Genetic and molecular analysis of the X chromosomal region 14B17-14C4 in Drosophila melanogaster: loss of function in NONA, a nuclear protein common to many cell types, results in specific physiological and behavioral defects

Structure of the heterodimer of human NONO and paraspeckle protein component 1 and analysis of its role in subnuclear body formation

Proteins of the Drosophila behavior/human splicing (DBHS) family include mammalian SFPQ (PSF), NONO (p54nrb), PSPC1, and invertebrate NONA and Hrp65. DBHS proteins are predominately nuclear, and are involved in transcriptional and posttranscriptional gene regulatory functions as well as DNA repair. DBHS proteins influence a wide gamut of biological processes, including the regulation of circadian rhythm, carcinogenesis, and progression of cancer. Additionally, mammalian DBHS proteins associate with the architectural long noncoding RNA NEAT1 (Menε/β) to form paraspeckles, subnuclear bodies that alter gene expression via the nuclear retention of RNA. Here we describe the crystal structure of the heterodimer of the multidomain conserved region of the DBHS proteins, PSPC1 and NONO. These proteins form an extensively intertwined dimer, consistent with the observation that the different DBHS proteins are typically copurified from mammalian cells, and suggesting that they act as obligate heterodimers. The PSPC1/NONO heterodimer has a right-handed antiparallel coiled-coil that positions two of four RNA recognition motif domains in an unprecedented arrangement on either side of a 20-Å channel. This configuration is supported by a protein:protein interaction involving the NONA/paraspeckle domain, which is characteristic of the DBHS family. By examining various mutants and truncations in cell culture, we find that DBHS proteins require an additional antiparallel coiled-coil emanating from either end of the dimer for paraspeckle subnuclear body formation. These results suggest that paraspeckles may potentially form through self-association of DBHS dimers into higher-order structures.

Expression of the apoptosis gene reaper in homeotic, segmentation and other mutants in Drosophila

Apoptosis is an essential process required for development and morphogenesis in metazoan organisms. The apoptosis pathway and cell death machinery have been extensively studied, but little is known how apoptosis genes are regulated in the course of development . In this study, we analyzed the transcriptional regulation of the pro-apoptotic gene reaper (rpr) by performing whole-mount in situ hybridization in embryos mutant for a number of transcription factor genes in Drosophila melanogaster. In sum, our data show that all factors studied have very specific temporal and spatial effects on rpr transcription . Thus, our results reinforce the concept that apoptosis is an essential process for morphogenesis and that apoptosis related genes very tight developmental factors identified in sculpting the morphology of various embryonic structures by modulating the apoptosis pathway.

Multifactorial regulation of a hox target gene

Hox proteins play fundamental roles in controlling morphogenetic diversity along the anterior-posterior body axis of animals by regulating distinct sets of target genes. Within their rather broad expression domains, individual Hox proteins control cell diversification and pattern formation and consequently target gene expression in a highly localized manner, sometimes even only in a single cell. To achieve this high-regulatory specificity, it has been postulated that Hox proteins co-operate with other transcription factors to activate or repress their target genes in a highly context-specific manner in vivo. However, only a few of these factors have been identified. Here, we analyze the regulation of the cell death gene reaper (rpr) by the Hox protein Deformed (Dfd) and suggest that local activation of rpr expression in the anterior part of the maxillary segment is achieved through a combinatorial interaction of Dfd with at least eight functionally diverse transcriptional regulators on a minimal enhancer. It follows that context-dependent combinations of Hox proteins and other transcription factors on small, modular Hox response elements (HREs) could be responsible for the proper spatio-temporal expression of Hox targets. Thus, a large number of transcription factors are likely to be directly involved in Hox target gene regulation in vivo.

Studies on the role of NonA in mRNA biogenesis

The NonA protein of Drosophila melanogaster is an abundant nuclear protein that belongs to the DBHS (Drosophila behavior, human splicing) protein family. The DBHS proteins bind both DNA and RNA in vitro and have been involved in different aspects of gene expression, including pre-mRNA splicing, transcription regulation and nuclear retention of mRNA. We have used double-stranded RNA interference in Drosophila S2 cells to silence the expression of NonA and to investigate its role in mRNA biogenesis. We show that knockdown of NonA does not affect transcription nor splicing. We demonstrate that NonA forms a complex with the essential nuclear export factor NXF1 in an RNA-dependent manner. We have constructed stable S2 cell lines that express full-length and truncated NXF1 fused to GFP in order to perform fluorescence recovery after photobleaching experiments. We show that knockdown of NonA reduces the intranuclear mobility of NXF1-GFP associated with poly(A)(+) RNA in vivo, while the mobility of the truncated NXF1-GFP that does not bind RNA is not affected. Our data suggest that NonA facilitates the intranuclear mobility of mRNP particles.

PERIOD1-associated proteins modulate the negative limb of the mammalian circadian oscillator

The clock proteins PERIOD1 (PER1) and PERIOD2 (PER2) play essential roles in a negative transcriptional feedback loop that generates circadian rhythms in mammalian cells. We identified two PER1-associated factors, NONO and WDR5, that modulate PER activity. The reduction of NONO expression by RNA interference (RNAi) attenuated circadian rhythms in mammalian cells, and fruit flies carrying a hypomorphic allele were nearly arrhythmic. WDR5, a subunit of histone methyltransferase complexes, augmented PER-mediated transcriptional repression, and its reduction by RNAi diminished circadian histone methylations at the promoter of a clock gene.

Phenotypic analysis of separation-of-function alleles of MEI-41, Drosophila ATM/ATR

ATM/ATR kinases act as signal transducers in eukaryotic DNA damage and replication checkpoints. Mutations in ATM/ATR homologs have pleiotropic effects that range from sterility to increased killing by genotoxins in humans, mice, and Drosophila. Here we report the generation of a null allele of mei-41, Drosophila ATM/ATR homolog, and the use of it to document a semidominant effect on a larval mitotic checkpoint and methyl methanesulfonate (MMS) sensitivity. We also tested the role of mei-41 in a recently characterized checkpoint that delays metaphase/anaphase transition after DNA damage in cellular embryos. We then compare five existing mei-41 alleles to the null with respect to known phenotypes (female sterility, cell cycle checkpoints, and MMS resistance). We find that not all phenotypes are affected equally by each allele, i.e., the functions of MEI-41 in ensuring fertility, cell cycle regulation, and resistance to genotoxins are genetically separable. We propose that MEI-41 acts not in a single rigid signal transduction pathway, but in multiple molecular contexts to carry out its many functions. Sequence analysis identified mutations, which, for most alleles, fall in the poorly characterized region outside the kinase domain; this allowed us to tentatively identify additional functional domains of MEI-41 that could be subjected to future structure-function studies of this key molecule.

Courtship and other behaviors affected by a heat-sensitive, molecularly novel mutation in the cacophony calcium-channel gene of Drosophila

The cacophony (cac) locus of Drosophila melanogaster, which encodes a calcium-channel subunit, has been mutated to cause courtship-song defects or abnormal responses to visual stimuli. However, the most recently isolated cac mutant was identified as an enhancer of a comatose mutation's effects on general locomotion. We analyzed the cac(TS2) mutation in terms of its intragenic molecular change and its effects on behaviors more complex than the fly's elementary ability to move. The molecular etiology of this mutation is a nucleotide substitution that causes a proline-to-serine change in a region of the polypeptide near its EF hand. Given that this motif is involved in channel inactivation, it was intriguing that cac(TS2) males generate song pulses containing larger-than-normal numbers of cycles--provided that such males are exposed to an elevated temperature. Similar treatments caused only mild visual-response abnormalities and generic locomotor sluggishness. These results are discussed in the context of calcium-channel functions that subserve certain behaviors and of defects exhibited by the original cacophony mutant. Despite its different kind of amino-acid substitution, compared with that of cac(TS2), cac(S) males sing abnormally in a manner that mimics the new mutant's heat-sensitive song anomaly.

Evolutionary behavioral genetics in Drosophila

Behavioral genes have a special evolutionary interest because they are potentially involved in speciation and in many forms of adaptation. Dozens of loci affecting different aspects of behavior have been already identified and cloned in Drosophila. Some of these genes determine variation in such ethologically complex phenotypes as the male "love song" that is produced during courtship and the locomotor "sleep-wake" activity cycles that are controlled by the circadian clock. Although the evolutionary analysis of most behavioral genes in Drosophila is relatively new, it has already given important insights into the forces shaping the molecular variation at these loci and their functional consequences.

Structures and dynamics of Drosophila Tpr inconsistent with a static, filamentous structure

Here we report immunofluorescence localizations of the Drosophila Tpr protein which are inconsistent with a filament-forming protein statically associated with nuclear pore complex-associated intranuclear filaments. Using tissues from throughout the Drosophila life cycle, we observe that Tpr is often localized to discontinuous, likely granular or particulate structures in the deep nuclear interior. These apparent granules have no obvious connectivity to pore complexes in the nuclear periphery, and are often localized on the surfaces of chromosomes and to the perinucleolar region. Most strikingly, after 1 h of heat shock, the great majority of the Tpr in the deep nuclear interior accumulates at a single heat shock puff, while Tpr in the nuclear periphery appears unchanged. This heat shock puff, 93D, is a known repository for many components of pre-mRNA metabolism during heat shock. Although we do not observe Tpr at sites of transcription under normal conditions, the 93D heat shock result leads us to favor a role for Tpr in mRNA metabolism, such as the transport of mRNA through the nuclear interior to nuclear pore complexes. Consistent with this, we observe networks of Tpr containing granules spanning between the nucleolus and the nuclear periphery which are also decorated by an anti-SR protein antibody. Since we also observe Drosophila Tpr in reticular or fibrous structures in other nuclei, such as salivary gland polytene nuclei, these results indicate that Tpr can exist in at least two structural forms, and suggest that Tpr may relocalize or even change structural forms in response to cellular needs.

The nonA gene in Drosophila conveys species-specific behavioral characteristics

The molecular basis of species-specific differences in courtship behavior, a critical factor in preserving species boundaries, is poorly understood. Genetic analysis of all but the most closely related species is usually impossible, given the inviability of hybrids. We have therefore applied interspecific transformation of a single candidate behavioral locus, no-on-transient A (nonA), between Drosophila virilis and D. melanogaster, to investigate whether nonA, like the period gene, might encode species-specific behavioral information. Mutations in nonA can disrupt both visual behavior and the courtship song in D. melanogaster. The lovesong of nonA(diss) mutant males superficially resembles that of D. virilis, a species that diverged from D. melanogaster 40-60 mya. Transformation of the cloned D. virilis nonA gene into D. melanogaster hosts carrying a synthetic deletion of the nonA locus restored normal visual function (the phenotype most sensitive to nonA mutation). However, the courtship song of transformant males showed several features characteristic of the corresponding D. virilis signal, indicating that nonA can act as a reservoir for species-specific information. This candidate gene approach, together with interspecific transformation, can therefore provide a direct avenue to explore potential speciation genes in genetically and molecularly tractable organisms such as Drosophila.

Molecular characterization of Ct-hrp65: identification of two novel isoforms originated by alternative splicing

Hrp65, a protein with two conserved RNA-binding domains, has been identified in Chironomus tentans as a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. We have cloned two novel hrp65 isoforms and characterized the structure of the hrp65 gene. Comparison of the hrp65 gene to the hrp65 cDNAs revealed that the multiple hrp65 isoforms, hrp65-1, hrp65-2 and hrp65-3, are generated by alternative splicing of a single pre-mRNA. The hrp65-3 mRNA is only detected in C. tentans tissue culture cells of embryonic origin, whereas hrp65-1 and hrp65-2 mRNAs appear to be constitutively expressed. The hrp65 mRNAs are generated by differential 3' splice site selection at the last exon of the gene. Thus, the three hrp65 transcripts contain different 3' UTRs and encode proteins that vary in their C-terminal ends. Interestingly, the variant C-terminal region determines the subcellular localization of the hrp65 proteins. In transient transfection assays, hrp65-1 is efficiently targetted to the nucleus, whereas hrp65-2 and hrp65-3 localize mainly to the cytoplasm. Moreover, hrp65-3 is associated with cytoplasmic actin fibers. All together, our findings suggest that the different hrp65 isoforms serve specialized roles related to mRNA localization/transport in the different cell compartments.

Comparative analysis of the nonA region in Drosophila identifies a highly diverged 5' gene that may constrain nonA promoter evolution

A genomic fragment from Drosophila virilis that contained all the no-on-transientA (nonA) coding information, plus several kilobases of upstream material, was identified. Comparisons of nonA sequences and the gene nonA-like in D. melanogaster, a processed duplication of nonA, suggest that it arose before the split between D. melanogaster and D. virilis. In both species, another gene that lies <350 bp upstream from the nonA transcription starts, and that probably corresponds to the lethal gene l(1)i19, was identified. This gene encodes a protein that shows similarities to GPI1, which is required for the biosynthesis of glycosylphosphatidylinositol (GPI), a component for anchoring eukaryotic proteins to membranes, and so we have named it dGpi1. The molecular evolution of nonA and dGpi1 sequences show remarkable differences, with the latter revealing a level of amino acid divergence that is as high as that of transformer and with extremely low levels of codon bias. Nevertheless, in D. melanogaster hosts, the D. virilis fragment rescues the lethality associated with a mutation of l(1)i19e, as well as the viability and visual defects produced by deletion of nonA(-). The presence of dGpi1 sequences so close to nonA appears to have constrained the evolution of the nonA promoter.

Molecular Dissection of the 5' Region of no-on-transientA of Drosophila melanogaster Reveals cis-Regulation by Adjacent dGpi1 Sequences

The nonA gene of Drosophila melanogaster is important for normal vision, courtship song, and viability and lies approximately 350 bp downstream of the dGpi1 gene. Full rescue of nonA mutant phenotypes can be achieved by transformation with a genomic clone that carries approximately 2 kb of 5' regulatory material and that encodes most of the coding sequence of dGpi1. We have analyzed this 5' region by making a series of deleted fragments, fusing them to yeast GAL4 sequences, and driving UAS-nonA expression in a mutant nonA background. Regions that both silence and enhance developmental tissue-specific expression of nonA and that are necessary for generating optomotor visual responses are identified. Some of these overlap the dGpi1 sequences, revealing cis-regulation by neighboring gene sequences. The largest 5' fragment was unable to rescue the normal electroretinogram (ERG) consistently, and no rescue at all was observed for the courtship song phenotype. We suggest that sequences within the nonA introns that were missing in the UAS-nonA cDNA may carry enhancer elements for these two phenotypes. Finally, we speculate on the striking observation that some of the cis-regulatory regions of nonA appear to be embedded within the coding regions of dGpi1.

The Drosophila genes disconnected and disco-related are redundant with respect to larval head development and accumulation of mRNAs from deformed target genes

HOM-C/hox genes specify body pattern by encoding regionally expressed transcription factors that activate the appropriate target genes necessary for differentiation of each body region. The current model of target gene activation suggests that interactions with cofactors influence DNA-binding ability and target gene activation by the HOM-C/hox proteins. Currently, little is known about the specifics of this process because few target genes and fewer cofactors have been identified. We undertook a deficiency screen in Drosophila melanogaster in an attempt to identify loci potentially encoding cofactors for the protein encoded by the HOM-C gene Deformed (Dfd). We identified a region of the X chromosome that, when absent, leads to loss of specific larval mouthpart structures producing a phenotype similar to that observed in Dfd mutants. The phenotype is correlated with reduced accumulation of mRNAs from Dfd target genes, though there appears to be no effect on Dfd protein accumulation. We show that these defects are due to the loss of two functionally redundant, neighboring genes encoding zinc finger transcription factors, disconnected and a gene we call disco-related. We discuss the role of these genes during differentiation of the gnathal segments and, in light of other recent findings, propose that regionally expressed zinc finger proteins may play a central role with the HOM-C proteins in establishing body pattern.

small wing encodes a phospholipase C-(gamma) that acts as a negative regulator of R7 development in Drosophila

Phospholipase C-(gamma) (PLC-(gamma)) is activated in many cell types following growth factor stimulation. Our understanding of the role of PLC-(gamma) in cell growth and differentiation has been severely limited by the dearth of mutations in any organism. In this study, we show that the Drosophila gene small wing (sl), identified by Bridges in 1915, encodes a PLC-(gamma). Mutations of sl result in extra R7 photoreceptors in the compound eye, consistent with overactivation of the receptor tyrosine kinase pathways that control R7 development. The data presented here provide the first genetic evidence that PLC-(gamma) is involved in Ras-mediated signaling and indicate that PLC-(gamma) acts as a negative regulator in such pathways in Drosophila.

RNA editing in the Drosophila DMCA1A calcium-channel alpha 1 subunit transcript

Messenger RNA editing of transcripts encoding voltage-sensitive ion channels has not been extensively analyzed--least of all in Drosophila, for which several channel-encoding genes are known. Previous sequence studies of D. melanogaster's cacophony gene, which encodes an alpha 1 calcium-channel subunit called Dmca1A, suggested that several nucleotides within the ORF of the primary transcript are edited such that "A-to-G" substitutions occur (these two nucleotides being the adenine that is found at the relevant sites in the sense strand of genomic DNA or the primary transcript, compared to the substitution of guanine that is detected at the level of cDNA analysis). Such A-to-G changes are the same kind of post-transcriptional variations originally discovered--in a neurobiological context--for a ligand-sensitive channel in vertebrates. Here, we extracted RNA from adult flies and revealed, by RT-PCR and restriction-enzyme analyses, that transcript heterogeneity exists in vivo for three distinct edited sites within the cac-encoded RNA. Each such nucleotide would lead to channel variability at the level of the Dmca1A polypeptide. Owing to cacophony being originally identified as a "behavioral gene," the possible significance of Dmca1A RNA editing for influencing the relevant neuro-functional phenotypes is discussed.

Genetic approaches to neuroethology

In neuroethology, the nervous system and behavior are analyzed in the context of the animal's natural habitat and evolutionary history. For the last 30 years the influence of genetics on neuroethology has steadily grown, particularly in Drosophila. Genetic variants reveal new properties of neurons; they help to dissect neuronal circuits and complex behavioral systems; genetics provides new methods to visualize certain brain structures and to assign behavioural functions to them; and, finally, genetic variants can be used to test ecological models. While single-gene mutations can hve highly specific behavioral effects, molecular analysis of the corresponding genes reveals that the latter normally have a much broader functional scope. The 'graininess' of a functional model of the brain, therefore, is defined by the independent regulatory units of the genes rather than by the genes themselves.

Cloning of the Drosophila melanogaster meiotic recombination gene mei-218: a genetic and molecular analysis of interval 15E

The mei-218 gene product is required for both meiotic crossing over and for the production of recombination modules, suggesting that these organelles are required for meiotic exchange. In this study the null phenotype of mei-218 was defined through the analysis of three preexisting and five new alleles. Consistent with previous studies, in homozygous mei-218 mutants meiotic crossing over is reduced to < 10% of normal levels. A molecular analysis of mei-218 was initiated with the isolation and mapping of lethal mutations and genome rearrangements in the region containing mei-218, polytene interval 15E on the X chromosome. This high resolution genetic map was aligned with a physical map constructed from cosmid and P1 clones by genetically mapping restriction fragment length polymorphisms and localizing rearrangement breakpoints. Within a region of 65 kb, we have identified seven transcription units, including mei-218 and the Minute(1)15D gene, which encodes ribosomal protein S5. The mei-218 mutant phenotype has been rescued by germline transformation with both a genomic fragment and a cDNA under the control of the hsp83 promoter. The mei-218 gene is predicted to produce an 1186-amino acid protein that has no significant similarities to any known proteins.

Temporally manipulated rescue of visual and courtship abnormalities caused by a nonA mutation in Drosophila

The no-on-transient-A gene was identified by independently isolated mutations causing visual-response abnormalities or courtship song defects. The nonA(diss) mutant is abnormal for all of these phenotypes. The pleiotropic effects of this dissonance allele dovetail with the widespread tissue expression of the nonA products. This gene, which encodes a putative RNA-binding protein, is expressed at essentially all stages of the life cycle. To determine whether the behavioral and physiological abnormalities exhibited by nonA mutant adults have a developmental etiology or are the result of an impaired mature nervous (or perhaps neuro-muscular) system, a conditional form of this gene was constructed. Animals from the resulting hsp-nonA (cDNA) transgenic strain were subjected to heat-shock regimes such that the gene's coding sequences were activated during development only, solely in the imaginal stage, or both. Surprisingly, expression during any of these time periods effected rescue of the visual-response and the courtship-song defects.

Bioassaying putative RNA-binding motifs in a protein encoded by a gene that influences courtship and visually mediated behavior in Drosophila: in vitro mutagenesis of nonA

The no-on-transient-A (nonA) gene of Drosophila melanogaster influences vision, courtship song, and viability. The nonA-encoded polypeptide is inferred to bind single-stranded nucleic acids. Although sequence-analysis of NONA implies that it belongs to a special interspecific family of this protein type, it does contain two classical RNA recognition motifs (RRM). Their behavioral significance was assayed by generating transgenic strains that were singly or multiply mutated within the relatively N-terminal motif (RRM1) or within RRM2. Neither class of mutation affected NONA binding to polytene chromosomes. The former mutations led to extremely low viability, accompanied by diminished adult longevities that were much worse than for a nonA-null mutant, implying that faulty interpolypeptide interactions might accompany the effects of the amino-acid substitutions within RRM1. All in vitro-mutated types caused optomotor blindness and an absence of transient spikes in the electroretinogram. Courtship analysis discriminated between the effects of the mutations: the RRM2-mutated type generated song pulses and trains that tended to be mildly mutant. These phenotypic abnormalities reinforce the notion that nonA's ubiquitous expression has its most important consequences in the optic lobes, the thoracic ganglia, or both, depending in part on the nonA allele.

The mating of a fly

Courtship in Drosophila is influenced by a wide variety of genes, in that many different kinds of pleiotropic mutations lead to defective courtship. This may seem to be a truism, but the broad temporal and spatial expression of most of the fly's "neuro genes" makes it difficult to exclude elements of such genes' actions as materially underlying reproductive behavior. "Courtship genes" that seem to play more particular roles were originally identified as sensory, learning, or rhythm mutations; their reproductive abnormalities have been especially informative for revealing components of male or female actions that might otherwise have gone unnoticed. Further behavioral mutations seemed originally to be courtship-specific, turned out not to have that property, and have led to a broadened perspective on the nature and action of Drosophila's sex-determination genes.

Behavioral and neurobiological implications of sex-determining factors in Drosophila

The function of the central nervous system as it controls sex-specific behaviors in Drosophila has been studied with renewed intensity, in the context of genetic factors that influence the development of sexually differentiated aspects of this insect. Three categories of genetic variations that cause anomalies in courtship and mating behaviors are discussed: (1) mutants isolated with regard to courtship defects, of which putatively courtship-specific variants such as the fruitless mutant are a subset; (2) general behavioral and neurological variants (including sensory and learning mutants), whose defects include subnormal reproductive performance; and (3) mutations of genes within the sex-determination regulatory hierarchy of Drosophila, the analysis of which has included studies of reproductive behavior. Recent studies of mutations in two of these categories have provided new insights into the control of neuronally based aspects of sex-specific behavior. The doublesex gene, the final factor acting in the sex-determination hierarchy, had been previously thought to regulate all aspects of sexual differentiation. Yet, it has been recently shown that doublesex does not control at least one neuronally-determined feature of sex-specific anatomy--a muscle in the male's abdomen, whose normal development is, however, dependent on the action of fruitless. These considerations prompted us to examine further (and in some cases re-examine) the influences exerted by sex-determination hierarchy genes on behavior. Our results--notably those obtained from assessments of doublesex mutations' effects on general reproductive actions and on a particular component of the courtship sequence (male "singing" behavior)--lead to the suggestion that there is a previously unrecognized branch within the sex-determination hierarchy, which controls the differentiation of the male- and female- specific phenotypes of Drosophila. This new branch separates from the doublesex-related one immediately before the action of that gene (just after transformer and transformer-2) and appears to control as least some aspects of neuronally determined sexual differentiation of males.