Organizational analysis of elav gene and functional analysis of ELAV protein of Drosophila melanogaster and Drosophila virilis

Monitoring cell-cell contacts in vivo in transgenic animals

We used a synthetic genetic system based on ligand-induced intramembrane proteolysis to monitor cell-cell contacts in animals. Upon ligand-receptor interaction in sites of cell-cell contact, the transmembrane domain of an engineered receptor is cleaved by intramembrane proteolysis and releases a protein fragment that regulates transcription in the interacting partners. We demonstrate that the system can be used to regulate gene expression between interacting cells, both in vitro and in vivo, in transgenic Drosophila We show that the system allows for detection of interactions between neurons and glia in the Drosophila nervous system. In addition, we observed that when the ligand is expressed in subsets of neurons with a restricted localization in the brain it leads to activation of transcription in a selected set of glial cells that interact with those neurons. This system will be useful to monitor cell-cell interactions in animals, and can be used to genetically manipulate cells that interact with one another.

The third RNA recognition motif of Drosophila ELAV protein has a role in multimerization

ELAV is a neuron-specific RNA-binding protein in Drosophila that is required for development and maintenance of neurons. ELAV regulates alternative splicing of Neuroglian and erect wing (ewg) transcripts, and has been shown to form a multimeric complex on the last ewg intron. The protein has three RNA recognition motifs (RRM1, 2 and 3) with a hinge region between RRM2 and 3. In this study, we used the yeast two-hybrid system to determine the multimerization domain of ELAV. Using deletion constructs, we mapped an interaction activity to a region containing most of RRM3. We found three conserved short sequences in RRM3 that were essential for the interaction, and also sufficient to give the interaction activity to RRM2 when introduced into it. In our in vivo functional assay, a mutation in one of the three sequences showed reduced activity in splicing regulation, underlining the functional importance of multimerization. However, RRM2 with the three RRM3 interaction sequences did not function as RRM3 in vivo, which suggested that multimerization is not the only function of RRM3. Our results are consistent with a model in which RRM3 serves as a bi-functional domain that interacts with both RNA and protein.

The functions of the multiproduct and rapidly evolving dec-1 eggshell gene are conserved between evolutionarily distant species of Drosophila

The Drosophila dec-1 gene encodes multiple proteins that are required for female fertility and proper eggshell morphogenesis. Genetic and immunolocalization data suggest that the different DEC-1 proteins are functionally distinct. To identify regions within the proteins with potential biological significance, we cloned and sequenced the D. yakuba and D. virilis dec-1 homologs. Interspecies comparisons of the predicted translation products revealed rapidly evolving sequences punctuated by blocks of conserved amino acids. Despite extensive amino acid variability, the proteins produced by the different dec-1 homologs were functionally interchangeable. The introduction of transgenes containing either the D. yakuba or the D. virilis dec-1 open reading frames into a D. melanogaster DEC-1 protein null mutant was sufficient to restore female fertility and wild-type eggshell morphology. Normal expression and extracellular processing of the DEC-1 proteins was correlated with the phenotypic rescue. The nature of the conserved features highlighted by the evolutionary comparison and the molecular resemblance of some of these features to those found in other extracellular proteins suggests functional correlates for some of the multiple DEC-1 derivatives.

Drosophila arginase is produced from a nonvital gene that contains the elav locus within its third intron

A Drosophila gene encoding a 351-amino acid-long predicted arginase (40% identity with vertebrate arginases) is reported. Interestingly, the third intron of the arginase gene includes the elav locus, whose coding sequence is on the complementary DNA strand to that of the arginase. Terrestrial vertebrates produce two arginases from duplicated genes. One form, essentially present in the liver, is a key enzyme of the urea cycle and eliminates excess ammonia through the excretion of urea. The function of the extrahepatic arginase, more ubiquitous, is not well understood. In macrophages, arginase competes with nitric-oxide synthase, which converts arginine into nitric oxide. Most organisms, including insects, produce only one type of arginase, whose function is not centered on ammonia detoxification. A Drosophila cDNA encoding a predicted arginase was isolated. It produces a 1.3-kilobase transcript present with highest levels toward the end of embryogenesis and thereafter. During embryogenesis, the arginase transcripts localize to the fat body. The first mutant allele of the Drosophila arginase gene was identified. It is predicted to produce a 199-amino acid-long C-terminally truncated protein, likely to be inactive. Preliminary characterization of the mutation shows that this recessive allele causes a developmental delay but does not affect viability.

Function of RRM domains of Drosophila melanogaster ELAV: Rnp1 mutations and rrm domain replacements with ELAV family proteins and SXL

Members of the ELAV family of proteins contain three RNA recognition motifs (RRMs), which are highly conserved. ELAV, a Drosophila melanogaster member of this family, provides a vital function and exhibits a predominantly nuclear localization. To investigate if the RNA-binding property of each of the ELAV RRMs is required for ELAV's in vivo function, amino acid residues critical in RNA binding for each RRM were individually mutated. A stringent genetic complementation test revealed that when the mutant protein was the sole source of ELAV, RNA-binding ability of each RRM was essential to ELAV function. To assess the degree to which each domain was specific for ELAV function and which domains perhaps performed a function common to related ELAV proteins, we substituted an ELAV RRM with the corresponding RRM from RBP9, the D. melanogaster protein most homologous to ELAV; HuD, a human ELAV family protein; and SXL, which, although evolutionarily related, is not an ELAV family member. This analysis revealed that RRM3 replacements were fully functional, but RRM1 and RRM2 replacements were largely nonfunctional. Under less stringent conditions RRM1 and RRM2 replacements from SXL and RRM1 replacement from RBP9 were able to provide supplemental function in the presence of a mutant hypomorphic ELAV protein.

Domain necessary for Drosophila ELAV nuclear localization: function requires nuclear ELAV

The neuron specific Drosophila ELAV protein belongs to the ELAV family of RNA binding proteins which are characterized by three highly conserved RNA recognition motifs, an N-terminal domain, and a hinge region between the second and third RNA recognition motifs. Despite their highly conserved RNA recognition motifs the ELAV family members are a group of proteins with diverse posttranscriptional functions including splicing regulation, mRNA stability and translatability and have a variety of subcellular localizations. The role of the ELAV hinge in localization and function was examined using transgenes encoding ELAV hinge deletions, in vivo. Subcellular localization of the hinge mutant proteins revealed that residues between amino acids 333–374 are necessary for nuclear localization. This delineated sequence has no significant homology to classical nuclear localization sequences, but it is similar to the recently characterized nucleocytoplasmic shuttling sequence, the HNS, from a human ELAV family member, HuR. This defined sequence, however, was insufficient for nuclear localization as tested using hinge-GFP fusion proteins. Functional assays revealed that mutant proteins that fail to localize to the nucleus are unable to provide ELAV vital function, but their function is significantly restored when translocated into the nucleus by a heterologous nuclear localization sequence tag.

ETR-1, a homologue of a protein linked to myotonic dystrophy, is essential for muscle development in Caenorhabditis elegans

Post-transcriptional gene processing by RNA-binding proteins (RBPs) has crucial roles during development [1] [2]. Here, we report the identification of ETR-1 (ELAV-type RNA-binding protein), a muscle-specific RBP in the nematode Caenorhabditis elegans. ETR-1 is related to the family of RBPs defined by the protein ELAV, which is essential for neurogenesis in the fruit fly Drosophila; members of the family possess two consecutive RNA recognition motifs (RRMs) separated from a third, carboxy-terminal RRM by a tether region of variable length [3] [4] [5] [6]. Its closest homologue, CUG-binding protein (CUG-bp), is a human RBP that has been implicated in the disease myotonic dystrophy and binds CUG repeats in the 3' untranslated region (UTR) of the mRNA for myotonic dystrophy protein kinase (DMPK) [7] [8]. Inactivation of etr-1 by RNA-mediated interference resulted in embryonic lethality. Embryos failed to elongate and became paralysed, a phenotype characteristic of C. elegans Pat mutants, which are defective in muscle formation and function [9]. The data indicate that etr-1 is essential for muscle development in C. elegans, perhaps by playing a role in post-transcriptional processing of some muscle component, and thus suggesting a possible conservation of gene function with human CUG-bp.

Evidence for 3' untranslated region-dependent autoregulation of the Drosophila gene encoding the neuronal nuclear RNA-binding protein ELAV

The Drosophila locus embryonic lethal abnormal visual system (elav) encodes a nuclear RNA-binding protein essential for normal neuronal differentiation and maintenance of neurons. ELAV is thought to play its role by binding to RNAs produced by other genes necessary for neuronal differentiation and consequently to affect their metabolism by an as yet unknown mechanism. ELAV structural homologues have been identified in a wide range of organisms, including humans, indicating an important conserved role for the protein. Analysis of elav germline transformants presented here shows that one copy of elav minigenes lacking a complete 3' untranslated region (3' UTR) rescues null mutations at elav, but that two copies are lethal. Additional in vivo experiments demonstrate that elav expression is regulated through the 3' UTR of the gene and indicate that this level of regulation is dependent upon ELAV itself. Because ELAV is an RNA-binding protein, the simplest model to account for these findings is that ELAV binds to the 3' UTR of its own RNA to autoregulate its expression. I discuss the implications of these results for normal elav function.

Gene organization and chromosome location of the neural-specific RNA binding protein Elavl4

We have isolated the gene that encodes the neural-specific RNA binding protein HuD in the mouse (Elavl4), and have mapped its location to the mid-distal region of chromosome 4, close to the neurological mutant clasper. The coding region of the Elavl4 gene covers approximately 44 kb; the first two RNA binding domains (RBDs) that are homologous to the two RBDs found in the Drosophila sex-lethal gene are each encoded in two exons, whereas the third RBD is encoded in a single exon. Elavl4 mRNAs are alternatively spliced in the region between RBDs 2 and 3 due to the variable use of two micro-exons, and RNase protection analysis indicates that two of four possible splice variants are the predominant isoforms expressed in the central nervous system. The high degree of sequence conservation between the Hu proteins suggests that the exon organization of all the Hu protein genes will be similar, if not identical, to the Elavl4 gene.

Characterization of a gene encoding a DNA-binding protein that interacts in vitro with vascular specific cis elements of the phenylalanine ammonia-lyase promoter

A study of the expression of a bean phenylalanine ammonia-lyase (PAL) promoter/beta-glucuronidase gene fusion in transgenic tobacco has shown that the PAL2 promoter has a modular organization. Expression of the PAL2 promoter in the vascular system involves positive and negative regulatory cis elements. Among these elements is an AC-rich motif implicated in xylem expression and a suppressing cis element for phloem expression. Using radiolabelled complementary oligonucleotides bearing the AC-rich motif, a cDNA clone encoding a DNA-binding protein has been isolated from a tobacco lambda gt11 expression library. This factor, named AC-rich binding factor (ACBF), showed binding specificity to the AC-rich region. The specificity of ACBF for the AC-rich region was also shown using a gel retardation assay with an ACBF recombinant protein extract. The deduced amino acid sequence from ACBF contains a long repeat of glutamine residues as found in well characterized transcription factors. Interestingly, ACBF shared sequence similarity to conserved amino acid motifs found in RNA-binding proteins. Genomic gel blot analysis indicated the presence of a small gene family of sequences related to ACBF within the tobacco nuclear genome. Analysis of tobacco mRNA using the ACBF cDNA as probe showed that while ACBF mRNA was present in all tissues examined, the highest transcript accumulation occurred in stem tissues. The functional characteristics of the AC-rich sequence were examined in transgenic tobacco. A heptamer of the AC-rich sequence, in front of a minimal 35S promoter from cauliflower mosaic virus (-46 to +4), conferred specific expression in xylem.

Subcellular distribution of Xenopus XEL-1 protein, a member of the neuron-specific ELAV/Hu family, revealed by epitope tagging

Drosophila and vertebrate elav/Hu genes are involved in the development and the maintenance of the nervous system. They all encode proteins that contain three RNA recognition motifs (RRM) and are thus expected to play a role in RNA metabolism. Drosophila ELAV and RBP9 proteins were reported to be exclusively distributed in nuclei of neurons, whereas known human Hu proteins display a bipartite nuclear and cytoplasmic distribution. We have previously isolated a member of this family in Xenopus, Xel-1, that is exclusively expressed in neural tissues from the early tailbud stage onward. In the present study, we report on the subcellular distribution of XEL-1 protein using myc epitope tagging, a strategy allowing the study of a single member of the ELAV/Hu family. We show that the subcellular distribution of exogenous XEL-1 protein in neural tissues depends on developmental stages. In the neural tube at the neurula stage, where endogenous Xel-1 is not expressed, exogenous tagged XEL-1 protein is localized in both the nucleus and the cytoplasm. At the tailbud stage, where endogenous Xel-1 is expressed, exogenous tagged XEL-1 protein is localized essentially in the cytoplasm of neural tube cells. In contrast, exogenous Drosophila ELAV protein localizes to the nucleus at all stages in Xenopus embryos. The variability in the subcellular localization of ELAV/Hu proteins in different species may have functional implications.

ELAV, a Drosophila neuron-specific protein, mediates the generation of an alternatively spliced neural protein isoform

BACKGROUND

Tissue-specific alternative pre-mRNA splicing is a widely used mechanism for gene regulation and the generation of different protein isoforms, but relatively little is known about the factors and mechanisms that mediate this process. Tissue-specific RNA-binding proteins could mediate alternative pre-mRNA splicing. In Drosophila melanogaster, the RNA-binding protein encoded by the elav (embryonic lethal abnormal visual system) gene is a candidate for such a role. The ELAV protein is expressed exclusively in neurons, and is important for the formation and maintenance of the nervous system.

RESULTS

In this study, photoreceptor neurons genetically depleted of ELAV, and elav-null central nervous system neurons, were analyzed immunocytochemically for the expression of neural proteins. In both situations, the lack of ELAV corresponded with a decrease in the immunohistochemical signal of the neural-specific isoform of Neuroglian, which is generated by alternative splicing. Furthermore, when ELAV was expressed ectopically in cells that normally express only the non-neural isoform of Neuroglian, we observed the generation of the neural isoform of Neuroglian.

CONCLUSIONS

Drosophila ELAV promotes the generation of the neuron-specific isoform of Neuroglian by the regulation of pre-mRNA splicing. The findings reported in this paper demonstrate that ELAV is necessary, and the ectopic expression of ELAV in imaginal disc cells is sufficient, to mediate neuron-specific alternative splicing.

Molecular and genetic analyses of lama, an evolutionarily conserved gene expressed in the precursors of the Drosophila first optic ganglion

Drosophila retinal axons trigger both the proliferation of their targets, the lamina neurons, as well as the final differentiation and migration of the lamina glia. To date, the molecular basis of these interactions has remained unclear. We have identified a new gene, lamina ancestor (lama). Both the lamina's neural and glial progenitors express lama, even though these cells have very different developmental origins. Expression of lama is down-regulated once the precursors begin their differentiation programs. Loss of function mutants are viable and fertile, and appear to have normally developed visual systems. lama encodes a novel protein that is 74% identical to its D. virilis homologue.

Two distinct temperature-sensitive alleles at the elav locus of Drosophila are suppressed nonsense mutations of the same tryptophan codon

The Drosophila gene elav encodes a 483-amino-acid-long nuclear RNA binding protein required for normal neuronal differentiation and maintenance. We molecularly analyzed the three known viable alleles of the gene, namely elavts1, elavFliJ1, and elavFliJ2, which manifest temperature-sensitive phenotypes. The modification of the elavFliJ1 allele corresponds to the change of glycine426 (GGA) into a glutamic acid (GAA). Surprisingly, elavts1 and elavFliJ2 were both found to have tryptophan419 (TGG) changed into two different stop codons, TAG and TGA, respectively. Unexpectedly, protein analysis from elavts1 and elavFliJ2 reveals not only the predicted 45-kD truncated ELAV protein due to translational truncation, but also a predominant full-size 50-kD ELAV protein, both at permissive and nonpermissive temperatures. The full-length protein present in elavts1 and elavFliJ2 can a priori be explained by one of several mechanisms leading to functional suppression of the nonsense mutation or by detection of a previously unrecognized ELAV isoform of similar size resulting from alternative splicing and unaffected by the stop codon. Experiments described in this article support the functional suppression of the nonsense mutation as the mechanism responsible for the full-length protein.

Sequence evolution of the Gpdh gene in the Drosophila virilis species group

The nucleotide sequence of the Gpdh gene from six taxa, D. virilis, D. lummei, D. novamexicana, D. a. americana, D. a. texana and D. ezoana, belonging to the virilis species group was determined to examine details of evolutionary change in the structure of the Gpdh gene. The Gpdh gene is comprised of one 5' non-translated region, eight exons, seven introns and three 3' non-translated regions. Exon/intron organization was identical in all the species examined, but different from that of mammals. Interspecific nucleotide divergence in the entire Gpdh gene followed the common pattern: it was low in the exon, high in the intron and intermediate in the non-translated regions. The degree of nucleotide divergence differed within these regions, suggesting that selection exerts constraints differentially on nucleotide change of the Gpdh gene. A phylogenetic tree of the virilis phylad constructed from nucleotide variation of total sequence was consistent with those obtained from other data.

The extra sex combs protein is highly conserved between Drosophila virilis and Drosophila melanogaster

Extra sex combs (esc) is one of the Polycomb Group genes, whose products are required for long term maintenance of the spatially restricted domains of homeotic gene expression initially established by the products of the segmentation genes. We recently showed that the esc protein contains five copies of the WD motif, which in other proteins has been directly implicated in protein-protein interactions. Mutations affecting the WD repeats of the esc protein indicate that they are essential for its function as a repressor of the homeotic genes. We proposed that they may mediate interactions between esc and other Polycomb Group proteins, recruiting them to their target genes, perhaps by additional interactions with transiently expressed repressors such as hunchback. To further investigate the functional importance of the WD motifs and identify other functionally important regions of the esc protein, we have begun to determine its evolutionary conservation by characterizing the esc gene from Drosophila virilis, a distantly related Drosophila species. We show that the esc protein is highly conserved between these species, particularly its WD motifs. Their high degree of conservation, particularly at positions which are not conserved in the WD consensus derived from alignment of all known WD motifs, suggests that each of the WD repeats in the esc protein is functionally specialized and that this specialization has been highly conserved during evolution. Its highly charged N-terminus exhibits the greatest divergence, but even these differences are conservative of its predicted physical properties. These observations suggest that the esc protein is functionally compact, nearly every residue making an important contribution to its function.

Isolation and embryonic expression of Xel-1, a nervous system-specific Xenopus gene related to the elav gene family

We have identified a new member of the elav gene family in Xenopus laevis. This gene, Xel-1, like the other elav-related genes, encodes a putative RNA-binding protein that contains three RNA Recognition Motifs and is solely expressed in the nervous system. Xel-1 is most likely the Xenopus homologue of Hel-N1, one of the three known human genes related to elav. Xel-1 is not expressed in early neural precursors but rather in differentiating neurons of the central nervous system, as well as in the cranial and the spinal ganglion cells. Xel-1 thus appears to be an early differentiation marker for both the central and the peripheral nervous system of Xenopus laevis.

Conservation of brown gene trans-inactivation in Drosophila

The mechanism underlying trans-inactivation associated with dominant position effect variegation (PEV) of the Drosophila melanogaster brown gene has been addressed by a comparison with its D. virilis homologue. This comparison revealed: 86% identity between conceptual translation products of the brown gene from these two species, functional homology, as the D. virilis gene rescues a D. melanogaster null brown mutation, and conservation of the sequences required for trans-inactivation, as the D. virilis gene in D. melanogaster is subject to dominant PEV. An extended region of sequence similarity upstream of the open reading frame is observed. As the D. virilis homologue is functionally interchangeable with the D. melanogaster gene, these genes must share regulatory sequences as well as protein coding homology. These results support a model in which trans-inactivation is mediated by a heterochromatin-sensitive transcription factor.

Gene elav of Drosophila melanogaster: a prototype for neuronal-specific RNA binding protein gene family that is conserved in flies and humans

Regulated gene activity is crucial to the formation and function of the nervous system. It is well known that gene regulation can occur at the transcriptional, post-transcriptional, translational, and post-translational levels. In this review our focus has been on the post-transcriptional regulation in neurons and on neural-specific RNA binding proteins that may be involved in post-transcriptional modulation of gene activity. We have taken advantage of this opportunity to review our work on the elav gene of Drosophila melanogaster which encodes a neural-specific RNA binding protein and relate it to other members of this elav-like gene family. We report new data that suggests that elav is post-transcriptionally regulated and we demonstrate that below-threshold levels of ELAV protein severely affects neuronal differentiation.