Detecting and quantifying stress granules in tissues of multicellular organisms with the Obj.MPP analysis tool.

Stress granules (SGs) are macromolecular assemblies induced by stress and composed of proteins and mRNAs stalled in translation initiation. SGs play an important role in the response to stress and in the modulation of signaling pathways. Furthermore, these structures are related to the pathological ribonucleoprotein (RNP) aggregates found in neurodegenerative disease contexts, highlighting the need to understand how they are formed and recycled in normal and pathological contexts. Although genetically tractable multicellular organisms have been key in identifying modifiers of RNP aggregate toxicity, in vivo analysis of SG properties and regulation has lagged behind, largely due to the difficulty of detecting SG from images of intact tissues. Here, we describe the object detector software Obj.MPP and show how it overcomes the limits of classical object analyzers to extract the properties of SGs from wide-field and confocal images of Caenorhabditis elegans and Drosophila tissues, respectively. We demonstrate that Obj.MPP enables the identification of genes modulating the assembly of endogenous and pathological SGs, and thus that it will be useful in the context of future genetic screens and in vivo studies.

Neuronal RNP granules: from physiological to pathological assemblies.

Neuronal cells rely on macro- and micro-cellular compartmentalization to rapidly process information, and respond locally to external stimuli. Such a cellular organization is achieved via the assembly of neuronal ribonucleoprotein (RNP) granules, dynamic membrane-less organelles enriched in RNAs and associated regulatory proteins. In this review, we discuss how these high-order structures transport mRNAs to dendrites and axons, and how they contribute to the spatio-temporal regulation of localized mRNA translation. We also highlight how recent biophysical studies have shed light on the mechanisms underlying neuronal RNP granule dynamic assembly, remodeling and maturation, in both physiological and pathological contexts.

Detecting Stress Granules in Drosophila Neurons.

Stress granules (SGs) are cytoplasmic ribonucleoprotein condensates that dynamically and reversibly assemble in response to stress. They are thought to contribute to the adaptive stress response by storing translationally inactive mRNAs as well as signaling molecules. Recent work has shown that SG composition and properties depend on both stress and cell types, and that neurons exhibit a complex SG proteome and a strong vulnerability to mutations in SG proteins. Drosophila has emerged as a powerful genetically tractable organism where to study the physiological regulation and functions of SGs in normal and pathological contexts. In this chapter, we describe a protocol enabling quantitative analysis of SG properties in both larval and adult Drosophila CNS samples. In this protocol, fluorescently tagged SGs are induced upon acute ex vivo stress or chronic in vivo stress, imaged at high-resolution via confocal microscopy and detected automatically, using a dedicated software.

Sumoylation regulates FMRP-mediated dendritic spine elimination and maturation.

Fragile X syndrome (FXS) is the most frequent inherited cause of intellectual disability and the best-studied monogenic cause of autism. FXS results from the functional absence of the fragile X mental retardation protein (FMRP) leading to abnormal pruning and consequently to synaptic communication defects. Here we show that FMRP is a substrate of the small ubiquitin-like modifier (SUMO) pathway in the brain and identify its active SUMO sites. We unravel the functional consequences of FMRP sumoylation in neurons by combining molecular replacement strategy, biochemical reconstitution assays with advanced live-cell imaging. We first demonstrate that FMRP sumoylation is promoted by activation of metabotropic glutamate receptors. We then show that this increase in sumoylation controls the homomerization of FMRP within dendritic mRNA granules which, in turn, regulates spine elimination and maturation. Altogether, our findings reveal the sumoylation of FMRP as a critical activity-dependent regulatory mechanism of FMRP-mediated neuronal function.

Kruppel-like factor 6 (KLF6) affects the promoter activity of the alpha1-proteinase inhibitor gene.

PURPOSE: Keratoconus is a progressive disease that thins and scars the cornea. In keratoconus corneas, levels of degradative enzymes, including lysosomal acid phosphatase (LAP) and cathepsin B, are elevated, and those of inhibitors alpha1-proteinase inhibitor (alpha1-PI) and alpha2-macroglobulin (alpha2-M) are reduced. The present study explored the possible involvement in keratoconus of Krüppel-like factor 6 (KLF6), a transcription factor previously described to be essential for the integrity of the corneal epithelium. The transcript and proteins level of KLF6 and its action in regulating the genes affected in keratoconus were examined in this study. METHODS: Semiquantitative RT-PCR, Western blot analysis, immunofluorescence and in situ hybridization were used to investigate the expression of KLF6 mRNA and protein in normal and keratoconus corneas. Modulation by KLF6 of the promoter activity of alpha1-PI, LAP, cathepsin B, and alpha2-M genes was studied after transient transfection of KLF6 expression plasmid into corneal epithelial cells using promoter-reporter gene assays. Chromatin immunoprecipitation (ChIP) assays were performed to confirm the interactions between KLF6 and promoters of the genes affected in keratoconus. RESULTS: A global increased expression of the transcription factor KLF6 in terms of mRNAs and proteins was observed in total cornea and/or the epithelium in a substantial number of the keratoconus specimens. The promoter activity of the human alpha1-PI gene was suppressed by expression of KLF6 in corneal epithelial cells. The ChIP assay confirmed a physical interaction between KLF6 and the alpha1-PI promoter. CONCLUSIONS: Transcription factor KLF6 downregulates the alpha1-PI gene in corneal epithelial cells and may thereby be involved in keratoconus.

Drosophila melanogaster p-glycoprotein: a membrane detoxification system toward polycyclic aromatic hydrocarbon pollutants.

Polycyclic aromatic hydrocarbons (PAHs) are well-known ubiquitous environmental contaminants. Permeability glycoprotein (P-gp) is a transmembrane detoxification efflux pump transporting various lipophilic xenobiotics, such as PAHs, out of the cells. The existence of a P-gp detoxification system inducible by PAHs was investigated in Drosophila melanogaster. Western blot experiments showed that D. melanogaster expressed a 140-kDa P-gp in S12 cells, embryos, and adult flies. Permeability glycoprotein was expressed in adult flies in the head, abdomen, and thorax and sublocalized in the sexual and olfactory organs. Flow cytometry experiments using Drosophila S12 cells in the presence of PAHs and target P-gp drug compounds revealed that Drosophila P-gp acted as an efflux detoxification pump. In Drosophila exposed to benzo[a]pyrene or to ambient air polluted by higher or lower PAH concentrations, P-gp expression was clearly showed a dose-dependent increase response. The P-gp induction was detected both in adult flies and in different fly parts, such as the head, thorax, and antennae. Drosophila P-gp acts as a membrane barrier against PAH pollutants.

Identification of the Drosophila progenitor of mammalian Krüppel-like factors 6 and 7 and a determinant of fly development.

The Krüppel-like transcription factors (KLFs) represent a family of 15 different zinc finger proteins of the C(2)H(2) type that are involved in vertebrate development and which control cell proliferation, growth and differentiation. Structural-functional considerations have segregated KLF6 and KLF7 into a phylogenetically distinct group. Here we report the identification of Luna, the Drosophila progenitor of the mammalian KLF6/KLF7 group. This conclusion is based on the near sequence identity, as well as the comparable location of the DNA-binding domains and nuclear localization signals of the insect and mammalian proteins. The homology extends to the composition and function of the amino-terminal segment of Luna which, similarly to the mammalian counterparts, stimulates transcription in a reporter gene assay. We also present preliminary in vivo evidence of Luna involvement in embryonic development and cell differentiation. First, luna RNA interference and luna overexpression during early Drosophila embryogenesis leads to developmental arrest at different embryonic stages. Second, targeted perturbation of luna expression in the forming compound eye interferes with terminal cell differentiation, but not cell specification. We therefore propose that Luna is a novel transcriptional determinant of Drosophila development.

Cell and tissue specific expression of human Krüppel-like transcription factors in human ocular surface.

PURPOSE: The ocular surface, composed of the conjunctiva and the cornea, is essential for vision. Its integrity depends on numerous molecular and cellular processes such as proliferation, differentiation, apoptosis, adhesion, and extracellular matrix homeostasis, whose deregulation can induce ophthalmological pathologies. The Krüppel-like transcription factors (KLFs) family is made up of 15 C2H2 zinc-finger proteins involved in vertebrate development and able to control cell proliferation, growth, and differentiation. In order to better define their respective roles in the human ocular surface, we decided to determine their pattern of expression in ocular tissues. We then focused on the expression of KLF4 and some of its target genes to establish KLF4's biological activities in human ocular surface. METHODS: Firstly, total mRNA was extracted from human total cornea, conjunctiva, corneal epithelial cells (primary culture and established cell line), corneal keratocytes (primary culture), corneal endothelial cells (established cell line), and conjunctival epithelial cells (established cell line) and submitted to RT-PCR experiments in order to determine the expression patterns of the different KLFs. Secondly, KLF4 protein localization was visualized by immunofluorescence assays at tissue and cell levels. Finally, KLF4 target genes (endoglin, ornithine decarboxylase) mRNA expression levels were determined by semi-quantitative RT-PCR, after KLF4 transient transfection in human corneal epithelium (HCE) cells. RESULTS: We detected the presence of twelve transcripts of KLFs in the cornea (KLF2, KLF3, KLF4, KLF5, KLF6, KLF7, KLF8, KLF10, KLF11, KLF12, KLF13, and KLF16) and eight in the conjunctiva (KLF2, KLF3, KLF4, KLF6, KLF7, KLF10, KLF11, and KLF12). Under our conditions, the transcripts encoding KLF1 and KLF9 were never detected. Specific expression patterns of each KLF were also determined for the major cellular components of the human cornea and conjunctiva. KLF4 immunolocalization assays indicated its presence in both the cytoplasmic and nuclear compartments of conjunctival and corneal cells. KLF4 transient overexpression in HCE cells down regulated both endoglin and ODC mRNA levels. CONCLUSIONS: For the first time, we established the presence of a KLF network in the human ocular surface and illustrated the conservation of KLF4's biological properties in a corneal derived epithelial cell line.

The ladybird homeobox genes are essential for the specification of a subpopulation of neural cells.

In Drosophila, neurons and glial cells are produced by neural precursor cells called neuroblasts (NBs), which can be individually identified. Each NB generates a characteristic cell lineage specified by a precise spatiotemporal control of gene expression within the NB and its progeny. Here we show that the homeobox genes ladybird early and ladybird late are expressed in subsets of cells deriving from neuroblasts NB 5-3 and NB 5-6 and are essential for their correct development. Our analysis revealed that ladybird in Drosophila, like their vertebrate orthologous Lbx1 genes, play an important role in cell fate specification processes. Among those cells that express ladybird are NB 5-6-derived glial cells. In ladybird loss-of-function mutants, the NB 5-6-derived exit glial cells are absent while overexpression of these genes leads to supernumerary glial cells of this type. Furthermore, aberrant glial cell positioning and aberrant spacing of axonal fascicles in the nerve roots observed in embryos with altered ladybird function suggest that the ladybird genes might also control directed cell movements and cell-cell interactions within the developing Drosophila ventral nerve cord.