Evaluation and validation of internal control genes for studying gene expression in the dinoflagellate Prorocentrum minimum using real-time PCR

Evaluation of reference genes for gene expression analysis by real-time quantitative PCR (qPCR) in different tissues from mice infected by Ascaris suum

Human ascariasis is the most prevalent helminth infection, affecting 445 million people worldwide. To better understand the impact of the immune system on the pathophysiology of individuals infected with Ascaris suum, mice have been used as experimental models. The RT-qPCR technique is a critical auxiliary tool of investigation used to quantify mRNA levels. However, proper normalization using reference genes is essential to ensure reliable outcomes to avoid analytical errors and false results. Despite the importance of reference genes for experimental A. suum infection studies, no specific reference genes have been identified yet. Therefore, we conducted a study to assess five potential reference genes (GAPDH, 18s, ACTB, B2M, and HPRT1) in different tissues (liver, lungs, small and large intestines) affected by A. suum larval migration in C57BL/6j mice. Tissue collection was carried out to analyze parasite burden and confirm the presence of larvae during the peak of migration in each tissue. Upon confirmation, we analyzed different genes in the tissues and found no common gene with stable expression. Our results highlight the importance of analyzing different genes and using different software programs to ensure reliable relative expression results. Based on our findings, B2M was ranked as the ideal reference gene for the liver, while 18S was the most stable gene in the lung and small intestine. ACTB, or a combination of ACTB with GAPDH, was deemed suitable as reference genes for the large intestine due to their stable expression and less variation between the control and infected groups. To further demonstrate the impact of using different reference genes, we normalized the expression of a chemokine gene (CXCL9) in all tissues. Significant differences in CXCL9 expression levels were observed between different groups in all tissues except for the large intestine. This underscores the importance of selecting appropriate reference genes to avoid overestimating target gene expression levels and encountering normalization-related issues that can lead to false results. In conclusion, our study highlights the significance of using reliable reference genes for accurate RT-qPCR analysis, especially in the context of A. suum infection studies in different tissues. Proper normalization is crucial to ensure the validity of gene expression data and avoid potential pitfalls in interpreting results.

Algicidal activity of a novel bacterium, Qipengyuania sp. 3-20A1M, against harmful Margalefidinium polykrikoides: Effects of its active compound

Margalefidinium polykrikoides causes significant economic losses in the aquaculture industry by red tide formation. Algicidal bacteria have attracted research interests as a potential bloom control approach without secondary pollution. Qipengyuania sp. 3-20A1M, isolated from surface seawater, exerted an algicidal effect on M. polykrikoides. However, it exhibited a significantly lower algicidal activity toward other microalgae. It reduced photosynthetic efficiency of M. polykrikoides and induced lipid peroxidation and cell disruption. The growth inhibition of M. polykrikoides reached 64.9 % after 24 h of co-culturing, and expression of photosynthesis-related genes was suppressed. It killed M. polykrikoides indirectly by secreting algicidal compounds. The algicide was purified and identified as pyrrole-2-carboxylic acid. After 24 h of treatment with pyrrole-2-carboxylic acid (20 μg/mL), 60.8 % of the M. polykrikoides cells were destroyed. Overall, our results demonstrated the potential utility of Qipengyuania sp. 3-20A1M and its algicidal compound in controlling M. polykrikoides blooms in the marine ecosystem.

Energy metabolism and genetic information processing mark major transitions in the life history of Scrippsiella acuminata (Dinophyceae)

Many dinoflagellates perform sexual reproduction and form cysts as a life history strategy to survive adverse environmental conditions and seed annual harmful algal blooms (HABs). The molecular mechanisms underpinning the life stage transitions can provide clues about how key environmental factors induce encystment and initiation of a HAB but are still poorly understood. Here, we conducted an integrated physiological and transcriptomic study to unravel the mechanisms in Scrippsiella acuminata. We established a culture from a bloom, induced cyst formation, and divided the process into four life stages. Transcriptomic analysis of these stages revealed 19,900 differentially expressed genes (DEGs). The expression of genes related to photosynthesis was significantly up-regulated from vegetative stage to immature cyst stage, consistent with the marked increase in cell contents of energy-storing macromolecules (carbohydrates and lipids). When proceeding to resting cysts, most photosynthesis genes were down-regulated while "genetic information processing" related genes were up-regulated. Comparing germinating cysts with resting cysts revealed 100 DEGs involved in energy metabolism, indicating a high energy requirement of germination. In addition, the transition from germinating cysts to vegetative cells featured up-regulation of photosynthesis. Our results demonstrate that energy storage and consumption play a pivotal role in cyst formation and germination respectively and genetic information processing is crucial in cyst dormancy.

Conservation and architecture of housekeeping genes in the model marine diatom Thalassiosira pseudonana

Housekeeping genes (HKGs) are constitutively expressed with low variation across tissues/conditions. They are thought to be highly conserved and fundamental to cellular maintenance, with distinctive genomic features. Here, we identify 1505 HKGs in the unicellular marine diatom Thalassiosira pseudonana based on an RNA-seq analysis of 232 samples taken under 12 experimental conditions over 0-72 h. We identify promising internal reference genes (IRGs) for T. pseudonana from the most stably expressed HKGs. A comparative analysis indicates < 18% of HKGs in T. pseudonana have orthologs in other eukaryotes, including other diatom species. Contrary to work on human tissues, T. pseudonana HKGs are longer than non-HKGs, due to elongated introns. More ancient HKGs tend to be shorter than more recent HKGs, and expression levels of HKGs decrease more rapidly with gene length relative to non-HKGs. Our results indicate that HKGs are highly variable across the tree of life and thus unlikely to be universally fundamental for cellular maintenance. We hypothesize that the distinct genomic features of HKGs of T. pseudonana may be a consequence of selection pressures associated with high expression and low variance across conditions.

Abundant synthesis of long-chain polyunsaturated fatty acids in Eutreptiella sp. (Euglenozoa) revealed by chromatographic and transcriptomic analyses

Algal lipids are important molecules to store energy in algae and transfer energy in the marine food chain, and are potential materials for high value nutraceuticals (e.g., omega-3 fatty acids) or biofuel production. However, how lipid biosynthesis is regulated is not well understood in many species including Eutreptiella from the phylum of Euglenozoa. Here, we characterized the fatty acid (FA) profile of an Eutreptiella species isolated from Long Island Sound, USA, using gas chromatography-tandem mass spectrometry (GC/MS/MS) and investigated their biosynthesis pathways by transcriptome sequencing. We discovered 24 types of FAs including a relatively high proportion of long-chain unsaturated FAs. The abundances of C16, C18, and saturated FAs decreased when phosphate in the culture medium was depleted. Among the 24 FAs, docosahexaenoic acid (C22:6^{∆4,7,10,13,16,19} ) was most abundant, suggesting that Eutreptiella sp. preferentially invests in the synthesis of long-chain polyunsaturated fatty acids (LC-PFAs). Further transcriptomic analysis revealed that Eutreptiella sp. likely synthesizes LC-PFAs via ∆8 pathway and uses type I and II fatty acid synthases. Using RT-qPCR, we found that some of the lipid synthesis genes, such as β-ketoacyl-ACP reductase, fatty acid desaturase, acetyl-CoA carboxylase, acyl carrier protein, ∆8 desaturase, and Acyl-ACP thioesterase, were more actively expressed during light period, and two carbon fixation genes were up-regulated in the high-lipid illuminated cultures, suggesting a linkage between photosynthesis and lipid production. The lipid profile renders Eutreptiella sp. a nutritional prey and valuable source for nutraceuticals, and the biosynthesis pathway documented here will be useful for future research and applications.

Selection and validation of reference genes for quantitative real-time PCR in the green microalgae Tetraselmis chui

Quantitative real-time reverse transcription PCR (RT-qPCR) is a highly sensitive technique that can be applied to analyze how genes are modulated by culture conditions, but identification of appropriate reference genes for normalization is a critical factor to be considered. For this reason, the expression stability of 18 candidate reference genes was evaluated for the green microalgae Tetraselmis chui using the widely employed algorithms geNorm, NormFinder, BestKeeper, the comparative ΔCT method, and RefFinder. Microalgae samples were collected from large scale outdoor photobioreactors during the growing phase (OUT_GP), and during the semi-continuous phase at different times of the day (OUT_DC). Samples from standard indoor cultures under highly controlled conditions (IND) were also collected to complement the other data. Different rankings for the candidate reference genes were obtained depending on the culture conditions and the algorithm employed. After comparison of the achieved ranks with the different methods, the references genes selected for samples from specific culture conditions were ALD and EFL in OUT_GP, RPL32 and UBCE in OUT_DC, and cdkA and UBCE in IND. Moreover, the genes EFL and cdkA or EFL and UBCE appeared as appropriate combinations for pools generated from all samples (ALL). Examination in the OUT_DC cultures of genes encoding the large and small subunits of ADP-glucose pyrophosphorylase (AGPL and AGPS, respectively) confirmed the reliability of the identified reference genes, RPL32 and UBCE. The present study represents a useful contribution for studies of gene expression in T. chui, and also represents the first step to set-up an RT-qPCR platform for quality control of T. chui biomass production in industrial facilities.

Atypical Membrane-Anchored Cytokine MIF in a Marine Dinoflagellate

Macrophage Migration Inhibitory Factors (MIF) are pivotal cytokines/chemokines for vertebrate immune systems. MIFs are typically soluble single-domain proteins that are conserved across plant, fungal, protist, and metazoan kingdoms, but their functions have not been determined in most phylogenetic groups. Here, we describe an atypical multidomain MIF protein. The marine dinoflagellate Lingulodinium polyedra produces a transmembrane protein with an extra-cytoplasmic MIF domain, which localizes to cell-wall-associated membranes and vesicular bodies. This protein is also present in the membranes of extracellular vesicles accumulating at the secretory pores of the cells. Upon exposure to biotic stress, L. polyedra exhibits reduced expression of the MIF gene and reduced abundance of the surface-associated protein. The presence of LpMIF in the membranes of secreted extracellular vesicles evokes the fascinating possibility that LpMIF may participate in intercellular communication and/or interactions between free-living organisms in multispecies planktonic communities.

Functional responses between PMP3 small membrane proteins and membrane potential

The Plasma Membrane Proteolipid 3 (PMP3, UPF0057 family in Uniprot) family consists of abundant small hydrophobic polypeptides with two predicted transmembrane helices. Plant homologues were upregulated in response to drought/salt-stresses and yeast deletion mutants exhibited conditional growth defects. We report here abundant expression of Group I PMP3 homologues (PMP3(i)hs) during normal vegetative growth in both prokaryotic and eukaryotic cells, at a level comparable to housekeeping genes, implicating the regular cellular functions. Expression of eukaryotic PMP3(i)hs was dramatically upregulated in response to membrane potential (Vm) variability (Vm_var ), whereas PMP3(i)hs deletion-knockdown led to Vm changes with conditional growth defects. Bacterial PMP3(i)h yqaE deletion led to a shift of salt sensitivity; Vm_var alternations with exogenous K⁺ addition downregulated prokaryotic PMP3(i)hs, suggesting [K⁺ ]-Vm_var axis being a significant feedback element in prokaryotic ionic homeostasis. Remarkably, the eukaryotic homologues functionally suppressed the conditional growth defects in bacterial deletion mutant, demonstrating the conserved cross-kingdom membrane functions by PMP3(i)hs. These data demonstrated a direct reciprocal relationship between PMP3(i)hs expression and Vm differentials in both prokaryotic and eukaryotic cells. Cumulative with PMP3(i)hs ubiquitous abundance, their lipid-binding selectivity and membrane protein colocalization, we propose [PMP3(i)hs]-Vm_var axis as a key element in membrane homeostasis.

The herbicide alachlor severely affects photosystem function and photosynthetic gene expression in the marine dinoflagellate Prorocentrum minimum

Alachlor is one of the most widely used herbicides and can remain in agricultural soils and wastewater. The toxicity of alachlor to marine life has been rarely studied; therefore, we evaluated the physiological and transcriptional responses in the marine dinoflagellate Prorocentrum minimum. The herbicide led to considerable decreases in P. minimum cell numbers and pigment contents. The EC₅₀ was determined to be 0.373 mg/L. Photosynthesis efficiency and chlorophyll autofluorescence dramatically decreased with increasing alachlor dose and exposure time. Real-time PCR analysis showed that the photosynthesis-related genes PmpsbA, PmatpB, and PmrbcL were induced the most by alachlor; the transcriptional level of each gene varied with time. PmrbcL expression increased after 30 min of alachlor treatment, whereas PmatpB and PmpsbA increased after 24 h. The PmpsbA expression level was highest (5.0 times compared to control) after 6 h of alachlor treatment. There was no significant change in PmpsaA expression with varying treatment time or concentration. Additionally, there was no notable change in the expression of antioxidant genes PmGST and PmKatG, or in ROS accumulation. These suggest that alachlor may affect microalgal photosystem function, with little oxidative stress, causing severe physiological damage to the cells, and even cell death.

Dur3 and nrt2 genes in the bloom-forming dinoflagellate Prorocentrum minimum: Transcriptional responses to available nitrogen sources

The increasing inflow of nitrogen (N) substrates into marine nearshore ecosystems induces proliferation of harmful algal blooms (HABs) of dinoflagellates, such as potentially toxic invasive species Prorocentrum minimum. In this study, we estimated the influence of NO3-, NH4+ and urea on transcription levels and urea transporter dur3 and nitrate transporter nrt2 genes expression in these dinoflagellates. We identified dur3 and nrt2 genes sequences in unannotated transcriptomes of P. minimum and other dinoflagellates presented in MMETSP database. Phylogenetic analysis showed that these genes of dinoflagellates clustered to the distinct clade demonstrating evolutionary relationship with the other known dur3 and nrt2 genes of microalgae. The evaluation of expression levels of dur3 and nrt2 genes by RT-qPCR revealed their sensitivity to input of the studied N sources. Dur3 expression levels were downregulated after the supplementation of additional N sources and were 1.7-2.6-fold lower than in the nitrate-grown culture. Nrt2 expression levels decreased 1.9-fold in the presence of NH4+. We estimated total RNA and DNA synthesis rates by the analysis of incorporation of 3H-thymidine and 3H-uridine in batch and continuous cultures. Addition of N compounds did not affect the DNA synthesis rates. Transcription levels increased up to 12.5-fold after the N supplementation in urea-limited treatments. Investigation of various nitrogen sources as biomarkers of dinoflagellate proliferation due to their differentiated impact on expression of dur3 and nrt2 genes and transcription rates in P. minimum cells allowed concluding about high potential of the studied parameters for future modeling of HABs under global N pollution.

Knockdown of Dinoflagellate Cellulose Synthase CesA1 Resulted in Malformed Intracellular Cellulosic Thecal Plates and Severely Impeded Cyst-to-Swarmer Transition

Cellulose synthesis (CS) is conducted by membrane-bound cellulose synthase complexes (CSCs), containing cellulose synthases (CesA), that are either arranged in hexagonal structures in higher plants or in linear arrays in most microbial organisms, including dinoflagellates. Dinoflagellates are a major phytoplankton group having linear-type CSCs and internal cellulosic thecal plates (CTPs) in large cortical vesicles. Immunological study suggested CesA1p were cortically localized to the periphery of CTPs. During cyst-to-swarmer transition (T_C–S), synchronized peaks of CesA1 transcription, CesA1p expression, CS and CTP formation occurred in respective order, over 12–16 h, strategically allowing the study of CS regulation and CTP biogenesis. CesA1-knockdown resulted in 40% reduction in CesA1p level and time required for swarmer cells reappearance. CTPs were severely malformed with reduced cellulose content. As CTPs are deposited in internal organelle, the present study demonstrated dinoflagellate CesA1 ortholog was adapted for non-surface deposition; this is different to paradigm of other CesAps which require plasmamembrane for cellulose fiber deposition. This pioneer gene-knockdown study demonstrated the requirement of a gene for dinoflagellate cell wall remodeling and proper T_C–S, which are prominent in dinoflagellate life-cycles.

Differential transcriptional responses of carotenoid biosynthesis genes in the marine green alga Tetraselmis suecica exposed to redox and non-redox active metals

The green microalga, Tetraselmis suecica, is commonly used in scientific, industrial, and aquacultural purposes because of its high stress tolerance and ease of culture in wide spectrums of environments. We hypothesized that carotenoids help to protect Tetraselmis cells from environmental stress by regulating genes in biosynthetic pathways. Here, we determined three major carotenogenic genes, phytoene synthase (PSY), phytoene desaturase (PDS), and β-lycopene cyclase (LCY-B) in T. suecica, and examined the physiological parameters and gene expression responses when exposed to redox-active metals and non-redox-active metals. Phylogenetic analyses of each gene indicated that T. suecica clustered well with other green algae. Real-time PCR analysis showed that TsPSY, TsPDS, and TsLCY-B genes greatly responded to the redox-active metals in CuSO₄ followed by CuCl₂, but not to the non-redox-active metals. The redox-active metals strongly affected the physiology of the cells, as determined by cell counting, reactive oxygen species (ROS) imaging, and photosynthetic efficiency. This suggests that carotenoids protect the cells from oxidative damage caused by metals, thereby contributing to cell survival under various stress conditions.

Origin and roles of a novel copper-zinc superoxide dismutase (CuZnSOD) gene from the harmful dinoflagellate Prorocentrum minimum

Superoxide dismutase (SOD) acts as the first line of defence against reactive oxygen species (ROS) within cells. In this study, we characterized a novel SOD gene (PmCuZnSOD) from the dinoflagellate Prorocentrum minimum, and examined its structural features, putative origin and gene expression. The SOD cDNA is 895 bp in length, containing dinoflagellate splice-leader (dinoSL) sequence, 714-bp ORF (237 aa), and poly (A) tail. In addition, PmCuZnSOD is coded on the dinoflagellate nuclear genome without introns and in a non-tandem repeat manner; however, the encoded protein is probably localized in chloroplasts. Phylogenetic analysis indicated that it might be acquired from cyanobacteria via horizontal gene transfer (HGT) and then the gene possibly relocated from the chloroplast to the nuclear genome. Excess copper dramatically increased the PmCuZnSOD transcripts and SOD activity in cells, caused by ROS generation and decrease of photosynthetic efficiency in the treated cells. These suggest that CuZnSOD may function to defend against oxidative stress for the survival of the dinoflagellate.

Genome-wide analysis of transcription and photosynthesis inhibition in the harmful dinoflagellate Prorocentrum minimum in response to the biocide copper sulfate

Copper is an essential trace metal for organisms; however, excess copper may damage cellular processes. Their efficiency and physiological effects of biocides have been well documented; however, molecular transcriptome responses to biocides are insufficiently studied. In the present study, a 6.0K oligonucleotide chip was developed to investigate the molecular responses of the harmful dinoflagellate Prorocentrum minimum to copper sulfate (CuSO₄) treatment. The results revealed that 515 genes (approximately 8.6%) responded to CuSO₄, defined as being within a 2-fold change. Further, KEGG pathway analysis showed that differentially expressed genes (DEGs) were involved in ribosomal function, RNA transport, carbon metabolism, biosynthesis of amino acids, photosystem maintenance, and other cellular processes. Among the DEGs, 49 genes were related to chloroplasts and mitochondria. Furthermore, the genes involved in the RAS signaling pathway, MAPK signaling pathway, and transport pathways were identified. An additional experiment showed that the photosynthesis efficiency decreased considerably, and reactive oxygen species (ROS) production increased in P. minimum after CuSO₄ exposure. These results suggest that CuSO₄ caused cellular oxidative stress in P. minimum, affecting the ribosome and mitochondria, and severely damaged the photosystem. These effects may potentially lead to cell death, although the dinoflagellate has developed a complex signal transduction process to combat copper toxicity.

Physiological and transcriptional responses to inorganic nutrition in a tropical Pacific strain of Alexandrium minutum: Implications for the saxitoxin genes and toxin production

Saxitoxins (STXs) constitute a family of potent sodium channel blocking toxins, causative agents of paralytic shellfish poisoning (PSP), and are produced by several species of marine dinoflagellates and cyanobacteria. Two STX-core genes, sxtA and sxtG, have been well elucidated in Alexandrium but the expression of these genes under various nutritional modes in tropical species remains unclear. This study investigates the physiological responses of a tropical Pacific strain of Alexandrium minutum growing with nitrate or ammonium, and with various nitrogen to phosphorus (N:P) supply ratios. The transcriptional responses of the sxt genes were observed. Likewise, a putative sxtI encoding O-carbamoyltransferase (herein designated as AmsxtI) was recovered from the transcriptomic data, and its expression was investigated. The results revealed that the cellular toxin quota (Q_t) was higher in P-depleted, nitrate-grown cultures. With cultures at similar N:P (<16), cells grown with excess ammonium showed a higher Q_t than those grown with nitrate. sxtA1 was not expressed under any culture conditions, suggesting that this gene might not be involved in STX biosynthesis by this strain. Conversely, sxtA4 and sxtG showed positive correlations with Q_t, and were up-regulated in P-depleted, nitrate-grown cultures and with excess ambient ammonium. On the other hand, AmsxtI was expressed only when induced by P-depletion, suggesting that this gene may play an important role in P-recycling metabolism, while simultaneously enhancing toxin production.

Physiological and Molecular Response of Prorocentrum minimum to Tannic Acid: An Experimental Study to Evaluate the Feasibility of Using Tannic Acid in Controling the Red Tide in a Eutrophic Coastal Water

Bioassay and gene expression experiments were conducted in order to evaluate the growth and physiology of Prorocentrum minimum isolated from a eutrophic coastal water in response to tannic acid. In the bioassay experiments, variations in abundance, chlorophyll (chl) a concentration, maximum fluorescence (in vivo Fm), and photosynthetic efficiency (Fv/Fm) were measured over the course of a seven-day incubation. Moreover, stress-related gene expression in both the control and an experimental (2.5 ppm TA treatment) group was observed for 24 h and 48 h. The molecular markers used in this study were the heat shock proteins (Hsp70 and Hsp90) and cyclophilin (CYP). The findings show that P. minimum can thrive and grow at low concentrations (<2.5 ppm) of tannic acid, and, above this concentration, cells begin to slow down development. In addition, TA concentration of 10 ppm halted photosynthetic activity. At the molecular level, treatment with tannic acid increased the expression of Hsp70, Hsp90, and CYP, and heat shock proteins are more upregulated than the cyclophilin gene. Exposure to tannic acid increased the expression of stress factors over time (48 h) by 10- to 27-fold the expression level of the control group. These results suggest that tannic acid can be used to control harmful algal blooms such as those containing P. minimum in eutrophic coastal waters.

Transcriptomic profiles reveal the genome-wide responses of the harmful dinoflagellate Cochlodinium polykrikoides when exposed to the algicide copper sulfate

Background

Harmful algal blooms (HABs) caused by the dinoflagellate Cochlodinium polykrikoides lead to severe environmental impacts in oceans worldwide followed by huge economic losses. Algicide agent copper sulfate (CuSO₄) is regard as an economical and effective agent for HABs mitigation; its biochemical and physiological effects were revealed in C. polykrikoides. However, molecular mechanisms of CuSO₄ effect on the C. polykrikoides, even other HAB species, have not been investigated. The present study investigated the transcriptional response of C. polykrikoides against CuSO₄ treatments, with the aim of providing certain molecular mechanism of CuSO₄ effect on the C. polykrikoides blooms.

Results

RNA-seq generated 173 million reads, which were further assembled to 191,212 contigs. 43.3 %, 33.9 %, and 15.6 % of contigs were annotated with NCBI NR, GO, and KEGG database, respectively. Transcriptomic analysis revealed 20.6 % differential expressed contigs, which grouped into 8 clusters according to K-means clustering analysis, responding to CuSO₄; 848 contigs were up-regulated and 746 contigs were down-regulated more than 2-fold changes from 12 h to 48 h exposure. KEGG pathway analysis of eukaryotic homologous genes revealed the differentially expressed genes (DEGs) were involved in diverse pathway; amongst, the genes involved in the translation, spliceosome, and/or signal transduction genes were highly regulated. Most of photosystem related genes were down-regulated and most of mitochondria related genes were up-regulated. In addition, the genes involved in the copper ion binding or transporting and antioxidant systems were identified. Measurement of chlorophyll fluorescence showed that photosynthesis was significantly inhibited by CuSO₄ exposure.

Conclusions

This study reported the first transcriptome of the C. polykrikoides. The widely differential expressed photosystem genes suggested photosynthetic machinery were severely affected, and may further contribute to the cell death. Furthermore, gene translation and transcription processes may be disrupted, inhibiting cell growth and proliferation, and possibly accelerating cell death. However, antioxidant systems resistant to CuSO₄ caused stress; mitochondrion may compensate for photosynthesis efficiency decreasing caused energy deficiency. In addition, various signal transduction pathways may be involved in the CuSO₄ induced regulation network in the C. polykrikoides. These data provide the potential transcriptomic mechanism to explain the algicide CuSO₄ effect on the harmful dinoflagellate C. polykrikoides.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-2341-3) contains supplementary material, which is available to authorized users.

A novel cyclophilin gene from the dinoflagellate Prorocentrum minimum and its possible role in the environmental stress response

Cyclophilins (CYPs) are a family of proteins that bind to cyclosporine and are thought to be involved in the stress response. In dinoflagellate algae, CYPs may function as a survival strategy in cells exposed to environmental stressors. Here, we identified a novel cyclophilin gene (referred to as PmCYP, comprising a 516-bp open reading frame, encoding a 171-aa protein with a molecular mass of 17.5kDa) from the dinoflagellate Prorocentrum minimum, and evaluated the role of dinoflagellate CYP in cells exposed to environmental pollutants copper and polychlorinated biphenyl. In addition, we assessed the cytoprotective role of nitric oxide in relation to the expression of PmCYP. These stressors strongly affected the physiology of the cells, as judged by cell counting, reactive oxygen species (ROS) imaging, and photosynthetic parameters (Fv/Fm and PIABS). PmCYP expression was significantly (P<0.05) induced upon exposure of the cells to all the test pollutants used in this study. These clearly indicate that PmCYP plays a vital role in the oxidative stress response in dinoflagellate survival, although the gene was initially known only for its housekeeping function.

Screening for Suitable Reference Genes for Quantitative Real-Time PCR in Heterosigma akashiwo (Raphidophyceae)

The raphidophyte Heterosigma akashiwo is a globally distributed harmful alga that has been associated with fish kills in coastal waters. To understand the mechanisms of H. akashiwo bloom formation, gene expression analysis is often required. To accurately characterize the expression levels of a gene of interest, proper reference genes are essential. In this study, we assessed ten of the previously reported algal candidate genes (rpL17-2, rpL23, cox2, cal, tua, tub, ef1, 18S, gapdh, and mdh) for their suitability as reference genes in this species. We used qRT-PCR to quantify the expression levels of these genes in H. akashiwo grown under different temperatures, light intensities, nutrient concentrations, and time points over a diel cycle. The expression stability of these genes was evaluated using geNorm and NormFinder algorithms. Although none of these genes exhibited invariable expression levels, cal, tub, rpL17-2 and rpL23 expression levels were the most stable across the different conditions tested. For further validation, these selected genes were used to normalize the expression levels of ribulose-1, 5-bisphosphate carboxylase/oxygenase large unite (HrbcL) over a diel cycle. Results showed that the expression of HrbcL normalized against each of these reference genes was the highest at midday and lowest at midnight, similar to the diel patterns typically documented for this gene in algae. While the validated reference genes will be useful for future gene expression studies on H. akashiwo, we expect that the procedure used in this study may be helpful to future efforts to screen reference genes for other algae.

Evaluation and selection of reference genes for ecotoxicogenomic study of the green alga Closterium ehrenbergii using quantitative real-time PCR

The green alga Closterium ehrenbergii occurs in fresh water environments and has been suggested as a model for ecotoxicological assessment. Quantitative real-time PCR (qRT-PCR), with its high sensitivity and specificity, is a preferred method for reliable quantification of gene expression levels. qRT-PCR requires reference genes to normalize the transcription level of the target gene, and selection of appropriate references is crucial. Here, we evaluated nine housekeeping genes, that is, 18S rRNA, ACT, TUA, TUB, eIF, H4, UBQ, rps4, and GAPDH, using 34 RNA samples of C. ehrenbergii cultured in various environments (e.g. exposure to heat shock, UV, metals, and non-metallic chemicals). Each housekeeping gene tested displayed different ranges of C T values for each experimental condition. The gene stability was determined using the descriptive statistic software geNorm, which showed that ACT, H4, and TUA were the most suitable reference genes for all the conditions tested. In addition, at least three genes were required for proper normalization. With these references, we assessed the expression level of the heat shock protein 70 (HSP70) gene in C. ehrenbergii cells exposed to thermal and toxic contaminant stress and found that it was significantly up-regulated by these stressors. This study provides potential reference genes for gene expression studies on C. ehrenbergii with qRT-PCR.

Sediment contaminated with the Azo Dye disperse yellow 7 alters cellular stress- and androgen-related transcription in Silurana tropicalis larvae

Azo dyes are the most commonly used type of dye, accounting for 60-70% of all organic dye production worldwide. They are used as direct dyes in the textile, leather, printing ink, and cosmetic industries. The aim of this study was to assess the lethal and sublethal effects of the disazo dye Disperse Yellow 7 (DY7) in frogs to address a knowledge gap regarding mechanisms of toxicity and the potential for endocrine disrupting properties. Larvae of Silurana tropicalis (Western clawed frog) were exposed to DY7-contaminated water (0 to 22 μg/L) and sediment (0 to 209 μg/g) during early larval development. The concentrations used included the range of similar azo dyes found in surface waters in Canada. A significant decrease in tadpole survivorship was observed at 209 μg/g while there was a significant increase in malformations at the two highest concentrations tested in sediment. In the 209 μg/g treatment, DY7 significantly induced hsp70 (2.5-fold) and hsp90 (2.4-fold) mRNA levels, suggesting that cells required oxidative protection. The same treatment also altered the expression of two androgen-related genes: decreased ar (2-fold) and increased srd5a2 (2.6-fold). Furthermore, transcriptomics generated new hypotheses regarding the mechanisms of toxic action of DY7. Gene network analysis revealed that high concentrations of DY7 in sediment induced cellular stress-related gene transcription and affected genes associated with necrotic cell death, chromosome condensation, and mRNA processing. This study is the first to report on sublethal end points for azo dyes in amphibians, a growing environmental pollutant of concern for aquatic species.

Identifying reference genes with stable expression from high throughput sequence data

Genes that are constitutively expressed across multiple environmental stimuli are crucial to quantifying differentially expressed genes, particularly when employing quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) assays. However, the identification of these potential reference genes in non-model organisms is challenging and is often guided by expression patterns in distantly related organisms. Here, transcriptome datasets from the diatom Thalassiosira pseudonana grown under replete, phosphorus-limited, iron-limited, and phosphorus and iron co-limited nutrient regimes were analyzed through literature-based searches for homologous reference genes, k-means clustering, and analysis of sequence counts (ASC) to identify putative reference genes. A total of 9759 genes were identified and screened for stable expression. Literature-based searches surveyed 18 generally accepted reference genes, revealing 101 homologs in T. pseudonana with variable expression and a wide range of mean tags per million. k-means analysis parsed the whole transcriptome into 15 clusters. The two most stable clusters contained 709 genes, but still had distinct patterns in expression. ASC analyses identified 179 genes that were stably expressed (posterior probability < 0.1 for 1.25 fold change). Genes known to have a stable expression pattern across the test treatments, like actin, were identified in this pool of 179 candidate genes. ASC can be employed on data without biological replicates and was more robust than the k-means approach in isolating genes with stable expression. The intersection of the genes identified through ASC with commonly used reference genes from the literature suggests that actin and ubiquitin ligase may be useful reference genes for T. pseudonana and potentially other diatoms. With the wealth of transcriptome sequence data becoming available, ASC can be easily applied to transcriptome datasets from other phytoplankton to identify reference genes.

Transcriptional responses of heat shock protein 70 (Hsp70) to thermal, bisphenol A, and copper stresses in the dinoflagellate Prorocentrum minimum

The heat shock protein 70 (Hsp70) family is an important part of the cell's machinery for protein folding, and helps to protect cells from environmental stress. Although Hsp70 functions have been discovered in various organisms, studies on dinoflagellate Hsps are limited, except for a few phylogenetic attempts. In this study, we sequenced the complete open reading frame of the dinoflagellate Prorocentrum minimum Hsp70 (PmHsp70), and characterized its molecular functions. The putative PmHsp70 protein contained 3 signature patterns of the Hsp70 family. Phylogenetic analysis revealed that PmHsp70 belonged to the dinoflagellate clade. Real-time (RT)-PCR analyses revealed that PmHsp70 was upregulated by thermal stress. Further, we examined the transcriptional response of PmHsp70 to copper (Cu) and bisphenol A (BPA) exposures. In toxicity assays, Cu and BPA exhibited EC(50)-72 h values of 1.07 ± 0.138 mg L(-1) and 1.51 ± 0.110 mg L(-1), respectively, in P. minimum. Expression of PmHsp70 was significantly upregulated in response to Cu and BPA exposures (one-way ANOVA, P<0.05). PmHsp70 displayed different expression patterns in response to different concentrations of Cu and BPA. This study evaluated typical characteristics and, for the first time, toxicant-related functions of PmHsp70. The results suggest that Hsp70 genes may play a vital role in the environmental stress responses of dinoflagellates.

Pseudogenes as weaknesses of ACTB (Actb) and GAPDH (Gapdh) used as reference genes in reverse transcription and polymerase chain reactions

The genes encoding β-actin (ACTB in human or Actb in mouse) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH in human or Gapdh in mouse) are the two most commonly used references for sample normalization in determination of the mRNA level of interested genes by reverse transcription (RT) and ensuing polymerase chain reactions (PCR). In this study, bioinformatic analyses revealed that the ACTB, Actb, GAPDH and Gapdh had 64, 69, 67 and 197 pseudogenes (PGs), respectively, in the corresponding genome. Most of these PGs are intronless and similar in size to the authentic mRNA. Alignment of several PGs of these genes with the corresponding mRNA reveals that they are highly homologous. In contrast, the hypoxanthine phosphoribosyltransferase-1 gene (HPRT1 in human or Hprt in mouse) only had 3 or 1 PG, respectively, and the mRNA has unique regions for primer design. PCR with cDNA or genomic DNA (gDNA) as templates revealed that our HPRT1, Hprt and GAPDH primers were specific, whereas our ACTB and Actb primers were not specific enough both vertically (within the cDNA) and horizontally (compared cDNA with gDNA). No primers could be designed for the Gapdh that would not mis-prime PGs. Since most of the genome is transcribed, we suggest to peers to forgo ACTB (Actb) and GAPDH (Dapdh) as references in RT-PCR and, if there is no surrogate, to use our primers with extra caution. We also propose a standard operation procedure in which design of primers for RT-PCR starts from avoiding mis-priming PGs and all primers need be tested for specificity with both cDNA and gDNA.