A Drosophila photoreceptor cell-specific protein, calphotin, binds calcium and contains a leucine zipper

Vitamin A deficiency affects gene expression in the Drosophila melanogaster head

Insufficient dietary intake of vitamin A causes various human diseases. For instance, chronic vitamin A deprivation causes blindness, slow growth, impaired immunity, and an increased risk of mortality in children. In contrast to these diverse effects of vitamin A deficiency (VAD) in mammals, chronic VAD in flies neither causes obvious developmental defects nor lethality. As in mammals, VAD in flies severely affects the visual system: it impairs the synthesis of the retinal chromophore, disrupts the formation of the visual pigments (Rhodopsins), and damages the photoreceptors. However, the molecular mechanisms that respond to VAD remain poorly understood. To identify genes and signaling pathways that are affected by VAD, we performed RNA-sequencing and differential gene expression analysis in Drosophila melanogaster. We found an upregulation of genes that are essential for the synthesis of the retinal chromophore, specific aminoacyl-tRNA synthetases, and major nutrient reservoir proteins. We also discovered that VAD affects several genes that are required for the termination of the light response: for instance, we found a downregulation of both arrestin genes that are essential for the inactivation of Rhodopsin. A comparison of the VAD-responsive genes with previously identified blue light stress-responsive genes revealed that the two types of environmental stress trigger largely nonoverlapping transcriptome responses. Yet, both stresses increase the expression of seven genes with poorly understood functions. Taken together, our transcriptome analysis offers insights into the molecular mechanisms that respond to environmental stresses.

Transcriptome profiling of aging Drosophila photoreceptors reveals gene expression trends that correlate with visual senescence

BACKGROUND

Aging is associated with functional decline of neurons and increased incidence of both neurodegenerative and ocular disease. Photoreceptor neurons in Drosophila melanogaster provide a powerful model for studying the molecular changes involved in functional senescence of neurons since decreased visual behavior precedes retinal degeneration. Here, we sought to identify gene expression changes and the genomic features of differentially regulated genes in photoreceptors that contribute to visual senescence.

RESULTS

To identify gene expression changes that could lead to visual senescence, we characterized the aging transcriptome of Drosophila sensory neurons highly enriched for photoreceptors. We profiled the nuclear transcriptome of genetically-labeled photoreceptors over a 40 day time course and identified increased expression of genes involved in stress and DNA damage response, and decreased expression of genes required for neuronal function. We further show that combinations of promoter motifs robustly identify age-regulated genes, suggesting that transcription factors are important in driving expression changes in aging photoreceptors. However, long, highly expressed and heavily spliced genes are also more likely to be downregulated with age, indicating that other mechanisms could contribute to expression changes at these genes. Lastly, we identify that circular RNAs (circRNAs) strongly increase during aging in photoreceptors.

CONCLUSIONS

Overall, we identified changes in gene expression in aging Drosophila photoreceptors that could account for visual senescence. Further, we show that genomic features predict these age-related changes, suggesting potential mechanisms that could be targeted to slow the rate of age-associated visual decline.

Genetic Determinants of RNA Editing Levels of ADAR Targets in Drosophila melanogaster

RNA editing usually affects only a fraction of expressed transcripts and there is a vast amount of variation in editing levels of ADAR (adenosine deaminase, RNA-specific) targets. Here we explore natural genetic variation affecting editing levels of particular sites in 81 natural strains of Drosophila melanogaster. The analysis of associations between editing levels and single-nucleotide polymorphisms allows us to map putative cis-regulatory regions affecting editing of 16 A-to-I editing sites (cis-RNA editing quantitative trait loci or cis-edQTLs, P < 10(-8)). The observed changes in editing levels are validated by independent molecular technique. All identified regulatory variants are located in close proximity of modulated editing sites. Moreover, colocalized editing sites are often regulated by same loci. Similar to expression and splicing QTL studies, the characterization of edQTLs will greatly expand our understanding of cis-regulatory evolution of gene expression.

Fractional Ca(2+) currents through TRP and TRPL channels in Drosophila photoreceptors

Light responses in Drosophila photoreceptors are mediated by two Ca(2+) permeable cation channels, transient receptor potential (TRP) and TRP-like (TRPL). Although Ca(2+) influx via these channels is critical for amplification, inactivation, and light adaptation, the fractional contribution of Ca(2+) to the currents (Pf) has not been measured. We describe a slow (τ ∼ 350 ms) tail current in voltage-clamped light responses and show that it is mediated by electrogenic Na(+)/Ca(2+) exchange. Assuming a 3Na:1Ca stoichiometry, we derive empirical estimates of Pf by comparing the charge integrals of the exchanger and light-induced currents. For TRPL channels, Pf was ∼17% as predicted by Goldman-Hodgkin-Katz (GHK) theory. Pf for TRP (29%) and wild-type flies (26%) was higher, but lower than the GHK prediction (45% and 42%). As predicted by GHK theory, Pf for both channels increased with extracellular [Ca(2+)], and was largely independent of voltage between -100 and -30 mV. A model incorporating intra- and extracellular geometry, ion permeation, diffusion, extrusion, and buffering suggested that the deviation from GHK predictions was largely accounted for by extracellular ionic depletion during the light-induced currents, and the time course of the Na(+)/Ca(2+) exchange current could be used to obtain estimates of cellular Ca(2+) buffering capacities.

Compartmentalization and Ca2+ buffering are essential for prevention of light-induced retinal degeneration

Fly photoreceptors are polarized cells, each of which has an extended interface between its cell body and the light-signaling compartment, the rhabdomere. Upon intense illumination, rhabdomeric calcium concentration reaches millimolar levels that would be toxic if Ca(2+) diffusion between the rhabdomere and cell body was not robustly attenuated. Yet, it is not clear how such effective attenuation is obtained. Here we show that Ca(2+) homeostasis in the photoreceptor cell relies on the protein calphotin. This unique protein functions as an immobile Ca(2+) buffer localized along the base of the rhabdomere, separating the signaling compartment from the cell body. Generation and analyses of transgenic Drosophila strains, in which calphotin-expression levels were reduced in a graded manner, showed that moderately reduced calphotin expression impaired Ca(2+) homeostasis while calphotin elimination resulted in severe light-dependent photoreceptor degeneration. Electron microscopy, electrophysiology, and optical methods revealed that the degeneration was rescued by prevention of Ca(2+) overload via overexpression of CalX, the Na(+)-Ca(2+) exchanger. In addition, Ca(2+)-imaging experiments showed that reduced calphotin levels resulted in abnormally fast kinetics of Ca(2+) elevation in photoreceptor cells. Together, the data suggest that calphotin functions as a Ca(2+) buffer; a possibility that we directly demonstrate by expressing calphotin in a heterologous expression system. We propose that calphotin-mediated compartmentalization and Ca(2+) buffering constitute an effective strategy to protect cells from Ca(2+) overload and light-induced degeneration.

Genomic and functional studies of Drosophila sex hierarchy regulated gene expression in adult head and nervous system tissues

The Drosophila sex determination hierarchy controls all aspects of somatic sexual differentiation, including sex-specific differences in adult morphology and behavior. To gain insight into the molecular-genetic specification of reproductive behaviors and physiology, we identified genes expressed in the adult head and central nervous system that are regulated downstream of sex-specific transcription factors encoded by doublesex (dsx) and fruitless (fru). We used a microarray approach and identified 54 genes regulated downstream of dsx. Furthermore, based on these expression studies we identified new modes of DSX-regulated gene expression. We also identified 90 and 26 genes regulated in the adult head and central nervous system tissues, respectively, downstream of the sex-specific transcription factors encoded by fru. In addition, we present molecular-genetic analyses of two genes identified in our studies, calphotin (cpn) and defective proboscis extension response (dpr), and begin to describe their functional roles in male behaviors. We show that dpr and dpr-expressing cells are required for the proper timing of male courtship behaviors.

The fruit fly Drosophila is an excellent model system to use to understand the molecular-genetic basis of male courtship behavior, as the potential for this behavior is specified by a well-understood genetic regulatory hierarchy, called the sex determination hierarchy. The sex hierarchy consists of a pre-mRNA splicing cascade that culminates in the production of sex-specific transcription factors, encoded by doublesex (dsx) and fruitless (fru). dsx specifies all the anatomical differences between the sexes, and fru is required for all aspects of male courtship behavior. In this study, we measure gene expression differences between males and females, and between sex hierarchy mutants and wild-type animals, to identify genes that underlie the differences between males and females. We have performed these studies on adult head and nervous system tissues, as these tissues are important for establishing the potential for behaviors. We have identified several genes regulated downstream of dsx and fru and more extensively characterized two genes that are more highly expressed in males. One gene regulated downstream of dsx is expressed in the retina and is known to have a function in visual transduction. The other gene, regulated downstream of fru, plays a role in the timing of male courtship behavior.

RNA editing in Drosophila melanogaster: New targets and functional consequences

Adenosine deaminases that act on RNA [adenosine deaminase, RNA specific (ADAR)] catalyze the site-specific conversion of adenosine to inosine in primary mRNA transcripts. These re-coding events affect coding potential, splice sites, and stability of mature mRNAs. ADAR is an essential gene, and studies in mouse, Caenorhabditis elegans, and Drosophila suggest that its primary function is to modify adult behavior by altering signaling components in the nervous system. By comparing the sequence of isogenic cDNAs to genomic DNA, we have identified and experimentally verified 27 new targets of Drosophila ADAR. Our analyses led us to identify new classes of genes whose transcripts are targets of ADAR, including components of the actin cytoskeleton and genes involved in ion homeostasis and signal transduction. Our results indicate that editing in Drosophila increases the diversity of the proteome, and does so in a manner that has direct functional consequences on protein function.

A crustacean Ca2+-binding protein with a glutamate-rich sequence promotes CaCO3 crystallization

The DD4 mRNA of the penaeid prawn Penaeus japonicus was shown previously to be expressed in the epidermis adjacent to the exoskeleton specifically during the post-moult period, when calcification of the exoskeleton took place. The encoded protein possessed a Ca2+-binding site, suggesting its involvement in the calcification of the exoskeleton. In the present study, an additional ORF (open reading frame) of 289 amino acids was identified at the 5' end of the previous ORF. The newly identified part of the encoded protein included a region of approx. 120 amino acids that was highly rich in glutamate residues, and contained one or more Ca2+-binding sites. In an immunohistochemical study, signals were detected within calcified regions in the endocuticular layer of the exoskeleton. Bacterially expressed partial segments of the protein induced CaCO3 crystallization in vitro. Finally, a reverse transcription-PCR study showed that the expression was limited to an early part of the post-moult period, preceding significant calcification of the exoskeleton. These observations argue for the possibility that the encoded protein, renamed crustocalcin (CCN), promotes formation of CaCO3 crystals in the exoskeleton by inducing nucleation.

Calcium homeostasis in fly photoreceptor cells

In fly photoreceptor cells, two processes dominate the Ca2+ homeostasis: light-induced Ca2+ influx through members of the TRP family of ion channels, and Ca2+ extrusion by Na+/Ca2+ exchange. Ca2+ release from intracellular stores is quantitatively insignificant. Both, the light-activated channels and the Ca2+-extruding exchangers are located in or close to the rhabdomeric microvilli, small protrusions of the plasma membrane. The microvilli also contain the molecular machinery necessary for generating quantum bumps, short electrical responses caused by the absorption of a single photon. Due to this anatomical arrangement, the light-induced Ca2+ influx results in two separate Ca2+ signals that have different functions: a global, homogeneous increase of the Ca2+ concentration in the cell body, and rapid but large amplitude Ca2+ transients in the microvilli. The global rise of the Ca2+ concentration mediates light adaptation, via regulatory actions on the phototransduction cascade, the voltage-gated K+ channels and small pigment granules controlling the light intensity. The local Ca2+ transients in the microvilli are responsible for shaping the quantum bumps into fast, all-or-nothing events. They achieve this by facilitating strongly the phototransduction cascade at early stages ofthe light response and subsequently inhibiting it. Many molecular targets of these feedback mechanisms have been identified and characterized due to the availability of numerous Drosophila mutant showing defects in the phototransduction.

Calcium binding to an elastic portion of connectin/titin filaments

Alpha-connectin/titin-1 exists as an elastic filament that links a thick filament with the Z-disk, keeping thick filaments centered within the sarcomere during force generation. We have shown that the connectin filament has an affinity for calcium ions and its binding site(s) is restricted to the beta-connectin/titin-2 portion. We now report the localization and the characterization of calcium-binding sites on beta-connectin. Purified beta-connectin was digested by trypsin into 1700- and 400-kDa fragments. which were then subjected to fluorescence calcium-binding assays. The 400-kDa fragment possesses calcium-binding activity; the binding constant was 1.0 x 10(7) M(-1) and the molar ratio of bound calcium ions to the 400-kDa fragment reached a maximum of 12 at a free calcium ion concentration of approximately 1.0 microM. Antibodies against the 400-kDa fragment formed a sharp dense stripe at the boundary of the A and the I bands, indicating that the calcium-binding domain constitutes the N-terminal region of beta-connectin, that is, the elastic portion of connectin filaments. Furthermore, we estimated the N-terminal location of beta-connectin of various origins (n = 26). Myofibrils were treated with a solution containing 0.1 mM CaCl2 and 70 microM leupeptin to split connectin filaments into beta-connectin and a subfragment, and chain weights of these polypeptides were estimated according to their mobility in 2% polyacrylamide slab gels. The subfragment exhibited a similar chain weight of 1200+/-33 kDa (mean+/-SD), while alpha- and beta-connectins were variable in size according to their origin. These results suggest that the apparent length of the 1200-kDa subfragment portion is almost constant in all instances, about 0.34 microm at the slack condition, therefore that the C-terminus of the 1200-kDa subfragment, that is, the N-terminus of the calcium-binding domain, is at the N2 line region of parent filaments in situ. Because the secondary structure of the 400-kDa fragment was changed by the binding of calcium ions, connectin filaments could be expected to alter their elasticity during the contraction-relaxation cycle of skeletal muscle.

The Drosophila homolog of Onecut homeodomain proteins is a neural-specific transcriptional activator with a potential role in regulating neural differentiation

We report here the characterization of the Drosophila homolog of the onecut homeobox gene, which encodes a protein product with one cut domain and one homeodomain. We present evidence that D-Onecut can bind to similar DNA sequences with high specificity and affinity as other Onecut proteins through the highly conserved cut domain and homeodomain. Interestingly, the cut domain alone can mediate DNA-binding, but the homeodomain cannot. However, depending upon the promoter context, we observed cooperative interactions between the two domains to confer high DNA-binding affinity and specificity. D-Onecut appears to be a moderate transcriptional activator and functions as a nuclear protein in neuronal tissues of both the CNS and PNS during development and in the adult. In the eye, D-Onecut expression is independent of glass, a transcriptional regulator of R cell differentiation. Taken together, our results suggest a role for D-Onecut in the regulation of some aspects of neural differentiation or maintenance. In support of this notion, overexpression of a putative dominant negative form of D-Onecut during eye development does not affect early cell fate specification, but severely affects photoreceptor differentiation.

Molecular cloning of the crustacean DD4 cDNA encoding a Ca(2+)-binding protein

A cDNA, named DD4, was identified in the prawn Penaeus japonicus in a search for genes that were expressed during calcification of the crustacean exoskeleton. DD4 transcripts were detected in the epidermal cells underlying the exoskeleton specifically during the postmolt stage, when the calcification takes place. In the DD4 cDNA an open reading frame of 542 amino acids was found. The deduced protein was acidic and proline-rich, and exhibited similarity to the Drosophila Ca(2+)-binding protein calphotin in the amino acid sequence and composition. The DD4 cDNA was expressed in Escherichia coli to characterize Ca(2+)-binding of the encoded protein, and Ca(2+) was found to bind to a central segment of 186 amino acids. The DD4 protein is suggested to play a role in the calcification of the crustacean exoskeleton.

A hydrophobic peptide (VAP-peptide) of the silkworm, Bombyx mori: structure, expression and an enhancing function of diapause hormone activity

We have recently identified a unique lipophilic peptide (VAP-peptide) with diapause egg inducing activity in the silkworm, Bombyx mori (Imai et al., 1996). The cloning and sequencing of cDNA encoding VAP-peptide have demonstrated that the deduced amino acid sequence consisted of 84 amino acid residues, from which the mature VAP-peptide of 68 amino acid residues was released by cleaving a signal sequence. Searches of the GenBank data base revealed no significant sequence similarity to other proteins including diapause hormone (DH). VAP-peptide gene was selectively expressed just before and at adult eclosion in the head and the thorax not in the abdomen. By a Western blot analysis, VAP-peptide was also localized in the head and the thorax of adults. The purified recombinant VAP-peptide could not induce diapause eggs even when injected at a high dose of 10 nmol/pupa. Whereas, injection of a mixture of VAP-peptide and DH clearly decreased a half-maximum dose (ED50 value) and a threshold dose (TD value) of DH, and these values decreased according to increasing molar ratios of VAP-peptide to DH. Thus, the VAP-peptide is concluded to be an endogenous protein acting as a potent enhancer of DH activity through interaction with DH.

Simian T cell leukemia virus type I from naturally infected feral monkeys from central and west Africa encodes a 91-amino acid p12 (ORF-I) protein as opposed to a 99-amino acid protein encoded by HTLV type I from humans

A single protein of 12 kDa, p12 is encoded by the HTLV-I genome from both the singly spliced mRNA pX-ORF-I and doubly spliced mRNA pX-rex-ORF-I. While many full-length sequences of HTLV-1 are known, data on the p12 regions of African STLV-I are unavailable. We have undertaken to sequence the p12 gene in STLV-I from Central and West Africa naturally infected primates, and have compared them to known p12 sequences of HTLV-I. Our data on sequence and in vitro transcription-translation analyses indicate that p12 is a 91-amino acid (aa) protein among STLV-I strains from Central and West Africa, in contrast to the 99-aa protein found among HTLV-I strains around the globe. The p12 sequences of STLV-I exhibit a marked genetic variability at the level of both nucleotide and peptide sequences. Hydropathic and helical wheel analyses reveal that 60% of residues in HTLV-I p12 are hydrophobic, in contrast to 55% in STLV-I from Africa. Although HTLV-I and STLV-I show a similar putative antigenic site, a second potential site was located exclusively in STLV-I from Africa. There are differences in the predicted transmembrane domains in p12 between STLV-I and HTLV-I. Furthermore, the secondary structure data according to the Chou and Fasman algorithm predict an alpha-helical domain at the carboxy terminus in HTLV-I, and this domain may be truncated in STLV-I p12. The amino acid sequence of p12 shows two leucine zipper motifs (LZMs) at the amino terminus and in the middle region, respectively. This is the first report describing the size differences in p12 protein between HTLV-I and STLV-I, which may provide insights into pathogenic mechanisms used by HTLV-I and STLV-I.

Protein-protein interactions: methods for detection and analysis

The function and activity of a protein are often modulated by other proteins with which it interacts. This review is intended as a practical guide to the analysis of such protein-protein interactions. We discuss biochemical methods such as protein affinity chromatography, affinity blotting, coimmunoprecipitation, and cross-linking; molecular biological methods such as protein probing, the two-hybrid system, and phage display: and genetic methods such as the isolation of extragenic suppressors, synthetic mutants, and unlinked noncomplementing mutants. We next describe how binding affinities can be evaluated by techniques including protein affinity chromatography, sedimentation, gel filtration, fluorescence methods, solid-phase sampling of equilibrium solutions, and surface plasmon resonance. Finally, three examples of well-characterized domains involved in multiple protein-protein interactions are examined. The emphasis of the discussion is on variations in the approaches, concerns in evaluating the results, and advantages and disadvantages of the techniques.

The czc operon of Alcaligenes eutrophus CH34: from resistance mechanism to the removal of heavy metals

The plasmid-borne czc operon ensures for resistance to Cd2+, Zn2+ and Co2+ ions through a tricomponent export pathway and is associated to various conjugative plasmids of A. eutrophus strains isolated from metal-contaminated industrial areas. The czc region of pMOL30 was reassessed especially for the segments located upstream and downstream the structural genes czc CBA. In cultures grown with high concentrations of heavy metals, czc-mediated efflux of cations is followed by a process of metal bioprecipitation. These observations led to the development of bioreactors designed for the removal of heavy metals from polluted effluents.

Calphotin: a Drosophila photoreceptor cell calcium-binding protein

Monoclonal antibody 23E9 identifies a calcium-binding protein, calphotin, in photoreceptor cells of the Drosophila melanogaster compound eyes and ocelli. The antigen is restricted to a defined cytoplasmic region; it is not present in the rhabdomeres, nuclei, mitochondria, or rough endoplasmic reticulum. A corresponding cDNA recognizes a 3-kb mRNA with retinal specificity similar to the antigen and maps to band 86E/F-87A/B on chromosome 3. An open reading frame of 2595 bp encodes an estimated 85-kDa protein of unusual amino acid composition, with > 50% proline, alanine, and valine and very few basic residues. The C-terminal segment contains a leucine zipper motif uninterrupted by prolines. We found no significant similarities with the GenBank or National Biomedical Resource Foundation data bases. The location of the protein within a distinct cytoplasmic region suggests that it might function as a calcium-sequestering "sponge" to regulate the amount of free cytoplasmic calcium.