Genomic analyses of gas (nitric oxide and carbon monoxide) and small molecule transmitter (acetylcholine, glutamate and GABA) signaling systems in Daphnia pulex

De novo assembly of the freshwater prawn Macrobrachium carcinus brain transcriptome for identification of potential targets for antibody development

Crustaceans are major constituents of aquatic ecosystems and, as such, changes in their behavior and the structure and function of their bodies can serve as indicators of alterations in their immediate environment, such as those associated with climate change and anthropogenic contamination. We have used bioinformatics and a de novo transcriptome assembly approach to identify potential targets for developing specific antibodies to serve as nervous system function markers for freshwater prawns of the Macrobrachium spp. Total RNA was extracted from brain ganglia of Macrobrachium carcinus freshwater prawns and Illumina Next Generation Sequencing was performed using an Eel Pond mRNA Seq Protocol to construct a de novo transcriptome. Sequencing yielded 97,202,662 sequences: 47,630,546 paired and 1,941,570 singletons. Assembly with Trinity resulted in 197,898 assembled contigs from which 30,576 were annotated: 9,600 by orthology, 17,197 by homology, and 3,779 by transcript families. We looked for glutamate receptors contigs, due to their main role in crustacean excitatory neurotransmission, and found 138 contigs related to ionotropic receptors, 32 related to metabotropic receptors, and 18 to unidentified receptors. After performing multiple sequence alignments within different biological organisms and antigenicity analysis, we were able to develop antibodies for prawn AMPA ionotropic glutamate receptor 1, metabotropic glutamate receptor 1 and 4, and ionotropic NMDA glutamate receptor subunit 2B, with the expectation that the availability of these antibodies will help broaden knowledge regarding the underlying structural and functional mechanisms involved in prawn behavioral responses to environmental impacts. The Macrobrachium carcinus brain transcriptome can be an important tool for examining changes in many other nervous system molecules as a function of developmental stages, or in response to particular conditions or treatments.

Characterization of neurotransmitters and related metabolites in Daphnia magna juveniles deficient in serotonin and exposed to neuroactive chemicals that affect its behavior: A targeted LC-MS/MS method

Neurotransmitters are endogenous metabolites that play a crucial role within an organism, at the chemical synapses. There is a growing interest in their analytical determination for understanding the neurotoxic effect of contaminants. Daphnia magna represents an excellent aquatic model for these environmental studies, due to its similarities with vertebrates in several neurotransmitters and related gene pathways and because of its wide application in ecotoxicological studies. Within this study, an accurate and sensible method of analysis of 17 neurotransmitters and related precursors and metabolites was developed. The method was validated in terms of sensitivity, reproducibility, precision, and accuracy, and also matrix effect was evaluated. As an independent probe of method validation and applicability, the method was applied to two different scenarios. First, it was used for the study of neurotransmitter levels in genetically mutated tryptophan hydrolase D. magna clones, confirming the absence of serotonin and its metabolite 5-HIAA. Additionally, the method was applied for determining the effects of chemical compounds known to affect different neurotransmitter systems and to alter Daphnia behavior. Significant changes were observed in 13 of the analyzed neurotransmitters across treatments, which were related to the neurotransmitter systems described as being affected by these neurochemicals. These two studies, which provide results on the ways in which the neurotransmitter systems in D. magna are affected, have corroborated the applicability of the presented method, of great importance due to the suitability of this organism for environmental neurotoxicity studies.

Involvement of glutamate and serotonin transmitter systems in male sex determination in Daphnia pulex

Environmental sex determination occurs in many organisms, however the means by which environmental stimuli are translated into endocrine messages remains poorly understood. The N-methyl-ᴅ-aspartate receptor (NMDAR) was evaluated as a candidate neural sensor of environmental signals linking environmental cues to endocrine responses using the crustacean Daphnia pulex. NMDAR agonists, modulators, and antagonists were evaluated for their ability to impact D. pulex male sex determination during early stages of reproductive maturity under conditions that simulated seasonal change. The antagonists MK-801 and desipramine significantly increased male sex determination. Both chemicals are also modulators of serotonergic and noradrenergic systems, thus, we evaluated several modulators of monoamine neurotransmission in an effort to discern which signaling pathways might contribute to male sex determination. Compounds that altered serotonergic signaling also stimulated male sex determination. The involvement of the glutamate and monoamine signaling in male sex determination was supported by the increase in mRNA levels of related receptors and transporters under conditions that stimulate male sex determination. Further, mRNA levels of components of the terminal endocrine pathway responsible for male sex determination were also elevated under stimulatory conditions. Overall, we provide evidence that glutamatergic and serotonergic systems function upstream of the endocrine regulation of male sex determination in early life stage daphnids.

Identification of putative amine receptor complement in the eyestalk of the crayfish, Procambarus clarkii

In decapod crustaceans, the amines dopamine, octopamine, serotonin, and histamine are known to serve as locally released and/or circulating neuromodulators. While many studies have focused on determining the modulatory actions of amines on decapod nervous systems, comparatively little is known about the identity of the receptors through which they exert their actions. Here, a crayfish, Procambarus clarkii, tissue-specific transcriptome was used to identify putative amine receptors in the eyestalk, a structure composed largely of the eyestalk ganglia, including the neuroendocrine X-organ-sinus gland system, and retina. Transcripts encoding 17 distinct putative amine receptors, three dopamine (one dopamine 1-like, one dopamine 2-like, and one dopamine/ecdysteroid-like), five octopamine (one alpha-like, three beta-like, and one octopamine/tyramine-like), three serotonin (two type-1-like and one type-7-like), and six histamine (five histamine-gated chloride channel A-like and one histamine-gated chloride channel B-like) were identified in the assembly. Comparison of the nucleotide sequence of the transcript encoding one predicted type-1-like serotonin receptor with that cloned previously from the P. clarkii nervous system shows the two sequences to be essentially identical, providing increased support for the validity of the transcripts used to deduce the proteins reported here. Reciprocal BLAST and structural/functional domain analyses support the protein family annotations ascribed to the putative P. clarkii receptors. These data represent the first large-scale description of amine receptors from P. clarkii, and as such provide a new resource for initiating gene-based studies of aminergic control of physiology/behavior at the level of receptors in this species.

Age-dependent survival, stress defense, and AMPK in Daphnia pulex after short-term exposure to a polystyrene nanoplastic

The widespread occurrence and accumulation of micro- and nanoplastics in aquatic environments has become a growing global concern. Generally, natural aquatic populations are characterized by a variety of multi-structured age groups, for which physiological and biochemical responses typically differ. The freshwater cladoceran, Daphnia pulex, is a model species used extensively in environmental monitoring studies and ecotoxicology testing. Here, the effects of a polystyrene nanoplastic on the physiological changes (i.e., survival) and expression levels of stress defense genes (i.e., those encoding antioxidant-mediated and heat shock proteins) in this freshwater flea were measured. Results from acute bioassays were used to determine the respective nanoplastic LC50 values for five age groups (1-, 4-, 7-, 14- and 21-day-old individuals): the obtained values for the 1- and 21-day-old D. pulex groups were similar (i.e., not significantly different). The expression levels of genes encoding key stress defense enzymes and proteins-SOD, CAT, GST, GPx, HSP70, and HSP90-were influenced by the nanoplastic in all the age groups, but not in the same way for each. Significant differences were observed among all age groups in their expression of the gene encoding the energy-sensing enzyme AMPK (adenosine monophosphate-activated protein kinase) α, β, and γ following exposure to the nanoplastic. Moreover, the expression of AMPK α was significantly increased in the 1-, 7-, and 21-day-old individuals exposed to nanoplastic relative to the control group. Together, these results indicate that age in D. pulex affects the sensitivity of its individuals to pollution from this nanoplastic, primarily via alterations to vital physiological and biochemical processes, such as cellular energy homeostasis and oxidation, which were demonstrated in vivo. We speculate that such age-related effects may extend to other nanoplastics and forms of pollution in D. pulex and perhaps similar marine organisms.

Molecular characterization of putative neuropeptide, amine, diffusible gas and small molecule transmitter biosynthetic enzymes in the eyestalk ganglia of the American lobster, Homarus americanus

The American lobster, Homarus americanus, is a model for investigating the neuromodulatory control of physiology and behavior. Prior studies have shown that multiple classes of chemicals serve as locally released/circulating neuromodulators/neurotransmitters in this species. Interestingly, while many neuroactive compounds are known from Homarus, little work has focused on identifying/characterizing the enzymes responsible for their biosynthesis, despite the fact that these enzymes are key components for regulating neuromodulation/neurotransmission. Here, an eyestalk ganglia-specific transcriptome was mined for transcripts encoding enzymes involved in neuropeptide, amine, diffusible gas and small molecule transmitter biosynthesis. Using known Drosophila melanogaster proteins as templates, transcripts encoding putative Homarus homologs of peptide precursor processing (signal peptide peptidase, prohormone processing protease and carboxypeptidase) and immature peptide modifying (glutaminyl cyclase, tyrosylprotein sulfotransferase, protein disulfide isomerase, peptidylglycine-α-hydroxylating monooxygenase and peptidyl-α-hydroxyglycine-α-amidating lyase) enzymes were identified in the eyestalk assembly. Similarly, transcripts encoding full complements of the enzymes responsible for dopamine [tryptophan-phenylalanine hydroxylase (TPH), tyrosine hydroxylase and DOPA decarboxylase (DDC)], octopamine (TPH, tyrosine decarboxylase and tyramine β-hydroxylase), serotonin (TPH or tryptophan hydroxylase and DDC) and histamine (histidine decarboxylase) biosynthesis were identified from the eyestalk ganglia, as were those responsible for the generation of the gases nitric oxide (nitric oxide synthase) and carbon monoxide (heme oxygenase), and the small molecule transmitters acetylcholine (choline acetyltransferase), glutamate (glutaminase) and GABA (glutamic acid decarboxylase). The presence and identity of the transcriptome-derived transcripts were confirmed using RT-PCR. The data presented here provide a foundation for future gene-based studies of neuromodulatory control at the level of neurotransmitter/modulator biosynthesis in Homarus.

Carbon Monoxide Ameliorates 6-Hydroxydopamine-Induced Cell Death in C6 Glioma Cells

Carbon monoxide (CO) is well-known as toxic gas and intrinsic signaling molecule such as neurotransmitter and blood vessel relaxant. Recently, it has been reported that low concentration of CO exerts therapeutic actions under various pathological conditions including liver failure, heart failure, gastric cancer, and cardiac arrest. However, little has been known about the effect of CO in neurodegenerative diseases like Parkinson's disease (PD). To test whether CO could exert a beneficial action during oxidative cell death in PD, we examined the effects of CO on 6-hydroxydopamine (6-OHDA)-induced cell death in C6 glioma cells. Treatment of CO-releasing molecule-2 (CORM-2) significantly attenuated 6-OHDA-induced apoptotic cell death in a dose-dependent manner. CORM-2 treatment decreased Bax/Bcl2 ratio and caspase-3 activity, which had been increased by 6-OHDA. CORM-2 increased phosphorylation of NF-E2-related factor 2 (Nrf2) which is a transcription factor regulating antioxidant proteins. Subsequently, CORM-2 also increased the expression of heme oxygenase-1 and superoxide dismutases (CuZnSOD and MnSOD), which were antioxidant enzymes regulated by Nrf2. These results suggest that CO released by CORM-2 treatment may have protective effects against oxidative cell death in PD through the potentiation of cellular adaptive survival responses via activation of Nrf2 and upregulation of heme oxygenase-1, leading to increasing antioxidant defense capacity.

Diversity of insulin-like peptide signaling system proteins in Calanus finmarchicus (Crustacea; Copepoda) - Possible contributors to seasonal pre-adult diapause

Calanus finmarchicus, an abundant calanoid copepod in the North Atlantic Ocean, is both a major grazer on phytoplankton and an important forage species for invertebrate and vertebrate predators. One component of the life history of C. finmarchicus is the overwintering dormancy of sub-adults, a feature key for the annual recruitment of this species in early spring. While little is known about the control of dormancy in C. finmarchicus, one hypothesis is that it is an insect-like diapause, where the endocrine system is a key regulator. One group of hormones implicated in the control of insect diapause is the insulin-like peptides (ILPs). Here, C. finmarchicus transcriptomic data were used to predict ILP signaling pathway proteins. Four ILP precursors were identified, each possessing a distinct A- and B-chain peptide; these peptides are predicted to form bioactive heterodimers via inter-chain disulfide bridging. Two ILP receptors, which likely represent splice variants of a common gene, were identified. Three insulin-degrading enzymes were also discovered, as were proteins encoding the transcription factor FOXO, a downstream target of ILP that has been implicated in the regulation of insect diapause, and insulin receptor substrate, a protein putatively linking the ILP receptor and FOXO. RNA-Seq data suggest that some C. finmarchicus insulin pathway transcripts are differentially expressed across development. As in insects, the ILP signaling system may be involved in controlling C. finmarchicus' organism-environment interactions (e.g., regulation of seasonal sub-adult diapause), a hypothesis that can now be investigated using these data.

De novo assembly and characterization of central nervous system transcriptome reveals neurotransmitter signaling systems in the rice striped stem borer, Chilo suppressalis

Background

Neurotransmitter signaling systems play crucial roles in multiple physiological and behavioral processes in insects. Genome wide analyses of de novo transcriptome sequencing and gene specific expression profiling provide rich resources for studying neurotransmitter signaling pathways. The rice striped stem borer, Chilo suppressalis is a destructive rice pest in China and other Asian countries. The characterization of genes involved in neurotransmitter biosynthesis and transport could identify potential targets for disruption of the neurochemical communication and for crop protection.

Results

Here we report de novo sequencing of the C. suppressalis central nervous system transcriptome, identification and expression profiles of genes putatively involved in neurotransmitter biosynthesis, packaging, and recycling/degradation. A total of 54,411 unigenes were obtained from the transcriptome analysis. Among these unigenes, we have identified 32 unigenes (31 are full length genes), which encode 21 enzymes and 11 transporters putatively associated with biogenic aminergic signaling, acetylcholinergic signaling, glutamatergic signaling and GABAergic signaling. RT-PCR and qRT-PCR results indicated that 12 enzymes were highly expressed in the central nervous system and all the transporters were expressed at significantly high levels in the central nervous system. In addition, the transcript abundances of enzymes and transporters in the central nervous system were validated by qRT-PCR. The high expression levels of these genes suggest their important roles in the central nervous system.

Conclusions

Our study identified genes potentially involved in neurotransmitter biosynthesis and transport in C. suppressalis and these genes could serve as targets to interfere with neurotransmitter production. This study presents an opportunity for the development of specific and environmentally safe insecticides for pest control.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1742-7) contains supplementary material, which is available to authorized users.

Distinct expression profiles of stress defense and DNA repair genes in Daphnia pulex exposed to cadmium, zinc, and quantum dots

The ever-increasing production and use of nanocrystaline semiconductors (Quantum dots; QDs) will inevitably result in increased appearance of these nanomaterials in the aquatic environment. However, the behavior and potential toxicity of heavy metal constituted nanoparticulates in aquatic invertebrates is largely unknown, especially with regard to molecular responses. The freshwater crustacean Daphnia pulex is a well-suited toxicological and ecological model to study molecular responses to environmental stressors. In this study, D. pulex were exposed for 48 h to sublethal doses of QDs (25% and 50% of LC50) with differing spectral properties (CdTe and CdSe/ZnS QDs) and Cd and Zn salts. Our data suggest that acute exposure to both CdSO4 and Cd-based QDs leads to Cd uptake in vivo, which was biologically supported by the observation of increased expression of metallothionein (MT-1). Furthermore, Cd, Zn, and CdSe/ZnS QDs induced different patterns of gene expression regarding stress defense and DNA repair, which furthers our knowledge regarding which response pathways are affected by nanoparticulate forms of metals versus ionic forms in aquatic crustaceans.

Identification of the molecular components of a Tigriopus californicus (Crustacea, Copepoda) circadian clock

Copepods of the genus Tigriopus have been proposed as marine models for investigations of environmental perturbation. One rapidly increasing anthropogenic stressor for intertidal organisms is light pollution. Given the sensitivity of circadian rhythms to exogenous light, the genes/proteins of a Tigriopus circadian pacemaker represent a potential system for investigating the influences of artificial light sources on circadian behavior in an intertidal species. Here, the molecular components of a putative Tigriopus californicus circadian clock were identified using publicly accessible transcriptome data; the recently deduced circadian proteins of the copepod Calanus finmarchicus were used as a reference. Transcripts encoding homologs of all commonly recognized ancestral arthropod core clock proteins were identified (i.e. CLOCK, CRYPTOCHROME 2, CYCLE, PERIOD and TIMELESS), as were ones encoding proteins likely to modulate the core clock (i.e. CASEIN KINASE II, CLOCKWORK ORANGE, DOUBLETIME, PROTEIN PHOSPHATASE 1, PROTEIN PHOSPHATASE 2A, SHAGGY, SUPERNUMERARY LIMBS and VRILLE) or to act as inputs to it (i.e. CRYPTOCHROME 1). PAR DOMAIN PROTEIN 1 was the only circadian-associated protein not identified in Tigriopus; it appears absent in Calanus too. These data represent just the third full set of molecular components for a crustacean circadian pacemaker (Daphnia pulex and C. finmarchicus previously), and only the second obtained from transcribed sequences (C. finmarchicus previously). Given Tigriopus' proposed status as a model for investigating the influences of anthropogenic stressors in the marine environment, these data provide the first suite of gene/protein targets for understanding how light pollution may influence circadian physiology and behavior in an intertidal organism.

Thrombospondin 1 promotes synaptic formation in bone marrow-derived neuron-like cells

In this study, a combination of growth factors was used to induce bone marrow mesenchymal stem cells differentiation into neuron-like cells, in a broader attempt to observe the role of thrombospondin 1 in synapse formation. Results showed that there was no significant difference in the differentiation rate of neuron-like cells between bone marrow mesenchymal stem cells with thrombospondin induction and those without. However, the cell shape was more complex and the neurites were dendritic, with unipolar, bipolar or multipolar morphologies, after induction with thrombospondin 1. The induced cells were similar in morphology to normal neurites. Immunohistochemical staining showed that the number of positive cells for postsynaptic density protein 95 and synaptophysin 1 protein was significantly increased after induction with thrombospondin 1. These findings indicate that thrombospondin 1 promotes synapse formation in neuron-like cells that are differentiated from bone marrow mesenchymal stem cells.

Diffusible gas transmitter signaling in the copepod crustacean Calanus finmarchicus: identification of the biosynthetic enzymes of nitric oxide (NO), carbon monoxide (CO) and hydrogen sulfide (H2S) using a de novo assembled transcriptome

Neurochemical signaling is a major component of physiological/behavioral control throughout the animal kingdom. Gas transmitters are perhaps the most ancient class of molecules used by nervous systems for chemical communication. Three gases are generally recognized as being produced by neurons: nitric oxide (NO), carbon monoxide (CO) and hydrogen sulfide (H2S). As part of an ongoing effort to identify and characterize the neurochemical signaling systems of the copepod Calanus finmarchicus, the biomass dominant zooplankton in much of the North Atlantic Ocean, we have mined a de novo assembled transcriptome for sequences encoding the neuronal biosynthetic enzymes of these gases, i.e. nitric oxide synthase (NOS), heme oxygenase (HO) and cystathionine β-synthase (CBS), respectively. Using Drosophila proteins as queries, two NOS-, one HO-, and one CBS-encoding transcripts were identified. Reverse BLAST and structural analyses of the deduced proteins suggest that each is a true member of its respective enzyme family. RNA-Seq data collected from embryos, early nauplii, late nauplii, early copepodites, late copepodites and adults revealed the expression of each transcript to be stage specific: one NOS restricted primarily to the embryo and the other was absent in the embryo but expressed in all other stages, no CBS expression in the embryo, but present in all other stages, and HO expressed across all developmental stages. Given the importance of gas transmitters in the regulatory control of a number of physiological processes, these data open opportunities for investigating the roles these proteins play under different life-stage and environmental conditions in this ecologically important species.

Peptidergic signaling in Calanus finmarchicus (Crustacea, Copepoda): in silico identification of putative peptide hormones and their receptors using a de novo assembled transcriptome

The copepod Calanus finmarchicus is the most abundant zooplankton species in the North Atlantic. While the life history of this crustacean is well studied, little is known about its peptidergic signaling systems despite the fact that these pathways are undoubtedly important components of its physiological/behavioral control systems. Here we have generated and used a de novo assembled transcriptome for C. finmarchicus (206,041 sequences in total) to identify peptide precursor proteins and receptors. Using known protein queries, 34 transcripts encoding peptide preprohormones and 18 encoding peptide receptors were identified. Using a combination of online software programs and homology to known arthropod isoforms, 148 mature peptides were predicted from the deduced precursors, including members of the allatostatin-A, allatostatin-B, allatostatin-C, bursicon, crustacean cardioactive peptide (CCAP), crustacean hyperglycemic hormone, diuretic hormone 31 (DH31), diuretic hormone 44 (DH44), FMRFamide-like peptide (myosuppressin, neuropeptide F [NPF] and extended FL/IRFamide subfamilies), leucokinin, neuroparsin, orcokinin, orcomyotropin, periviscerokinin, RYamide and tachykinin-related peptide (TRP) families. The identified receptors included ones for allatostatin-A, allatostatin-C, bursicon, CCAP, DH31, DH44, ecdysis-triggering hormone, NPF, short NPF, FMRFamide, insulin-like peptide, leucokinin, periviscerokinin, pigment dispersing hormone, and TRP. Developmental profiling of the identified transcripts in embryos, early nauplii, late nauplii, early copepodites, late copepodites, and adult females was also undertaken, with all showing the highest expression levels in the naupliar and copepodite stages. Collectively, these data radically expand the catalog of known C. finmarchicus peptidergic signaling proteins and provide a foundation for experiments directed at understanding the physiological roles served by them in this species.

Prediction of the protein components of a putative Calanus finmarchicus (Crustacea, Copepoda) circadian signaling system using a de novo assembled transcriptome

Diel vertical migration and seasonal diapause are critical life history events for the copepod Calanus finmarchicus. While much is known about these behaviors phenomenologically, little is known about their molecular underpinnings. Recent studies in insects suggest that some circadian genes/proteins also contribute to the establishment of seasonal diapause. Thus, it is possible that in Calanus these distinct timing regimes share some genetic components. To begin to address this possibility, we used the well-established Drosophila melanogaster circadian system as a reference for mining clock transcripts from a 200,000+ sequence Calanus transcriptome; the proteins encoded by the identified transcripts were also deduced and characterized. Sequences encoding homologs of the Drosophila core clock proteins CLOCK, CYCLE, PERIOD and TIMELESS were identified, as was one encoding CRYPTOCHROME 2, a core clock protein in ancestral insect systems, but absent in Drosophila. Calanus transcripts encoding proteins known to modulate the Drosophila core clock were also identified and characterized, e.g. CLOCKWORK ORANGE, DOUBLETIME, SHAGGY and VRILLE. Alignment and structural analyses of the deduced Calanus proteins with their Drosophila counterparts revealed extensive sequence conservation, particularly in functional domains. Interestingly, reverse BLAST analyses of these sequences against all arthropod proteins typically revealed non-Drosophila isoforms to be most similar to the Calanus queries. This, in combination with the presence of both CRYPTOCHROME 1 (a clock input pathway protein) and CRYPTOCHROME 2 in Calanus, suggests that the organization of the copepod circadian system is an ancestral one, more similar to that of insects like Danaus plexippus than to that of Drosophila.