture. Studies of plant immune mechanisms have led to strategies of engineering resistant crops through ectopic transcription of plants’ own defence genes, such as the master immune regulatory gene NPR1 (ref. 1 ). However, enhanced resistance obtained through such strategies is often associated with substantial penalties to fitness 2 , making the resulting products undesirable for agricultural applications. To remedy this problem, we sought more stringent mechanisms of expressing defence proteins. On the basis of our latest finding that translation of key immune regulators, such as TBF1 (ref. 3 ), is rapidly and transiently induced upon pathogen challenge (see accompanying paper 4 ), we developed a ‘TBF1-cassette’ consisting of not only the immune-inducible promoter but also two pathogen-responsive upstream open reading frames (uORFs TBF1 ) of the TBF1 gene. Here we demonstrate that inclusion of uORFs TBF1 -mediated translational control over the production of snc1-1 (an autoactivated immune receptor) in Arabidopsis thaliana and At NPR1 in rice enables us to engineer broad-spectrum disease resistance without compromising plant fitness in the laboratory or in the field. This broadly applicable strategy may lead to decreased pesticide use and reduce the selective pressure for resistant pathogens.

Dysfunction of the epidermal permeability barrier can result in dehydration, electrolyte imbalance and poor thermoregulation. Immature skin is a portal of entry for infectious agents and potential toxins in topically applied substances. As the skin is one of the last organs to mature in utero, premature infants born before 34 weeks gestation are at great risk for complications. The transcription factor kruppel-like factor 4 (Klf4), has been shown by a targeted ablation, to have an essential function in barrier acquisition. We investigated whether Klf4 expression in utero is sufficient to establish the epidermal barrier. Specifically, we generated lines of mice that express Klf4 from a tetracycline inducible promoter when crossed with transgenic mice expressing the tetracycline transactivator tTA from the epidermal keratin 5 promoter. These mice exhibit acceleration in barrier acquisition as manifest by the exclusion of a dye solution one day earlier in development than controls. Underlying this dye impermeability are morphological changes, including an increased number of stratified layers, expression of terminal differentiation markers and assembly of cornified envelopes. By all criteria, Klf4 ectopic expression accelerates the normal process of terminal differentiation. Premature barrier acquisition in these mice follows the normal pattern rather than the pattern of the transgene promoter, indicating that there are fields of competence in which KLF4 acts. Although other transgenic mice have perturbed barrier acquisition, these mice are the first to accelerate the process of barrier establishment. These studies show that KLF4 regulates barrier acquisition and provides an animal model for studying how to accelerate the process of barrier acquisition for the premature infant.

The cytosolic accumulation of mitochondrial precursors is hazardous to cellular fitness and is associated with a number of diseases. However, it is not observed under physiological conditions. Individual mechanisms that allow cells to avoid cytosolic accumulation of mitochondrial precursors have recently been discovered, but their interplay and regulation remain elusive. Here, we show that cells rapidly launch a global transcriptional programme to restore cellular proteostasis after induction of a ‘clogger’ protein that reduces the number of available mitochondrial import sites. Cells upregulate the protein folding and proteolytic systems in the cytosol and downregulate both the cytosolic translation machinery and many mitochondrial metabolic enzymes, presumably to relieve the workload of the overstrained mitochondrial import system. We show that this transcriptional remodelling is a combination of a ‘wideband’ core response regulated by the transcription factors Hsf1 and Rpn4 and a unique mitoprotein-induced downregulation of the oxidative phosphorylation components, mediated by an inactivation of the HAP complex. Boos et al. show that impairing mitochondrial protein import induces a global transcriptional response to activate the ubiquitin–proteasome system and heat stress response and repress oxidative phosphorylation genes.​

The CXXC domains of TET2 (encoded by the distinct gene IDAX ) and TET3 are found to have previously unknown roles in the regulation of TET proteins through the activation of caspases and subsequent reduction in TET catalytic activity; this regulation is dependent on DNA binding through the CXXC domain. IDAX regulates TET2 protein expression TET family proteins modify the methylation status of DNA by oxidizing 5-methylcytosine to 5-hydroxymethylcytosine (5hmC, sometimes called the 'fifth base' of DNA) and other intermediates. TET1 and TET3 contain a CXXC domain but the ancestral CXXC domain of TET2 is encoded by a distinct gene, IDAX (or CXXC4 ). This paper demonstrates that IDAX binds unmethylated CpG-rich DNA via its CXXC domain and recruits TET2. The separate and linked CXXC domains of TET2 and TET3 are shown to act as regulators of caspase activation and TET enzymatic activity. The authors suggest that future studies should focus on the genomic targets of TET2, IDAX and the IDAX-related protein CXXC5 in normal development and in cancer. TET (ten-eleven-translocation) proteins are Fe( ii )- and α-ketoglutarate-dependent dioxygenases 1 , 2 , 3 that modify the methylation status of DNA by successively oxidizing 5-methylcytosine to 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxycytosine 1 , 3 , 4 , 5 , potential intermediates in the active erasure of DNA-methylation marks 5 , 6 . Here we show that IDAX (also known as CXXC4), a reported inhibitor of Wnt signalling 7 that has been implicated in malignant renal cell carcinoma 8 and colonic villous adenoma 9 , regulates TET2 protein expression. IDAX was originally encoded within an ancestral TET2 gene that underwent a chromosomal gene inversion during evolution, thus separating the TET2 CXXC domain from the catalytic domain. The IDAX CXXC domain binds DNA sequences containing unmethylated CpG dinucleotides, localizes to promoters and CpG islands in genomic DNA and interacts directly with the catalytic domain of TET2. Unexpectedly, IDAX expression results in caspase activation and TET2 protein downregulation, in a manner that depends on DNA binding through the IDAX CXXC domain, suggesting that IDAX recruits TET2 to DNA before degradation. IDAX depletion prevents TET2 downregulation in differentiating mouse embryonic stem cells, and short hairpin RNA against IDAX increases TET2 protein expression in the human monocytic cell line U937. Notably, we find that the expression and activity of TET3 is also regulated through its CXXC domain. Taken together, these results establish the separate and linked CXXC domains of TET2 and TET3, respectively, as previously unknown regulators of caspase activation and TET enzymatic activity.

Cortical hyperexcitability and mislocalization of the RNA-binding protein TDP43 are highly conserved features in amyotrophic lateral sclerosis (ALS). Nevertheless, the relationship between these phenomena remains poorly defined. Here, we showed that hyperexcitability recapitulates TDP43 pathology by upregulating shortened TDP43 (sTDP43) splice isoforms. These truncated isoforms accumulated in the cytoplasm and formed insoluble inclusions that sequestered full-length TDP43 via preserved N-terminal interactions. Consistent with these findings, sTDP43 overexpression was toxic to mammalian neurons, suggesting neurodegeneration arising from complementary gain- and loss-of-function mechanisms. In humans and mice, sTDP43 transcripts were enriched in vulnerable motor neurons, and we observed a striking accumulation of sTDP43 within neurons and glia of ALS patients. Collectively, these studies uncover a pathogenic role for alternative TDP43 isoforms in ALS, and implicate sTDP43 as a key contributor to the susceptibility of motor neurons in this disorder.

The authors identify brain RNA targets for TDP-43, a RNA binding protein linked to ALS. RNAs derived from genes with very long introns were more affected by TDP-43 levels. TDP-43 also auto-regulated its own synthesis, partly by binding and enhancing the splicing of an intron in its 3′ UTR We used cross-linking and immunoprecipitation coupled with high-throughput sequencing to identify binding sites in 6,304 genes as the brain RNA targets for TDP-43, an RNA binding protein that, when mutated, causes amyotrophic lateral sclerosis. Massively parallel sequencing and splicing-sensitive junction arrays revealed that levels of 601 mRNAs were changed (including Fus (Tls), progranulin and other transcripts encoding neurodegenerative disease–associated proteins) and 965 altered splicing events were detected (including in sortilin, the receptor for progranulin) following depletion of TDP-43 from mouse adult brain with antisense oligonucleotides. RNAs whose levels were most depleted by reduction in TDP-43 were derived from genes with very long introns and that encode proteins involved in synaptic activity. Lastly, we found that TDP-43 autoregulates its synthesis, in part by directly binding and enhancing splicing of an intron in the 3′ untranslated region of its own transcript, thereby triggering nonsense-mediated RNA degradation.

Notch signaling is shown to regulate the browning of adipocytes and whole-body energy expenditure, with inhibition leading to protection from diet-induced obesity in mice. Beige adipocytes in white adipose tissue (WAT) are similar to classical brown adipocytes in that they can burn lipids to produce heat. Thus, an increase in beige adipocyte content in WAT browning would raise energy expenditure and reduce adiposity. Here we report that adipose-specific inactivation of Notch1 or its signaling mediator Rbpj in mice results in browning of WAT and elevated expression of uncoupling protein 1 (Ucp1), a key regulator of thermogenesis. Consequently, as compared to wild-type mice, Notch mutants exhibit elevated energy expenditure, better glucose tolerance and improved insulin sensitivity and are more resistant to high fat diet–induced obesity. By contrast, adipose-specific activation of Notch1 leads to the opposite phenotypes. At the molecular level, constitutive activation of Notch signaling inhibits, whereas Notch inhibition induces, Ppargc1a and Prdm16 transcription in white adipocytes. Notably, pharmacological inhibition of Notch signaling in obese mice ameliorates obesity, reduces blood glucose and increases Ucp1 expression in white fat. Therefore, Notch signaling may be therapeutically targeted to treat obesity and type 2 diabetes.

The maintenance of immune homeostasis requires regulatory T cells (Tregs). Given their intrinsic self-reactivity, Tregs must stably maintain a suppressive phenotype to avoid autoimmunity. We report that impaired expression of the transcription factor (TF) Helios by FoxP3+ CD4 and Qa-1–restricted CD8 Tregs results in defective regulatory activity and autoimmunity in mice. Helios-deficient Tregs develop an unstable phenotype during inflammatory responses characterized by reduced FoxP3 expression and increased effector cytokine expression secondary to diminished activation of the STAT5 pathway. CD8 Tregs also require Helios-dependent STAT5 activation for survival and to prevent terminal T cell differentiation. The definition of Helios as a key transcription factor that stabilizes Tregs in the face of inflammatory responses provides a genetic explanation for a core property of Tregs.

Growing up on a dairy farm protects children from allergy, hay fever, and asthma. A mechanism linking exposure to this endotoxin (bacterial lipopolysaccharide)–rich environment with protection has remained elusive. Here we show that chronic exposure to low-dose endotoxin or farm dust protects mice from developing house dust mite (HDM)–induced asthma. Endotoxin reduced epithelial cell cytokines that activate dendritic cells (DCs), thus suppressing type 2 immunity to HDMs. Loss of the ubiquitin-modifying enzyme A20 in lung epithelium abolished the protective effect. A single-nucleotide polymorphism in the gene encoding A20 was associated with allergy and asthma risk in children growing up on farms. Thus, the farming environment protects from allergy by modifying the communication between barrier epithelial cells and DCs through A20 induction.

Epithelial renewal in the Drosophila intestine is orchestrated by Intestinal Stem Cells (ISCs). Following damage or stress the intestinal epithelium produces ligands that activate the epidermal growth factor receptor (EGFR) in ISCs. This promotes their growth and division and, thereby, epithelial regeneration. Here we demonstrate that the HMG-box transcriptional repressor, Capicua (Cic), mediates these functions of EGFR signaling. Depleting Cic in ISCs activated them for division, whereas overexpressed Cic inhibited ISC proliferation and midgut regeneration. Epistasis tests showed that Cic acted as an essential downstream effector of EGFR/Ras signaling, and immunofluorescence showed that Cic's nuclear localization was regulated by EGFR signaling. ISC-specific mRNA expression profiling and DNA binding mapping using DamID indicated that Cic represses cell proliferation via direct targets including string (Cdc25), Cyclin E, and the ETS domain transcription factors Ets21C and Pointed (pnt). pnt was required for ISC over-proliferation following Cic depletion, and ectopic pnt restored ISC proliferation even in the presence of overexpressed dominant-active Cic. These studies identify Cic, Pnt, and Ets21C as critical downstream effectors of EGFR signaling in Drosophila ISCs.