Expression analysis of ABC transporters reveals differential functions of tandemly duplicated genes in Caenorhabditis elegans

We have previously identified 60 predicted ABC transporter genes in the Caenorhabditis elegans genome and classified them into eight groups. As an initial step towards understanding how these putative ABC genes work in worms, we generated promoter-fluorescent protein fusions for the entire family to address when and where these genes are turned on in vivo. Both Aequoria green fluorescent protein (GFP) and Discosoma red fluorescent protein (RFP) were used as reporters in our transgenic assay. Observable expression is more frequently seen from fusions to genes in subfamilies B, C, D and E than those in subfamilies A and G. Sixteen worm ABC genes are found in tandem duplications, forming two four-gene clusters and four two-gene clusters. Fifteen out of the 16 duplicated gene promoters drove different or partially overlapping expression patterns, suggesting active functions for these duplicated genes. Furthermore, our results suggest that an internal promoter can cause differential expression of genes within an operon. Finally, our observations suggest that it is possible for coding sequences to function as a regulatory region for a neighbouring gene.     

Expression of in vivo-inducible Salmonella enterica promoters during infection of Caenorhabditis elegans

In vitro mimicking of the stimuli controlling in vivo-inducible bacterial promoters during infection of the host can be complex. Therefore, the use of the nematode Caenorhabditis elegans was evaluated, as a surrogate host to examine the expression of Salmonella enterica promoters. Green fluorescent protein (GFP+) was put under the control of the promoters of the pagC, mgtB, sseA, pgtE and fur genes of S. enterica. After infection of C. elegans with an S. enterica serovar Typhimurium vaccine strain expressing these constructs, clear bacterial expression of GFP+ was observed under the control of all five promoters, although significant expression was not always obtained in vitro. It is concluded that C. elegans constitutes a useful model system for the study of the in vivo expression of Salmonella promoters.     

Efficient and cell specific knock-down of gene function in targeted C. elegans neurons

The nematode C. elegans has become an important model for understanding how genes influence behavior. However, in this organism the available approaches for identifying the neuron(s) where the function of a gene is required for a given behavioral trait are time consuming and restricted to non essential genes for which mutants are available. We describe a simple reverse genetics approach for reducing, in chosen C. elegans neurons, the function of genes. The method is based on the expression, under cell specific promoters, of sense and antisense RNA corresponding to a gene of interest. By targeting the genes osm-10, osm-6 and the Green Fluorescent Protein gene, gfp, we show that this approach leads to efficient, heritable and cell autonomous knock-downs of gene function, even in neurons usually refractory to classic RNA interference (RNAi). By targeting the essential and ubiquitously expressed gene, gpb-1, which encodes a G protein beta subunit, we identify for the first time two distinct sets of neurons in which the function of gpb-1 is required to regulate two distinct behaviors: egg-laying and avoidance of repellents. The cell specific knock-downs obtained with this approach provide information that is complementary to that provided by the cell specific rescue of loss-of-function mutations and represents a useful new tool for dissecting the role that genes play in selected neurons.     

Autophagy genes protect against disease caused by polyglutamine expansion proteins in Caenorhabditis elegans

Expanded polyglutamine (polyQ) proteins aggregate intracellularly in Huntington's disease and other neurodegenerative disorders. The lysosomal degradation pathway, autophagy, is known to promote clearance of polyQ protein aggregates in cultured cells. Moreover, basal autophagy in neuronal cells in mice prevents neurodegeneration by suppressing the accumulation of abnormal intracellular proteins. However, it is not yet known whether autophagy genes play a role in vivo in protecting against disease caused by mutant aggregate-prone, expanded polyQ proteins. To examine this question, we used two models of polyQ-induced toxicity in C. elegans, including the expression of polyQ40 aggregates in muscle and the expression of a human huntingtin disease fragment containing a polyQ tract of 150 residues (Htn-Q150) in ASH sensory neurons. Here, we show that genetic inactivation of autophagy genes accelerates the accumulation of polyQ40 aggregates in C. elegans muscle cells and exacerbates polyQ40-induced muscle dysfunction. Autophagy gene inactivation also increases the accumulation of Htn-Q150 aggregates in C. elegans ASH sensory neurons and results in enhanced neurodegeneration. These data provide in vivo genetic evidence that autophagy genes suppress the accumulation of polyQ aggregates and protect cells from disease caused by polyQ toxicity.     

Fluoxetine-resistance genes in Caenorhabditis elegans function in the intestine and may act in drug transport

Fluoxetine (Prozac) is one of the most widely prescribed pharmaceuticals, yet important aspects of its mechanism of action remain unknown. We previously reported that fluoxetine and related antidepressants induce nose muscle contraction of C. elegans. We also reported the identification and initial characterization of mutations in seven C. elegans genes that cause defects in this response (Nrf, nose resistant to fluoxetine). Here we present genetic evidence that the known nrf genes can be divided into two subgroups that confer sensitivity to fluoxetine-induced nose contraction by distinct pathways. Using both tissue-specific promoters and genetic mosaic analysis, we show that a gene from one of these classes, nrf-6, functions in the intestine to confer fluoxetine sensitivity. Finally, we molecularly identify nrf-5, another gene in the same class. The NRF-5 protein is homologous to a family of secreted lipid-binding proteins with broad ligand specificity. NRF-5 is expressed in the intestine and is likely secreted into the pseudocoelomic fluid, where it could function to transport fluoxetine. One model that explains these findings is that NRF-5 binds fluoxetine and influences its presentation or availability to in vivo targets.     

The divergent orphan nuclear receptor ODR-7 regulates olfactory neuron gene expression via multiple mechanisms in Caenorhabditis elegans

Nuclear receptors regulate numerous critical biological processes. The C. elegans genome is predicted to encode approximately 270 nuclear receptors of which >250 are unique to nematodes. ODR-7 is the only member of this large divergent family whose functions have been defined genetically. ODR-7 is expressed in the AWA olfactory neurons and specifies AWA sensory identity by promoting the expression of AWA-specific signaling genes and repressing the expression of an AWC-specific olfactory receptor gene. To elucidate the molecular mechanisms of action of a divergent nuclear receptor, we have identified residues and domains required for different aspects of ODR-7 function in vivo. ODR-7 utilizes an unexpected diversity of mechanisms to regulate the expression of different sets of target genes. Moreover, these mechanisms are distinct in normal and heterologous cellular contexts. The odr-7 ortholog in the closely related nematode C. briggsae can fully substitute for all ODR-7-mediated functions, indicating conservation of function across 25-120 million years of divergence.