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

Targeting amino acid metabolism in cancer

Metabolic rewiring is a characteristic hallmark of cancer cells. This phenomenon sustains uncontrolled proliferation and resistance to apoptosis by increasing nutrients and energy supply. However, reprogramming comes together with vulnerabilities that can be used against tumor and can be applied in targeted therapy. In the last years, the genetic background of tumors has been identified thoroughly and new therapies targeting those mutations tested. Nevertheless, we propose that targeting the phenotype of cancer cells could be another way of treatment aiming to avoid drug resistance and non-responsiveness of cancer patients. Amino acid metabolism is part of the altered processes in cancer cells. Amino acids are building blocks and also sensors of signaling pathways regulating main biological processes. In this comprehensive review, we described four amino acids (asparagine, arginine, methionine, and cysteine) which have been actively investigated as potential targets for anti-tumor therapy. Asparagine depletion is successfully used for decades in the treatment of acute lymphoblastic leukemia and there is a strong implication to apply it to other types of tumors. Arginine auxotrophic tumors are great candidates for arginine-starvation therapy. Higher requirement for essential amino acids such as methionine and cysteine point out promising targetable weaknesses of cancer cells.

Acute hypoxia elevates arginase 2 and induces polyamine stress response in zebrafish via evolutionarily conserved mechanism

Living organisms repeatedly encounter stressful events and apply various strategies to survive. Polyamines are omnipresent bioactive molecules with multiple functions. Their transient synthesis, inducible by numerous stressful stimuli, is termed the polyamine stress response. Animals developed evolutionarily conserved strategies to cope with stresses. The urea cycle is an ancient attribute that deals with ammonia excess in terrestrial species. Remarkably, most fish retain the urea cycle genes fully expressed during the early stages of development and silenced in adult animals. Environmental challenges instigate urea synthesis in fish despite substantial energetic costs, which poses the question of the urea cycle's evolutionary significance. Arginase plays a critical role in oxidative stress-dependent reactions being the final urea cycle enzyme. Its unique subcellular localization, high inducibility, and several regulation levels provide a supreme ability to control the polyamine synthesis rate. Notably, oxidative stress instigates the arginase-1 activity in mammals. Arginase is also dysregulated in aging organisms' brain and muscle tissues, indicating its role in the pathogenesis of age-associated diseases. We designed a study to investigate the levels of the urea cycle and polyamine synthesis-related enzymes in a fish model of acute hypoxia. We evidence synchronized elevation of arginase-2 and ornithine decarboxylase following oxidative stress in adult fish and aging animals signifying the specific function of arginase-2 in fish. Moreover, we demonstrate oxidative stress-associated polyamine synthesis' induction and urea cycle' arrest in adult fish. The subcellular arginase localization found in the fish seems to correspond to its possible evolutionary roles.

Histomorphology of the Malpighian Tubules and the Chemical Composition of the Spherocrystals in the Tubule Epithelial Cells of Adult Leptophyes albovittata (Kollar, 1833) (Orthoptera, Tettigoniidae)

In insects, the number, cytological and histological structures, and the spherocrystals of the Malpighian tubules (MTs) can vary considerably in different insect groups. These differences are considered important because they can be used as taxonomic characters. For this purpose, the ultrastructure of the MT epithelial cells in Leptophyes albovittata (Kollar, 1833) (Orthoptera, Tettigoniidae) was examined by light microscopy, scanning electron microscopy, and transmission electron microscopy. The wall of each tubule consists of a single layer of cells. These cells have round-shaped nuclei. Two different cell types were demonstrated in the tubule cell. These are cells that have electron-dense cytoplasm and electron-lucent cytoplasm. It was observed that the cytoplasm of these cells has many spherocrystals. The chemical composition of the spherocrystals was found to be high in carbon, phosphorus, and manganese in tubule cells.

Alzheimer's disease as a chronic maladaptive polyamine stress response

Polyamines are nitrogen-rich polycationic ubiquitous bioactive molecules with diverse evolutionary-conserved functions. Their activity interferes with numerous genes' expression resulting in cell proliferation and signaling modulation. The intracellular levels of polyamines are precisely controlled by an evolutionary-conserved machinery. Their transient synthesis is induced by heat stress, radiation, and other traumatic stimuli in a process termed the polyamine stress response (PSR). Notably, polyamine levels decline gradually with age; and external supplementation improves lifespan in model organisms. This corresponds to cytoprotective and reactive oxygen species scavenging properties of polyamines. Paradoxically, age-associated neurodegenerative disorders are characterized by upsurge in polyamines levels, indicating polyamine pleiotropic, adaptive, and pathogenic roles. Specifically, arginase overactivation and arginine brain deprivation have been shown to play an important role in Alzheimer's disease (AD) pathogenesis. Here, we assert that a universal short-term PSR associated with acute stimuli is beneficial for survival. However, it becomes detrimental and maladaptive following chronic noxious stimuli, especially in an aging organism. Furthermore, we regard cellular senescence as an adaptive response to stress and suggest that PSR plays a central role in age-related neurodegenerative diseases' pathogenesis. Our perspective on AD proposes an inclusive reassessment of the causal relationships between the classical hallmarks and clinical manifestation. Consequently, we offer a novel treatment strategy predicated upon this view and suggest fine-tuning of arginase activity with natural inhibitors to preclude or halt the development of AD-related dementia.

Adapting Drosophila melanogaster Cell Lines to Serum-Free Culture Conditions

Successful Drosophila cell culture relies on media containing xenogenic components such as fetal bovine serum to support continuous cell proliferation. Here, we report a serum-free culture condition that supports the growth and proliferation of Drosophila S2R+ and Kc167 cell lines. Importantly, the gradual adaptation of S2R+ and Kc167 cells to a media lacking serum was supported by supplementing the media with adult Drosophila soluble extract, commonly known as fly extract. The utility of these adapted cells lines is largely unchanged. The adapted cells exhibited robust proliferative capacity and a transfection efficiency that was comparable to control cells cultured in serum-containing media. Transcriptomic data indicated that the S2R+ cells cultured with fly extract retain their hemocyte-specific transcriptome profile, and there were no global changes in the transcriptional output of cell signaling pathways. Our metabolome studies indicate that there were very limited metabolic changes. In fact, the cells were likely experiencing less oxidative stress when cultured in the serum-free media supplemented with fly extract. Overall, the Drosophila cell culture conditions reported here consequently provide researchers with an alternative and physiologically relevant resource to address cell biological research questions.

Intestinal response to dietary manganese depletion inDrosophila

Metabolic adaptations to manganese deficiency.

Evolutionary compromises to metabolic toxins: Ammonia and urea tolerance in Drosophila suzukii and Drosophila melanogaster

The invasive pest Drosophila suzukii has evolved morphological and behavioural adaptations to lay eggs under the skin of fresh fruits. This results in severe damage to a wide range of small fruits. Drosophila suzukii females typically lay few eggs per fruit, preferring healthy fruits. Hence, larvae are exposed to a reduced amount of nitrogenous waste. Differently, the innocuous Drosophila melanogaster lays eggs on fermented fruits already infested by conspecifics, with larvae developing in a crowded environment with the accumulation of nitrogenous waste such as ammonia and urea. These compounds derive from nitrogen metabolism, protein degradation, and amino acids catabolism and are relatively toxic at high concentrations in an organism. The observed differences in oviposition site and larval ecological niche suggest that these species might differ in behavioural and physiological mechanisms used to cope with nitrogenous waste. We investigated how different concentrations of ammonia and urea affect oviposition and larval development in both species. Females and larvae of D. suzukii showed greater susceptibility to high concentrations of both compounds, with a dramatic decrease in the number of eggs laid and egg viability. Moreover, we tested the chemotactic response of third instar larvae to high concentrations of the compounds. Interestingly, ammonia resulted in a repulsive behaviour in respect of the control and urea groups. To better understand the pathways underlying these differences, we evaluated the effect on ornithine aminotransferase and glutathione-S-transferase, two enzymes involved in nitrogen metabolism and stress response that are expressed during larval development. Both ammonia and urea significantly reduced the expression of these enzymes in D. suzukii compared to D. melanogaster. This shows how the ecological shift of D. suzukii to fresh fruit is accompanied by less efficient detoxifying and excretory mechanisms, with important implications for evolutionary biology and applied research. Our data suggest that the ecological shift of D. suzukii to fresh fruit as oviposition substrate is accompanied by a reduced tolerance to metabolic toxins during larval development.

Biogenesis of zinc storage granules in Drosophila melanogaster

Membrane transporters and sequestration mechanisms concentrate metal ions differentially into discrete subcellular microenvironments for use in protein cofactors, signalling, storage or excretion. Here we identify zinc storage granules as the insect's major zinc reservoir in principal Malpighian tubule epithelial cells of Drosophila melanogaster The concerted action of Adaptor Protein-3, Rab32, HOPS and BLOC complexes as well as of the white-scarlet (ABCG2-like) and ZnT35C (ZnT2/ZnT3/ZnT8-like) transporters is required for zinc storage granule biogenesis. Due to lysosome-related organelle defects caused by mutations in the homologous human genes, patients with Hermansky-Pudlak syndrome may lack zinc granules in beta pancreatic cells, intestinal paneth cells and presynaptic vesicles of hippocampal mossy fibers.

Iron Sulfur and Molybdenum Cofactor Enzymes Regulate the Drosophila Life Cycle by Controlling Cell Metabolism

Iron sulfur (Fe-S) clusters and the molybdenum cofactor (Moco) are present at enzyme sites, where the active metal facilitates electron transfer. Such enzyme systems are soluble in the mitochondrial matrix, cytosol and nucleus, or embedded in the inner mitochondrial membrane, but virtually absent from the cell secretory pathway. They are of ancient evolutionary origin supporting respiration, DNA replication, transcription, translation, the biosynthesis of steroids, heme, catabolism of purines, hydroxylation of xenobiotics, and cellular sulfur metabolism. Here, Fe-S cluster and Moco biosynthesis in Drosophila melanogaster is reviewed and the multiple biochemical and physiological functions of known Fe-S and Moco enzymes are described. We show that RNA interference of Mocs3 disrupts Moco biosynthesis and the circadian clock. Fe-S-dependent mitochondrial respiration is discussed in the context of germ line and somatic development, stem cell differentiation and aging. The subcellular compartmentalization of the Fe-S and Moco assembly machinery components and their connections to iron sensing mechanisms and intermediary metabolism are emphasized. A biochemically active Fe-S core complex of heterologously expressed fly Nfs1, Isd11, IscU, and human frataxin is presented. Based on the recent demonstration that copper displaces the Fe-S cluster of yeast and human ferredoxin, an explanation for why high dietary copper leads to cytoplasmic iron deficiency in flies is proposed. Another proposal that exosomes contribute to the transport of xanthine dehydrogenase from peripheral tissues to the eye pigment cells is put forward, where the Vps16a subunit of the HOPS complex may have a specialized role in concentrating this enzyme within pigment granules. Finally, we formulate a hypothesis that (i) mitochondrial superoxide mobilizes iron from the Fe-S clusters in aconitase and succinate dehydrogenase; (ii) increased iron transiently displaces manganese on superoxide dismutase, which may function as a mitochondrial iron sensor since it is inactivated by iron; (iii) with the Krebs cycle thus disrupted, citrate is exported to the cytosol for fatty acid synthesis, while succinyl-CoA and the iron are used for heme biosynthesis; (iv) as iron is used for heme biosynthesis its concentration in the matrix drops allowing for manganese to reactivate superoxide dismutase and Fe-S cluster biosynthesis to reestablish the Krebs cycle.

Dietary L-arginine accelerates pupation and promotes high protein levels but induces oxidative stress and reduces fecundity and life span in Drosophila melanogaster

L-Arginine, a precursor of many amino acids and of nitric oxide, plays multiple important roles in nutrient metabolism and regulation of physiological functions. In this study, the effects of L-arginine-enriched diets on selected physiological responses and metabolic processes were assessed in Drosophila melanogaster. Dietary L-arginine at concentrations 5-20 mM accelerated larval development and increased body mass, and total protein concentrations in third instar larvae, but did not affect these parameters when diets contained 100 mM arginine. Young (2 days old) adult flies of both sexes reared on food supplemented with 20 and 100 mM L-arginine possessed higher total protein concentrations and lower glucose and triacylglycerol concentrations than controls. Additionally, flies fed 20 mM L-arginine had higher proline and uric acid concentrations. L-Arginine concentration in the diet also affected oxidative stress intensity in adult flies. Food with 20 mM L-arginine promoted lower protein thiol concentrations and higher catalase activity in flies of both sexes and higher concentrations of low molecular mass thiols in males. When flies were fed on a diet with 100 mM L-arginine, lower catalase activities and concentrations of protein thiols were found in both sexes as well as lower low molecular mass thiols in females. L-Arginine-fed males demonstrated higher climbing activity, whereas females showed higher cold tolerance and lower fecundity, compared with controls. Food containing 20 mM L-arginine shortened life span in both males and females. The results suggest that dietary L-arginine shows certain beneficial effects at the larval stage and in young adults. However, the long-term consumption of L-arginine-enriched food had unfavorable effects on D. melanogaster due to decreasing fecundity and life span.

Characterisation of arginase paralogues in salmonids and their modulation by immune stimulation/ infection

In this study we show that four arginase isoforms (arg1a, arg1b, arg2a, arg2b) exist in rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar). We have characterised these molecules in terms of a) sequence analysis, b) constitutive expression in different tissues, and modulated expression following c) stimulation of head kidney macrophages in vitro, or d) vaccination/infection with Yersinia ruckeri and e) parasite infection (AGD caused by Paramoeba perurans and PKD caused by Tetracapsuloides bryosalmonae). Synteny analysis suggested that these arginase genes are paralogues likely from the Ss4R duplication event, and amino acid identity/similarity analyses showed that the proteins are relatively well conserved across species. In rainbow trout constitutive expression of one or both paralogues was seen in most tissues but different constitutive expression patterns were observed for the different isoforms. Stimulation of rainbow trout head kidney macrophages with PAMPs and cytokines also revealed isoform specific responses and kinetics, with arg1a being particularly highly modulated by the PAMPs and pro-inflammatory cytokines. In contrast the type II arginase paralogues were induced by rIl-4/13, albeit to a lesser degree. Vaccination and infection with Y. ruckeri also revealed isoform specific responses, with variation in tissue expression level and kinetics. Lastly, the impact of parasite infection was studied, where down regulation of arg1a and arg1b was seen in two different models (AGD in salmon and PKD in trout) and of arg2a in AGD. The differential responses seen are discussed in the context of markers of type II responses in fish and paralogue subfunctionalization.

Evidence of metabolic microevolution of the limpet Nacella concinna to naturally high heavy metal levels in Antarctica

The gastropod Nacella concinna is the most conspicuous macroinvertebrate of the intertidal zone of the Antarctic Peninsula and adjacent islands. Naturally high levels of copper and cadmium in coastal marine ecosystems are accumulated in N. concinna tissues. We aimed to study the effects of metal cations on N. concinna arginase in the context of possible adaptive microevolution. Gills and muscle had the highest argininolytic activity, which was concentrated in the cytosol in both tissues. Gills had the highest levels of arginase and may be involved in the systemic control of l-arginine levels. The relatively high argininolytic activity of the N. concinna muscular foot, with K_M=25.3±3.4mmolL^-1, may be involved in the control of l-arginine levels during phosphagen breakdown. N. concinna arginases showed the following preferences for metal cations: Ni²⁺>Mn²⁺>Co²⁺>Cu²⁺ in muscle and Mn²⁺>Cu²⁺ in gills. Cu²⁺ activation is a unique characteristic of N. concinna arginases, as copper is a potent arginase inhibitor. Cu²⁺ partly neutralized N. concinna arginase inhibition by Cd²⁺, worked synergistically in muscle arginase activation by Co²⁺ and neutralized muscle arginase activation by Ni²⁺. Mn²⁺ was able to activate muscle arginase in the presence of Fe³⁺ and Pb²⁺. The selection of arginases that are activated by Cu²⁺ and resistant to inhibition by Cd²⁺ in the presence of Cu²⁺ over evolutionary timescales may have favored N. concinna occupation of copper- and cadmium-rich niches.

Evolutionary Aspects of Macrophages Polarization

Macrophages constitute a heterogeneous population of myeloid cells that are essential for maintaining homeostasis and as a first line of innate responders controlling and organizing host defenses against pathogens. Monocyte-macrophage lineage cells are among the most functionally diverse and plastic cells of the immune system. They undergo specific activation into functionally distinct phenotypes in response to immune signals and microbial products. In mammals, macrophage functional heterogeneity is defined by two activation states, M1 and M2, which represent two polar ends of a continuum exhibiting pro-inflammatory and tissue repair activities, respectively. While the ancient evolutionary origin of macrophages as phagocytic defenders is well established, the evolutionary roots of the specialized division of macrophages into subsets with polarized activation phenotypes is less well defined. Accordingly, this chapter focuses on recent advances in the understanding of the evolution of macrophage polarization and functional heterogeneity with a focus on ectothermic vertebrates.

Immune modulation by MANF promotes tissue repair and regenerative success in the retina

Regenerative therapies are limited by unfavorable environments in aging and diseased tissues. A promising strategy to improve success is to balance inflammatory and anti-inflammatory signals and enhance endogenous tissue repair mechanisms. Here, we identified a conserved immune modulatory mechanism that governs the interaction between damaged retinal cells and immune cells to promote tissue repair. In damaged retina of flies and mice, platelet-derived growth factor (PDGF)-like signaling induced mesencephalic astrocyte-derived neurotrophic factor (MANF) in innate immune cells. MANF promoted alternative activation of innate immune cells, enhanced neuroprotection and tissue repair, and improved the success of photoreceptor replacement therapies. Thus, immune modulation is required during tissue repair and regeneration. This approach may improve the efficacy of stem-cell-based regenerative therapies.

Evolutionary roots of arginase expression and regulation

Two main types of macrophage functions are known: classical (M1), producing nitric oxide, NO, and M2, in which arginase activity is primarily expressed. Ornithine, the product of arginase, is a substrate for synthesis of polyamines and collagen, important for growth and ontogeny of animals. M2 macrophages, expressing high level of mitochondrial arginase, have been implicated in promoting cell division and deposition of collagen during ontogeny and wound repair. Arginase expression is the default mode of tissue macrophages, but can also be amplified by signals, such as IL-4/13 or transforming growth factor-β (TGF-β) that accelerates wound healing and tissue repair. In worms, the induction of collagen gene is coupled with induction of immune response genes, both depending on the same TGF-β-like pathway. This suggests that the main function of M2 “heal” type macrophages is originally connected with the TGF-β superfamily of proteins, which are involved in regulation of tissue and organ differentiation in embryogenesis. Excretory–secretory products of metazoan parasites are able to induce M2-type of macrophage responses promoting wound healing without participation of Th2 cytokines IL-4/IL-13. The expression of arginase in lower animals can be induced by the presence of parasite antigens and TGF-β signals leading to collagen synthesis. This also means that the main proteins, which, in primitive metazoans, are involved in regulation of tissue and organ differentiation in embryogenesis are produced by innate immunity. The signaling function of NO is known already from the sponge stage of animal evolution. The cytotoxic role of NO molecule appeared later, as documented in immunity of marine mollusks and some insects. This implies that the M2-wound healing promoting function predates the defensive role of NO, a characteristic of M1 macrophages. Understanding when and how the M1 and M2 activities came to be in animals is useful for understanding how macrophage immunity, and immune responses operate.

Urea synthesis and excretion in Aedes aegypti mosquitoes are regulated by a unique cross-talk mechanism

Aedes aegypti mosquitoes do not have a typical functional urea cycle for ammonia disposal such as the one present in most terrestrial vertebrates. However, they can synthesize urea by two different pathways, argininolysis and uricolysis. We investigated how formation of urea by these two pathways is regulated in females of A. aegypti. The expression of arginase (AR) and urate oxidase (UO), either separately or simultaneously (ARUO) was silenced by RNAi. The amounts of several nitrogen compounds were quantified in excreta using mass spectrometry. Injection of mosquitoes with either dsRNA-AR or dsRNA-UO significantly decreased the expressions of AR or UO in the fat body (FB) and Malpighian tubules (MT). Surprisingly, the expression level of AR was increased when UO was silenced and vice versa, suggesting a cross-talk regulation between pathways. In agreement with these data, the amount of urea measured 48 h after blood feeding remained unchanged in those mosquitoes injected with dsRNA-AR or dsRNA-UO. However, allantoin significantly increased in the excreta of dsRNA-AR-injected females. The knockdown of ARUO mainly led to a decrease in urea and allantoin excretion, and an increase in arginine excretion. In addition, dsRNA-AR-injected mosquitoes treated with a specific nitric oxide synthase inhibitor showed an increase of UO expression in FB and MT and a significant increase in the excretion of nitrogen compounds. Interestingly, both a temporary delay in the digestion of a blood meal and a significant reduction in the expression of several genes involved in ammonia metabolism were observed in dsRNA-AR, UO or ARUO-injected females. These results reveal that urea synthesis and excretion in A. aegypti are tightly regulated by a unique cross-talk signaling mechanism. This process allows blood-fed mosquitoes to regulate the synthesis and/or excretion of nitrogen waste products, and avoid toxic effects that could result from a lethal concentration of ammonia in their tissues.

Candidate innate immune system gene expression in the ecological model Daphnia

The last ten years have witnessed increasing interest in host-pathogen interactions involving invertebrate hosts. The invertebrate innate immune system is now relatively well characterised, but in a limited range of genetic model organisms and under a limited number of conditions. Immune systems have been little studied under real-world scenarios of environmental variation and parasitism. Thus, we have investigated expression of candidate innate immune system genes in the water flea Daphnia, a model organism for ecological genetics, and whose capacity for clonal reproduction facilitates an exceptionally rigorous control of exposure dose or the study of responses at many time points. A unique characteristic of the particular Daphnia clones and pathogen strain combinations used presently is that they have been shown to be involved in specific host-pathogen coevolutionary interactions in the wild. We choose five genes, which are strong candidates to be involved in Daphnia-pathogen interactions, given that they have been shown to code for immune effectors in related organisms. Differential expression of these genes was quantified by qRT-PCR following exposure to the bacterial pathogen Pasteuria ramosa. Constitutive expression levels differed between host genotypes, and some genes appeared to show correlated expression. However, none of the genes appeared to show a major modification of expression level in response to Pasteuria exposure. By applying knowledge from related genetic model organisms (e.g. Drosophila) to models for the study of evolutionary ecology and coevolution (i.e. Daphnia), the candidate gene approach is temptingly efficient. However, our results show that detection of only weak patterns is likely if one chooses target genes for study based on previously identified genome sequences by comparison to homologues from other related organisms. Future work on the Daphnia-Pasteuria system will need to balance a candidate gene approach with more comprehensive approaches to de novo identify immune system genes specific to the Daphnia-Pasteuria interaction.

Identification of two arginases generated by alternative splicing in the silkworm, Bombyx mori

Arginase (EC 3.5.3.1) catalyzes the hydrolysis of arginine to ornithine and urea. Here, we have cloned two arginase cDNAs from the silkworm, Bombyx mori. The analysis of exon/intron structures showed that the two mRNAs named bmarg-r and bmarg-f were generated from a single gene by alternative usage of exons. The bmarg-r and bmarg-f were predicted to encode almost the same amino acid sequences, except that the latter had additional ten N-terminal residues. Recombinant bmARG-r and bmARG-f in Escherichia coli cell lysates were roughly similar to each other in enzymatic characteristics, which did not show large difference from those of arginases assayed by using tissue extracts. Differential RT-PCR experiments and tissue distribution analyses of arginase activity indicated that the bmarg-r gene is expressed in the male reproductive organs, especially in the glandula lacteola and vesicular seminalis, from which it is secreted to the seminal fluid and transferred to the female during copulation, whereas the bmarg-f gene is expressed in the larval and adult nonreproductive organs including the fat body and muscle, where the produced arginase proteins are considered to stay in the cells. Thus, the two silkworm arginase isoforms may have a difference in whether or not the product is excreted out of the cells in which it is synthesized.

Immunity in a variable world

Immune function is likely to be a critical determinant of an organism's fitness, yet most natural animal and plant populations exhibit tremendous genetic variation for immune traits. Accumulating evidence suggests that environmental heterogeneity may retard the long-term efficiency of natural selection and even maintain polymorphism, provided alternative host genotypes are favoured under different environmental conditions. 'Environment' in this context refers to abiotic factors such as ambient temperature or availability of nutrient resources, genetic diversity of pathogens or competing physiological demands on the host. These factors are generally controlled in laboratory experiments measuring immune performance, but variation in them is likely to be very important in the evolution of resistance to infection. Here, we review some of the literature emphasizing the complexity of natural selection on immunity. Our aim is to describe how environmental and genetic heterogeneities, often excluded from experimentation as 'noise', may determine the evolutionary potential of populations or the potential for interacting species to coevolve.

Rapid functional diversification in the structurally conserved ELAV family of neuronal RNA binding proteins

BACKGROUND

The Drosophila gene embryonic lethal abnormal visual system (elav) is the prototype of a gene family present in all metazoans. Its members encode structurally conserved neuronal proteins with three RNA Recognition Motifs (RRM) but they paradoxically act at diverse levels of post-transcriptional regulation. In an attempt to understand the history of this family, we searched for orthologs in eleven completely sequenced genomes, including those of humans, D. melanogaster and C. elegans, for which cDNAs are available.

RESULTS

We analyzed 23 orthologs/paralogs of elav, and found evidence of gain/loss of gene copy number. For one set of genes, including elav itself, the coding sequences are free of introns and their products most resemble ELAV. The remaining genes show remarkable conservation of their exon organization, and their products most resemble FNE and RBP9, proteins encoded by the two elav paralogs of Drosophila. Remarkably, three of the conserved exon junctions are both close to structural elements, involved respectively in protein-RNA interactions and in the regulation of sub-cellular localization, and in the vicinity of diverse sequence variations.

CONCLUSION

The data indicate that the essential elav gene of Drosophila is newly emerged, restricted to dipterans and of retrotransposed origin. We propose that the conserved exon junctions constitute potential sites for sequence/function modifications, and that RRM binding proteins, whose function relies upon plastic RNA-protein interactions, may have played an important role in brain evolution.

Shared RNA-binding sites for interacting members of the Drosophila ELAV family of neuronal proteins

The product of the Drosophila embryonic lethal abnormal visual system is a conserved protein (ELAV) necessary for normal neuronal differentiation and maintenance. It possesses three RNA-binding domains and is involved in the regulation of RNA metabolism. The long elav 3'-untranslated region (3'-UTR) is necessary for autoregulation. We used RNA-binding assays and in vitro selection to identify the ELAV best binding site in the elav 3'-UTR. This site resembles ELAV-binding sites identified previously in heterologous targets, both for its nucleotide sequence and its significant affinity for ELAV (K(d) 40 nM). This finding supports our model that elav autoregulation depends upon direct interaction between ELAV and elav RNA. We narrowed down the best binding site to a 20 nt long sequence A(U5)A(U3)G(U2)A(U6) in an alternative 3' exon. We propose and test a model in which the regulated use of this alternative 3' exon is involved in normal elav regulation. Found in NEurons (FNE), another neuronal RNA-binding protein paralogous to ELAV, also binds this site. These observations provide a molecular basis for the in vivo interactions reported previously between elav and fne.

Proteome of Aedes aegypti larvae in response to infection by the intracellular parasite Vavraia culicis

We report on the modification of the Aedes aegypti larval proteome following infection by the microsporidian parasite Vavraia culicis. Mosquito larvae were sampled at 5 and 15 days of age to compare the effects of infection when the parasite was in two different developmental stages. Modifications of the host proteome due to the stress of infection were distinguished from those of a more general nature by treatments involving hypoxia. We found that the major reaction to stress was the suppression of particular protein spots. Older (15 days) larvae reacted more strongly to infection by V. culicis (46% of the total number of spots affected; 17% for 5 days larvae), while the strongest reaction of younger (5 days) larvae was to hypoxia for pH range 5-8 and to combined effects of infection and hypoxia for pH range 3-6. MALDI-TOF results indicate that proteins induced or suppressed by infection are involved directly or indirectly in defense against microorganisms. Finally, our MALDI-TOF results suggest that A. aegypti larvae try to control or clear V. culicis infection and also that V. culicis probably impairs the immune defense of this host via arginases-NOS competition.

Dogmas and controversies in the handling of nitrogenous wastes: expression of arginase Type I and II genes in rainbow trout: influence of fasting on liver enzyme activity and mRNA levels in juveniles

Through analysis of a cDNA library and third-party annotation of available database sequences, we characterized the full-length coding regions of rainbow trout (Oncorhynchus mykiss) Type I, Onmy-ARG01, and Type II, Onmy-ARG02, arginase genes. Two partial related arginase sequences, Onmy-ARG01b and Onmy-ARG02b, and a full-length zebrafish arginase coding region (Danio rerio), Dare-ARG02, are also reported. Comparison of vertebrate arginase sequences shows that both Type I and Type II genes in bony fishes contain a mitochondrial targeting N-terminal domain. This suggests that the cytosolic Type I arginase found in ureotelic vertebrates arose in the common ancestor of amphibia and mammals. Onmy-ARG01 and Onmy-ARG02 mRNA was detected in liver, kidney, gill, intestine, red muscle and heart tissues. Onmy-ARG01 was expressed at a significantly higher level relative to Onmy-ARG02 in liver and red muscle tissue. To investigate whether there was differential regulation of Onmy-ARG01 and Onmy-ARG02, juvenile trout were fasted for 6 weeks and hepatic enzyme activities and mRNA levels were compared with those of fed control fish. There was a 3-fold increase in liver arginase activity and a 2-fold increase in Onmy-ARG02 mRNA levels but no change in Onmy-ARG01 mRNA levels in fasted fish relative to fed fish. These findings indicate that both types of arginase genes are present and expressed in rainbow trout and that the pattern of expression varies between tissues. The increase in liver arginase activity after a 6-week fast is due, in part, to an increase in the expression of Onmy-ARG02 mRNA levels.

Identification and characterization of human MUS81-MMS4 structure-specific endonuclease

Replication forks may stall when they reach a block on the DNA template such as DNA damage, and the recovery of such stalled replication forks plays a crucial role in the maintenance of genomic stability. Holliday junctions, which are X-shaped DNA structures, are formed at the stalled replication forks and can accumulate if they are not cleaved by structure-specific endonucleases. Recently, a novel nuclease involved in resolving Holliday junction-like structures, Mus81, has been reported in yeast and humans. MUS81 has sequence homology to another DNA nuclease, XPF, which, with its partner ERCC1, makes the 5' incision during nucleotide excision repair. MUS81 also has a binding partner named Mms4 in Saccharomyces cerevisiae and Eme1 in Schizosaccharomyces pombe, but no such partner was identified in human cells. Here, we report identification of the binding partner of human MUS81, which we designate hMMS4. Using immunoaffinity purification we show that hMUS81 or hMMS4 alone have no detectable nuclease activity, but that the hMUS81.hMMS4 complex is a structure-specific nuclease that is capable of resolving fork structures.

found in neurons, a third member of the Drosophila elav gene family, encodes a neuronal protein and interacts with elav

elav, a gene necessary for neuronal differentiation and maintenance in Drosophila, encodes the prototype of a family of conserved proteins involved in post-transcriptional regulation. We identified found in neurons (fne), a gene encoding a new ELAV paralogue. We showed that FNE binds RNA in vitro. fne transcripts are present throughout development and contain long untranslated regions. Transcripts and proteins are restricted to neurons of the CNS and PNS during embryogenesis. These features are reminiscent of elav. However, fne expression is delayed compared to elav's, and FNE protein appears cytoplasmic, while ELAV is nuclear. GAL4-directed overexpression of fne in neurons leads to a reduction of stable transcripts produced from both the fne and elav endogenous loci, suggesting that fne autoregulates and also regulates elav.

Identification and characterization of murine Brunol4, a new member of the elav/bruno family

RNA-binding proteins are involved in post-transcriptional processes like mRNA stabilization, post-transcriptional modification, and transport and have been suggested to play an important role in developmental gene regulation. We report here the cloning and characterization of Brunol4, a novel mouse cDNA closely related to the elav-type family of genes encoding for RNA-binding proteins and a subfamily recently named after the bruno gene of Drosophila. Murine Brunol4 is localized near the centromere of chromosome 18. The cDNA sequence of Brunol4 is separated by 12 introns and the size of Brunol4 may be around 250 kb due to the large size of several introns. Brunol4 expression is detectable in the developing embryo and, later on becomes mainly restricted to cerebral structures, in particular the cerebellum where it persists in the adult organism. We predict a role of Brunol4 and the respective human homologue in differentiation and maintenance of neuronal structures.

Mechanisms of urea tolerance in urea-adapted populations ofDrosophila melanogaster

When behavioral avoidance cannot prevent an animal from being exposed to novel environmental toxins, physiological mechanisms must cope with the toxin and its effects. We are investigating the basis of urea tolerance in populations of Drosophila melanogaster that have been selected to survive and develop in food containing 300mmoll−1 urea. Previous research has demonstrated that the urea-selected larvae have lower levels of urea in their body than control larvae reared under the same conditions. The current series of experiments focuses on three possible ways of reducing urea levels in the body: urea metabolism, increased urea excretion and decreased urea uptake from the environment. We tested for urea metabolism directly, by assaying for activity of two urea-metabolizing enzymes, and indirectly, by looking for reduced urea content of their medium. To measure urea excretion rates in whole animals, we reared control and urea-selected larvae on urea-containing food (urea food), switched them to normal food and monitored the loss of urea from their hemolymph. We measured urea uptake by rearing control and selected larvae on normal food, switching them to urea food and monitoring the rate of urea appearance in the hemolymph. We found no evidence for urea metabolism by either direct or indirect methods. Control larvae excreted urea at a higher rate than selected, probably because they contained more urea than the selected larvae and thus had a greater gradient for urea loss. The rate of urea uptake in selected larvae was 2mmoll−1h−1 slower than the rate in control larvae, a difference that could account for the measured differences in body urea levels. Thus the selected larvae appear to have adapted to urea exposure primarily by decreasing the ability of urea to enter their body in the first place. The mechanism responsible for this reduction in uptake is uncertain.

Characterization of two promoters of the Xenopus laevis elrD gene

The Xenopus laevis elrD gene belongs to the multigenic elav/Hu family. elrD is exclusively expressed in neural cells, where it could be involved in the posttranscriptional control of mRNAs. Here we report the isolation and characterization of the genomic elrD 5'-flanking region. We localized the transcription initiation sites and thus identified two distinct transcripts, elrD1 and elrD2 by 5' RACE PCR. The two transcripts derive from the use of alternative promoters located 915 bp apart. We show that sequences upstream of the elrD1 and elrD2 transcription units can direct expression of the reporter luciferase gene in Xenopus embryos. We also observed length variation of the ELRD first RNA recognition motif (RRM1).