Development of an efficient RNA interference method by feeding for the microcrustacean Daphnia

Chemical tolerance related to the ABC transporter gene and DNA methylation in cladocera (Daphnia magna)

We performed multigenerational tests to clarify the chemical tolerance mechanisms of a nontarget aquatic organism, Daphnia magna. We continuously exposed D. magna to a carbamate insecticide (pirimicarb) at lethal or sublethal concentrations (0, 3.8, 7.5, and 15 μg/L) for 15 generations (F0-F14). We then determined the 48 h-EC50 values and mRNA expression levels of acetylcholinesterase, glutathione S-transferase, and ATP (Adenosine triphosphate)-binding cassette transporter (ABCt) in neonates (<24 h old) from F0, F4, F9, and F14. To ascertain the effects of DNA methylation on pirimicarb sensitivity, we measured 5-methylcytosine levels (DNA methylation levels) in neonates of parents in the last generation (F14). In addition, we cultured groups exposed to 0 and 7.5 μg/L (the latter of which acquired chemical tolerance to pirimicarb) with or without 5-azacytidine (de-methylating agent) and determined methylation levels and 48 h-EC50 values in neonates (<24 h old) from the treated parents. The EC50 values (30.3-31.6 μg/L) in F14 of the 7.5 and 15 μg/L groups were approximately two times higher than that in the control (16.0 μg/L). A linear mixed model analysis showed that EC50 and ABCt mRNA levels were significantly increased with generational alterations; further analysis showed that the ABCt mRNA level was positively related to the EC50 . Therefore, ABCt may be associated with altered pirimicarb sensitivity. In addition, the EC50 value and DNA methylation levels in pirimicarb-tolerant clones decreased after exposure to 5-azacytidine, suggesting that DNA methylation contributes to chemical tolerance. These findings improved our knowledge regarding the acquisition of chemical tolerance in aquatic organisms.

Cloning and functional analysis of the molting gene CYP302A1 of Daphnia sinensis

BACKGROUND

Molting is an important physiological process in the growth and development of arthropoda, which is mainly regulated by juvenile hormone and ecdysone. CYP302A1 is a key enzyme which plays a critical role in the synthesis of ecdysone in insects, but it has not been identified in cladocera.

RESULTS

The CYP302Al gene of Daphnia sinensis was cloned and its function was analyzed in this paper. The CYP302Al gene of D. sinensis was 5926 bp in full-length, with an open reading frame (ORF) of 1596 bp that encoded 531 amino acids (aa), a molecular weight of 60.82 kDa and an isoelectric point of 9.29. The amino acid sequence analysis revealed that there were five characteristic conserved regions of cytochrome P450 family (namely helix-C, helix-K, helix-I, PERF and heme-binding). In dsRNA mediated experiment, the expression level of CYP302A1 gene decreased significantly (knock-down of 56.22%) in the 5% Escherichia coli concentration treatment. In addition, the expression levels of EcR and USP and HR3 genes in the downstream were also significantly decreased, whereas that of FTZ-f1 gene increased significantly. In the 5% E. coli treatment, the molting time at maturity of D. sinensis prolonged, and the development of embryos in the incubation capsule appeared abnormal or disintegrated. The whole-mount in situ hybridization showed that the CYP302A1 gene of D. sinensis had six expression sites before RNA interference (RNAi), which located in the first antennal ganglion, ovary, cecae, olfactory hair, thoracic limb and tail spine. However, the expression signal of the CYP302A1 gene of D. sinensis disappeared in the first antennal ganglion and obviously attenuated in the ovary after RNAi.

CONCLUSION

The CYP302A1 gene played an important role in the ecdysone synthesis pathway of D. sinensis, and the knock-down of the gene affected the molting and reproduction of D. sinensis.

Protective effects of small heat shock proteins in Daphnia magna against heavy metal exposure

Daphnia magna is one of the most commonly used model organisms to assess toxicity of heavy metal and other xenobiotics. However, the lack of knowledge about important stress-resistant molecules limits our understanding of the alteration of phenotypic and physiological traits of D. magna upon stress exposures. In this study, we focused on a chaperone family of small heat shock protein (sHSP) that has been found in archaea, bacteria and eukaryotes and plays an important role in stress tolerance. A total of eleven sHSP genes (termed DmsHSP1 - DmsHSP11) were identified from the D. magna genome, whose expression profiles during exposure to heavy metal (Cd²⁺, Cu²⁺ and Zn²⁺) and a few other potential pollutants were evaluated via qRT-PCR and RNA-Seq analysis. The results highlighted the predominant role of DmsHSP1 with the highest basal expression level in adults and robust upregulation upon exposure to heavy metals (Cu²⁺ > Cd²⁺ > Zn²⁺). In vivo, recombinant protein rDmsHSP1-21 and rDmsHSP11-12.8 could not only prevent model substrates agglutination induced by heavy metals or reducer dithiotreitol (DTT), but also protect tissue proteins and enzymes from denaturation and inactivation caused by heavy metals or high temperature. Ectopically expression of DmsHSP1-21 or DmsHSP11-12.8 in E. coli conferred host enhanced resistance against various abiotic stresses including Cd²⁺, Cu²⁺ and phenazine methosulfate (PMS). Knockdown of DmsHSP1-21 by RNAi, but not for DmsHSP11-12.8, significantly increased the vulnerability of D. magna to heavy metal exposure. Our work provides systematic information on the evolution and function of sHSPs in D. magna and leads to important insights into the mechanisms by which D. magna survive in adverse environments.

Daphnia as a versatile model system in ecology and evolution

Water fleas of the genus Daphnia have been a model system for hundreds of years and is among the best studied ecological model organisms to date. Daphnia are planktonic crustaceans with a cyclic parthenogenetic life-cycle. They have a nearly worldwide distribution, inhabiting standing fresh- and brackish water bodies, from small temporary pools to large lakes. Their predominantly asexual reproduction allows for the study of phenotypes excluding genetic variation, enabling us to separate genetic from non-genetic effects. Daphnia are often used in studies related to ecotoxicology, predator-induced defence, host–parasite interactions, phenotypic plasticity and, increasingly, in evolutionary genomics. The most commonly studied species are Daphnia magna and D. pulex, for which a rapidly increasing number of genetic and genomic tools are available. Here, I review current research topics, where the Daphnia model system plays a critical role.

Potential differences in chitin synthesis ability cause different sensitivities to diflubenzuron among three strains of Daphnia magna

Ecotoxicity testing of crustaceans using Daphnia magna has been implemented in the chemical management systems of various countries. While the chemical sensitivity of D. magna varies depending on genetically different clonal lineages, the strain used in ecotoxicity tests, including the acute immobilization test (OECD TG202), has not been specified. We hypothesized that comprehensive gene expression profiles could provide useful information on phenotypic differences among strains, including chemical sensitivity. To test this hypothesis, we performed mRNA sequencing on three different strains (NIES, England, and Clone 5) of D. magna under culture conditions. The resulting expression profile of the NIES strain was clearly different compared to the profiles of the other two strains. Gene ontology (GO) enrichment analysis suggested that chitin metabolism was significantly enriched in the NIES strain compared to that in the England strain. Consistent with the GO analysis, evidence of high levels of chitin metabolism in the NIES strain were observed across multiple levels of biological organization, such as expression of chitin synthase genes, chitin content, and chitinase activity, which suggested that the different strains would exhibit different sensitivities to chemicals used to inhibit chitin synthesis. We found that among all strains, the NIES strain was more tolerant to diflubenzuron, a chitin synthesis inhibitor, with a 14-fold difference in the 48 h-EC₅₀ value for the acute immobilization test compared to the England strain. The present study demonstrates that the differences among strains in chitin metabolism may lead to sensitivity difference to diflubenzuron, and serves as a case study of the usefulness of comprehensive gene expression profiles in finding sensitivity differences.

RNA Interference by Ingested Dsrna-Expressing Bacteria to Study Porphyrin Pigmentation in Crassostrea gigas

Porphyrins are a widespread group of pigments in nature which are believed to contribute to shell colors in mollusks. Previous studies have provided candidate genes for porphyrin shell coloration, however, the linkage analysis between functional genes and porphyrin pigmentation remains unclear in mollusks. RNA interference is a powerful molecular tool for analyzing the loss of functions of genes in vivo and alter gene expression. In this study, we used unicellular alga Platymonas subcordiformis and Nitzschia closterium f. minutissima as vectors to feed oysters with Escherichia coli strain HT115 engineered to express double-stranded RNAs targeting specific genes involved in porphyrin synthesis. A strain of Crassostrea gigas with orange shell was used to target key haem pathway genes expression using the aforementioned approach. We show here that feeding the oysters with E. coli, containing dsRNA targeting pigmentation genes, can cause changes in the color of the newly deposited shell. For example, the RNAi knockdown of CgALAS and CgPBGD resulted in the loss of uroporphyrin pigmentation from the shell due to the accumulation of the pigment in the oyster's mantle. The study probed the crucial role of ALAS and PBGD genes potential functions of uroporphyrin production and shell color pigmentation in C. gigas.

De novo transcriptome assembly of the green alga Ankistrodesmus falcatus

Ankistrodesmus falcatus is a globally distributed freshwater chlorophyte that is a candidate for biofuel production, is used to study the effects of toxins on aquatic communities, and is used as food in zooplankton research. Each of these research fields is transitioning to genomic tools. We created a reference transcriptome for of A. falcatus using NextGen sequencing and de novo assembly methods including Trinity, Velvet-Oases, and EvidentialGene. The assembled transcriptome has a total of 17,997 contigs, an N50 value of 2,462, and a GC content of 64.8%. BUSCO analysis recovered 83.3% of total chlorophyte BUSCOs and 82.5% of the eukaryotic BUSCOs. A portion (7.9%) of these supposedly single-copy genes were found to have transcriptionally active, distinct duplicates. We annotated the assembly using the dammit annotation pipeline, resulting in putative functional annotation for 68.89% of the assembly. Using available rbcL sequences from 16 strains (10 species) of Ankistrodesmus, we constructed a neighbor-joining phylogeny to illustrate genetic distances of our A. falcatus strain to other members of the genus. This assembly will be valuable for researchers seeking to identify Ankistrodesmus sequences in metatranscriptomic and metagenomic field studies and in experiments where separating expression responses of zooplankton and their algal food sources through bioinformatics is important.

Expression and functional analysis of the Akt gene from Daphnia pulex

Daphnia pulex is a nutrient-rich freshwater crustacean with two different reproduction methods. Akt is a serine/threonine protein kinase that plays an important role in cell growth, survival, and lifespan regulation. To explore the function of Akt in the growth and aging process of Daphnia pulex, we cloned the cDNA sequence of the open reading frame (ORF) of the akt gene based on the bioinformatic analysis of the transcriptome data of D. pulex, and analyzed the structural features of the Akt protein. Gene silencing was performed using RNA interference (RNAi), and the expression of the Akt gene and protein before and after interference were analyzed using qPCR and western blotting. The results showed that the expression of akt in D. pulex at different ages showed a "W" pattern, being significantly higher at 20 days than at 10 days and 15 days (P < .05). The expression trend of Akt protein and mRNA were similar, with lower expression at a younger age (1-5 day), after which expression gradually increased from 10 days age, and showed no significant change after 25 days, which might be caused by a lag of protein translation. RNAi reduced the expression of the Akt gene and protein by at least 76%, and the survival rate and reproductive capacity of D. pulex were significantly lower in the RNAi group compared with those in the control group. This study provides a better understanding of the function of the akt gene in D. pulex.

Characterization of an adulticidal and larvicidal interfering RNA pesticide that targets a conserved sequence in mosquito G protein-coupled dopamine 1 receptor genes

G protein-coupled receptors (GPCRs), key regulators of a variety of critical biological processes, are attractive targets for insecticide development. Given the importance of these receptors in many organisms, including humans, it is critical that novel pesticides directed against GPCRs are designed to be species-specific. Here, we present characterization of an interfering RNA pesticide (IRP) targeting the mosquito GPCR-encoding dopamine 1 receptor (dop1) genes. A small interfering RNA corresponding to dop1 was identified in a screen for IRPs that kill Aedes aegypti during both the adult and larval stages. The 25 bp sequence targeted by this IRP is conserved in the dop1 genes of multiple mosquito species, but not in non-target organisms, indicating that it could function as a biorational mosquito insecticide. Aedes aegypti adults treated through microinjection or attractive toxic sugar bait delivery of small interfering RNA corresponding to the target site exhibited severe neural and behavioral defects and high levels of adult mortality. Likewise, A. aegypti larval consumption of dried inactivated yeast tablets prepared from a Saccharomyces cerevisiae strain engineered to express short hairpin RNA corresponding to the dop1 target site resulted in severe neural defects and larval mortality. Aedes albopictus and Anopheles gambiae adult and larval mortality was also observed following treatment with dop1 IRPs, which were not toxic to non-target arthropods. The results of this investigation indicate that dop1 IRPs can be used for species-specific targeting of dop1 GPCRs and may represent a new biorational strategy for control of both adult and larval mosquitoes.

RNA interference may result in unexpected phenotypes in Caenorhabditis elegans

RNA interference (RNAi) is a valuable technique to determine gene function. In Caenorhabditis elegans, RNAi can be achieved by feeding worms bacteria carrying a plasmid expressing double-stranded RNA (dsRNA) targeting a gene of interest. The most commonly used plasmid vector for this purpose is L4440. However, it has been noticed that sequences within L4440 may elicit unspecific effects. Here, we provide a comprehensive characterization of these effects and their mechanisms and describe new unexpected phenotypes uncovered by the administration of unspecific exogenous dsRNA. An example involves dsRNA produced by the multiple cloning site (MCS) of L4440, which shares complementary sequences with some widely used reporter vectors and induces partial transgene silencing via the canonical and antiviral RNAi pathway. Going beyond transgene silencing, we found that the reduced embryonic viability of mir-35-41(gk262) mutants is partially reversed by exogenous dsRNA via a mechanism that involves canonical RNAi. These results indicate cross-regulation between different small RNA pathways in C. elegans to regulate embryonic viability. Recognition of the possible unspecific effects elicited by RNAi vectors is important for rigorous interpretation of results from RNAi-based experiments.

RNA Interference by Ingested dsRNA-Expressing Bacteria to Study Shell Biosynthesis and Pigmentation in Crassostrea gigas

RNA interference (RNAi) is an important molecular tool for analysis of gene function in vivo. Although the Pacific oyster Crassostrea gigas is an economically important species with fully sequenced genome, very few mechanistic studies have been carried out due to the lack of molecular techniques to alter gene expression without inducing stress. In this present study, we used unicellular alga Platymonas subcordiformis and Nitzschia closterium f. minutissima as a vector to feed oysters with Escherichia coli strain HT115 engineered to express double-stranded RNAs (dsRNAs) targeting specific genes involved in shell pigmentation. A C. gigas strain with black shell was used to target tyrosinase or peroxidase gene expression by RNAi using the above-mentioned approach. The results showed that feeding oyster with dsRNA of tyrosinase could knock down the expression of corresponding tyrosinase and hinder the developed shell growth. Feeding oyster with dsRNA of peroxidase could knock down the expression of the corresponding peroxidase and result in reduced black pigmentation in the newly developed shell. This non-invasive RNAi study demonstrated that tyrosinase played a vital role in the assembly and maturation of shell matrices and peroxidase was essential for black pigmentation in the shell. Moreover, the RNA interference by ingested dsRNA-expressing bacteria is a relatively simple and effective method for knockdown of a gene expression in adult oysters, thus further advances the use of C. gigas as model organism in functional genomic studies.

Genomic integration and ligand-dependent activation of the human estrogen receptor α in the crustacean Daphnia magna

The freshwater crustacean Daphnia have a long history in water quality assessments and now lend themselves to detection of targeted chemicals using genetically encoded reporter gene due to recent progress in the development of genome editing tools. By introducing human genes into Daphnia, we may be able to detect chemicals that affect the human system, or even apply it to screening potentially useful chemicals. Here, we aimed to develop a transgenic line of Daphnia magna that contains the human estrogen receptor alpha (hERα) and shows a fluorescence response to exposure of estrogens. We designed plasmids to express hERα in Daphnia (EF1α1:esr1) and to report estrogenic activity via red fluorescence (ERE:mcherry) under the control of estrogen response element (ERE). After confirmation of functionality of the plasmids by microinjection into embryos, the two plasmids were joined, a TALE site was added and integrated into the D. magna genome using TALEN. When the resulting transgenic Daphnia named the ES line was exposed to Diethylstilbestrol (DES) or 17β-Estradiol (E2), the ES line could reliably expressed red fluorescence derived from mCherry in a ligand-dependent manner, indicating that an estrogen-responsive line of D. magna was established. This is the first time a human gene was expressed in Daphnia, showcasing potential for further research.

Hemoglobin Levels Modulate Nitrite Toxicity to Daphnia magna

Nitrogenous compounds enter the environment through various anthropogenic sources. Among these are nitrate (NO₃⁻) and nitrite (NO₂⁻) which can oxidize the heme moiety of hemoglobin and reduce the oxygen-carrying capacity of the molecule resulting in toxicity. Of the two anions, nitrite is more toxic. Hemoglobin levels are influenced by environmental conditions; thus, we hypothesized that hemoglobin levels would influence the toxicity of nitrite with low hemoglobin levels resulting in enhanced toxicity and high hemoglobin levels resulting in reduced toxicity. We tested this hypothesis by elevating hemoglobin levels with pyriproxyfen treatment and lowering hemoglobin levels using siRNA in Daphnia magna. Exposure to pyriproxyfen significantly elevated hemoglobin mRNA levels and induced copper coloration of the organisms, indicative of increased hemoglobin protein accumulation. siRNA treatment significantly reduced hemoglobin mRNA levels in both untreated and pyriproxyfen-treated organisms and attenuated copper coloration. Pyriproxyfen treatment increased the tolerance of daphnids to the acute toxicity of nitrite approximately 2-fold while siRNA treatment significantly decreased the tolerance of daphnids to nitrite toxicity. Results indicate that increased hemoglobin levels increase the tolerance of daphnids to nitrite toxicity which may serve to protect daphnids in environments subject to hemoglobin-elevating hypoxia or elevated temperatures.

Full and partial hydrolysis of poly(2-oxazoline)s and the subsequent post-polymerization modification of the resulting polyethylenimine (co)polymers

This review discusses the full and partial hydrolysis of poly(2-oxazoline)s as well as the synthetic methods that have been reported to modify the resulting secondary amine groups.

Identification of a novel toll gene (Shtoll3) from the freshwater crab Sinopotamon henanense and its expression pattern changes in response to cadmium followed by Aeromonas hydrophila infection

Toll signaling is essential for expression of immune genes which are important for defense against bacterial, fungal and viral infections in invertebrates. Although several toll genes have been identified in the crustaceans, none of them has been investigated in freshwater crab Sinopotamon henanense. Moreover, the effect of cadmium (Cd) on toll gene expression has never been examined on the freshwater crabs which live in the sediments and are prone to heavy metal bioaccumulation. Our transcriptomic analysis of hepatopancreas tissue reveals that toll3 gene expression has been decreased when treated with Cd. In this study, we cloned one toll gene (hereby designated Shtoll3) from the crab. The full-length cDNA of Shtoll3 was 4488 bp, with an ORF of 3693 bp encoding a putative protein of 1230 amino acids, a 5'-untranslated region of 414 bp and a 3'-untranslated region of 781 bp. Phylogenetic analysis showed that ShToll3 was clustered into the group of DmToll8. The tissue distribution results showed that Shtoll3 was expressed widely in different tissues, with the highest in gills, and the lowest in hemocytes. Shtoll3 expression was down-regulated only in midguts after Aeromonas hydrophila infection. With Cd presence, Shtoll3 expression in response to A. hydrophila were up-regulated in midguts and gills, which was further confirmed by western blotting analysis. Moreover, the mRNA level of two antimicrobial peptides (AMPs) crustin and c-lys, which possibly responded to Cd and A. hydrophila stimulation through Shtoll3, were analysised. Thus, we conclude that Cd changes the susceptibility of Shtoll3 to A. hydrophila infection in gills and midguts. This suggest that Shtoll3 may contribute to the innate immune defense of S. henanense to A. hydrophila and Cd can modify the immune function in epithelium.

Trojan Horse Strategy for Non-invasive Interference of Clock Gene in the Oyster Crassostrea gigas

RNA interference is a powerful method to inhibit specific gene expression. Recently, silencing target genes by feeding has been successfully carried out in nematodes, insects, and small aquatic organisms. A non-invasive feeding-based RNA interference is reported here for the first time in a mollusk bivalve, the pacific oyster Crassostrea gigas. In this Trojan horse strategy, the unicellular alga Heterocapsa triquetra is the food supply used as a vector to feed oysters with Escherichia coli strain HT115 engineered to express the double-stranded RNA targeting gene. To test the efficacy of the method, the Clock gene, a central gene of the circadian clock, was targeted for knockout. Results demonstrated specific and systemic efficiency of the Trojan horse strategy in reducing Clock mRNA abundance. Consequences of Clock disruption were observed in Clock-related genes (Bmal, Tim1, Per, Cry1, Cry2, Rev.-erb, and Ror) and triploid oysters were more sensitive than diploid to the interference. This non-invasive approach shows an involvement of the circadian clock in oyster bioaccumulation of toxins produced by the harmful alga Alexandrium minutum.

A New Reference Genome Assembly for the Microcrustacean Daphnia pulex

Comparing genomes of closely related genotypes from populations with distinct demographic histories can help reveal the impact of effective population size on genome evolution. For this purpose, we present a high quality genome assembly of Daphnia pulex (PA42), and compare this with the first sequenced genome of this species (TCO), which was derived from an isolate from a population with >90% reduction in nucleotide diversity. PA42 has numerous similarities to TCO at the gene level, with an average amino acid sequence identity of 98.8 and >60% of orthologous proteins identical. Nonetheless, there is a highly elevated number of genes in the TCO genome annotation, with ∼7000 excess genes appearing to be false positives. This view is supported by the high GC content, lack of introns, and short length of these suspicious gene annotations. Consistent with the view that reduced effective population size can facilitate the accumulation of slightly deleterious genomic features, we observe more proliferation of transposable elements (TEs) and a higher frequency of gained introns in the TCO genome.

Involvement of Daphnia pulicaria Sir2 in regulating stress response and lifespan

The ability to appropriately respond to proteotoxic stimuli is a major determinant of longevity and involves induction of various heat shock response (HSR) genes, which are essential to cope with cellular and organismal insults throughout lifespan. The activity of NAD+-dependent deacetylase Sir2, originally discovered in yeast, is known to be essential for effective HSR and longevity. Our previous work on HSR inDaphnia pulicaria indicated a drastic reduction of the HSR in older organisms. In this report we investigate the role of Sir2 in regulating HSR during the lifespan of D. pulicaria. We cloned Daphnia Sir2 open reading frame (ORF) to characterize the enzyme activity and confirmed that the overall function of Sir2 was conserved in Daphnia. The Sir2 mRNA levels increased while the enzyme activity declined with age and considering that Sir2 activity regulates HSR, this explains the previously observed age-dependent decline in HSR. Finally, we tested the effect of Sir2 knockdown throughout adult life by using our new RNA interference (RNAi) method by feeding. Sir2 knockdown severely reduced both the median lifespan as well as significantly increased mortality following heat shock. Our study provides the first characterization and functional study of Daphnia Sir2.

Population Genomics of Daphnia pulex

Using data from 83 isolates from a single population, the population genomics of the microcrustacean Daphnia pulex are described and compared to current knowledge for the only other well-studied invertebrate, Drosophila melanogaster These two species are quite similar with respect to effective population sizes and mutation rates, although some features of recombination appear to be different, with linkage disequilibrium being elevated at short ([Formula: see text] bp) distances in D. melanogaster and at long distances in D. pulex The study population adheres closely to the expectations under Hardy-Weinberg equilibrium, and reflects a past population history of no more than a twofold range of variation in effective population size. Fourfold redundant silent sites and a restricted region of intronic sites appear to evolve in a nearly neutral fashion, providing a powerful tool for population genetic analyses. Amino acid replacement sites are predominantly under strong purifying selection, as are a large fraction of sites in UTRs and intergenic regions, but the majority of SNPs at such sites that rise to frequencies [Formula: see text] appear to evolve in a nearly neutral fashion. All forms of genomic sites (including replacement sites within codons, and intergenic and UTR regions) appear to be experiencing an [Formula: see text] higher level of selection scaled to the power of drift in D. melanogaster, but this may in part be a consequence of recent demographic changes. These results establish D. pulex as an excellent system for future work on the evolutionary genomics of natural populations.