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

A decade of dinoflagellate genomics illuminating an enigmatic eukaryote cell

Dinoflagellates are a remarkable group of protists, not only for their association with harmful algal blooms and coral reefs but also for their numerous characteristics deviating from the rules of eukaryotic biology. Genome research on dinoflagellates has lagged due to their immense genome sizes in most species (~ 1-250 Gbp). Nevertheless, the last decade marked a fruitful era of dinoflagellate genomics, with 27 genomes sequenced and many insights attained. This review aims to synthesize information from these genomes, along with other omic data, to reflect on where we are now in understanding dinoflagellates and where we are heading in the future. The most notable insights from the decade-long genomics work include: (1) dinoflagellate genomes have been expanded in multiple times independently, probably by a combination of rampant retroposition, accumulation of repetitive DNA, and genome duplication; (2) Symbiodiniacean genomes are highly divergent, but share about 3,445 core unigenes concentrated in 219 KEGG pathways; (3) Most dinoflagellate genes are encoded unidirectionally and are not intron-poor; (4) The dinoflagellate nucleus has undergone extreme evolutionary changes, including complete or nearly complete loss of nucleosome and histone H1, and acquisition of dinoflagellate viral nuclear protein (DVNP); (5) Major basic nuclear protein (MBNP), histone-like protein (HLP), and bacterial HU-like protein (HCc) belong to the same protein family, and MBNP can be the unifying name; (6) Dinoflagellate gene expression is regulated by poorly understood mechanisms, but microRNA and other epigenetic mechanisms are likely important; (7) Over 50% of dinoflagellate genes are "dark" and their functions remain to be deciphered using functional genetics; (8) Initial insights into the genomic basis of parasitism and mutualism have emerged. The review then highlights functionally unique and interesting genes. Future research needs to obtain a finished genome, tackle large genomes, characterize the unknown genes, and develop a quantitative molecular ecological model for addressing ecological questions.

Two novel glutathione S-transferase (GST) genes in the toxic marine dinoflagellate Alexandrium pacificum and their transcriptional responses to environmental contaminants

The present study identified two novel glutathione S-transferase (GST) genes from the toxic dinoflagellate Alexandrium pacificum and examined their molecular characteristics and transcriptional responses to algicides and environmental contaminants. Bioinformatic analysis revealed that both ApGSTs are cytosolic, belonging to the chi-like class (ApGST1) and an undefined class (ApGST2). The overall expression of ApGSTs showed similar patterns depending on the exposed contaminants, while they were differently regulated by polychlorinated biphenyl (PCB). Copper treatments (CuCl2 and CuSO4) did not significantly induce the expression of ApGSTs. The highest up-regulations of ApGST1 and ApGST2 were under 6-h treatments of 0.10 and 0.50 mg L-1 NaOCl. Interestingly, only ApGST1 increased significantly after 0.10, 0.50, and 1.00 mg L-1 of PCB exposure (6 h). Intracellular reactive oxygen species (ROS) increased considerably under NaOCl; however, it was not significantly higher in the PCB-treated cells. GST activity was increased by NaOCl and PCB treatments, but only PCB caused apoptosis. These results suggest that GSTs are involved in the first line of phase II detoxification, protecting dinoflagellate cells against oxidative damage.

Characterization and regulation of salt upregulated cyclophilin from a halotolerant strain of Penicillium oxalicum

Penicillium species are an industrially important group of fungi. Cyclophilins are ubiquitous proteins and several members of this family exhibit peptidyl-prolyl cis-trans isomerase (PPIase) activity. We had earlier demonstrated that the salt-induced PPIase activity in a halotolerant strain of P. oxalicum was associated with enhanced expression of a cyclophilin gene, PoxCYP18. Cloning and characterization of PoxCYP18 revealed that its cDNA consists of 522 bp encoding a protein of 173 amino acid residues, with predicted molecular mass and pI values of 18.91 kDa and 8.87, respectively. The recombinant PoxCYP18 can catalyze cis-trans isomerization of peptidyl-prolyl bond with a catalytic efficiency of 1.46 × 107 M-1 s-1 and is inhibited specifically only by cyclosporin A, with an inhibition constant of 5.04 ± 1.13 nM. PoxCYP18 consists of two cysteine residues at positions - 45 and - 170, and loses its activity under oxidizing conditions. Substitution of these residues alone or together by site-directed mutagenesis revealed that the PPIase activity of PoxCYP18 is regulated through a redox mechanism involving the formation of disulfide linkages. Heterologous expression of PoxCYP18 conferred enhanced tolerance to salt stress in transgenic E. coli cells, implying that this protein imparts protection to cellular processes against salt-induced damage.

Transcriptomic analysis reveals distinct mechanisms of adaptation of a polar picophytoplankter under ocean acidification conditions

Human emissions of carbon dioxide are causing irreversible changes in our oceans and impacting marine phytoplankton, including a group of small green algae known as picochlorophytes. Picochlorophytes grown in natural phytoplankton communities under future predicted levels of carbon dioxide have been demonstrated to thrive, along with redistribution of the cellular metabolome that enhances growth rate and photosynthesis. Here, using next-generation sequencing technology, we measured levels of transcripts in a picochlorophyte Chlorella, isolated from the sub-Antarctic and acclimated under high and current ambient CO2 levels, to better understand the molecular mechanisms involved with its ability to acclimate to elevated CO2. Compared to other phytoplankton taxa that induce broad transcriptomic responses involving multiple parts of their cellular metabolism, the changes observed in Chlorella focused on activating gene regulation involved in different sets of pathways such as light harvesting complex binding proteins, amino acid synthesis and RNA modification, while carbon metabolism was largely unaffected. Triggering a specific set of genes could be a unique strategy of small green phytoplankton under high CO2 in polar oceans.

Effects of zinc and mercury on ROS-mediated oxidative stress-induced physiological impairments and antioxidant responses in the microalga Chlorella vulgaris

The rapid growth of industrialization and urbanization results in deterioration of freshwater systems around the world, rescinding the ecological balance. Among many factors that lead to adverse effects in aquatic ecology, metals are frequently discharged into aquatic ecosystems from natural and anthropogenic sources. Metals are highly persistent and toxic substances in trace amounts and can potentially induce severe oxidative stress in aquatic organisms. In this study, adverse effects of the two metal elements zinc (maximum concentration of 167.25 mg/L) and mercury (104.2 mg/L) were examined using Chlorella vulgaris under acute and chronic exposure period (48 h and 7 days, respectively). The metal-induced adverse effects have been analyzed through photosynthetic pigment content, total protein content, reactive oxygen species (ROS) generation, antioxidant enzymatic activities, namely catalase and superoxide dismutase (SOD) along with morphological changes in C. vulgaris. Photosynthetic pigments were gradually reduced (~32-100% reduction) in a dose-dependent manner. Protein content was initially increased during acute (~8-12%) and chronic (~57-80%) exposure and decreased (~44-56%) at higher concentration of the two metals (80%). Under the two metal exposures, 5- to 7-fold increase in ROS generation indicated the induction of oxidative stress and subsequent modulations in antioxidant activities. SOD activity was varied with an initial increase (58-129%) followed by a gradual reduction (~3.7-79%), while ~1- to 12-fold difference in CAT activity was observed in all experimental condition (~83 to 1605%). A significant difference was observed in combined toxic exposure (Zn+Hg), while comparing the toxic endpoint data of individual metal exposure (Zn and Hg alone). Through this work, lethal effects caused by single and combined toxicity of zinc and mercury were assessed, representing the significance of appropriate monitoring system to trim down the release of metal contaminants into the aquatic ecosystems.

Nitric oxide production and signalling in algae

Nitric oxide (NO) was the first identified gaseous messenger and is now well established as a major ubiquitous signalling molecule. The rapid development of our understanding of NO biology in embryophytes came with the partial characterization of the pathways underlying its production and with the decrypting of signalling networks mediating its effects. Notably, the identification of proteins regulated by NO through nitrosation greatly enhanced our perception of NO functions. In comparison, the role of NO in algae has been less investigated. Yet, studies in Chlamydomonas reinhardtii have produced key insights into NO production through the identification of NO-forming nitrite reductase and of S-nitrosated proteins. More intriguingly, in contrast to embryophytes, a few algal species possess a conserved nitric oxide synthase, the main enzyme catalysing NO synthesis in metazoans. This latter finding paves the way for a deeper characterization of novel members of the NO synthase family. Nevertheless, the typical NO-cyclic GMP signalling module transducing NO effects in metazoans is not conserved in algae, nor in embryophytes, highlighting a divergent acquisition of NO signalling between the green and the animal lineages.

Plant Cyclophilins: Multifaceted Proteins With Versatile Roles

Cyclophilins constitute a family of ubiquitous proteins that bind cyclosporin A (CsA), an immunosuppressant drug. Several of these proteins possess peptidyl-prolyl cis-trans isomerase (PPIase) activity that catalyzes the cis-trans isomerization of the peptide bond preceding a proline residue, essential for correct folding of the proteins. Compared to prokaryotes and other eukaryotes studied until now, the cyclophilin gene families in plants exhibit considerable expansion. With few exceptions, the role of the majority of these proteins in plants is still a matter of conjecture. However, recent studies suggest that cyclophilins are highly versatile proteins with multiple functionalities, and regulate a plethora of growth and development processes in plants, ranging from hormone signaling to the stress response. The present review discusses the implications of cyclophilins in different facets of cellular processes, particularly in the context of plants, and provides a glimpse into the molecular mechanisms by which these proteins fine-tune the diverse physiological pathways.

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.

Small heat shock protein genes of the green algae Closterium ehrenbergii: Cloning and differential expression under heat and heavy metal stresses

The freshwater green algae Closterium ehrenbergii has been considered as a model for eco-toxicological assessment in aquatic systems. Heat shock proteins (HSPs) are a class of highly conserved proteins produced in all living organisms, which participate in environmental stress responses. In the present study, we determined the cDNA sequences of small heat shock protein 10 (sHSP10) and sHSP17.1 from C. ehrenbergii, and examined the physiological changes and transcriptional responses of the genes after exposure to thermal shock and toxicants treatments. The open reading frame (ORF) of CeHSP10 was 300 bp long, encoding 99 amino acid (aa) residues (10.53 kDa) with a GroES chaperonin conserved site of 22 aa. The CeHSP17.1 had a 468 bp ORF, encoding 155 aa with a conserved C-terminal α-crystallin domain. For heat stress, cells presented pigment loss and possible chloroplast damage, with an up-regulation in the expression of both sHSP10 and sHSP17.1 genes. As for the heavy metal stressors, an increase in the production of reactive oxygen species was registered in a dose dependent manner, with a significant up-regulation of both sHSP10 and sHSP17.1 genes. These results suggest that sHSP genes in C. ehrenbergii may play a role in responses to stress environments, and they could be used as an early detection parameter as biomarker genes in molecular toxicity assessments.

Physiological and molecular responses of Prorocentrum donghaiense to dissolved inorganic phosphorus limitation

Prorocentrum donghaiense is an important dinoflagellate as it frequently forms harmful algal blooms that cause serious damage to marine ecosystems and fisheries in the coast of East China Sea. Previous studies showed that phosphorus acquisition (especially inorganic phosphorus) was the limiting factor for P. donghaiense growth. However, the responsive mechanism of this microalga under dissolved inorganic phosphorus (DIP) limitation is poorly understood. In this work, the physiological parameters and differentially expressed genes in P. donghaiense response to DIP limitation were comparatively analyzed. DIP-depleted P. donghaiense displayed decreased growth rate, enlarged cell size, decreased cellular phosphorus content, and high AP activities. A forward suppression subtractive hybridization (SSH) library representing differentially upregulated genes in P. donghaiense under DIP-depleted conditions was constructed, and 134 ESTs were finally identified, with a significant identity (E values<1×10^-4) to the deposited genes (proteins) in the corresponding databases. Five representative genes, namely, NAD-dependent deacetylase, phosphoglycolate phosphatase, heat shock protein (HSP) 90, rhodopsin, and HSP40 were investigated through real-time quantitative PCR to verify the effectiveness of the established SSH library. Results showed that all the selected genes were differentially expressed and thus indicated that the established SSH library generally represented differentially expressed genes. These genes were classified into 11 categories according to their gene ontology annotations of biological processes. The members involved in functional responses such as cell defense/homeostasis, phosphorus metabolism, and cellular cycles were specially discussed. This study is the first to perform a global analysis of differentially expressed functional genes in P. donghaiense under DIP-depleted condition. It provided new insights into the molecular adaptive mechanisms of dinoflagellate in response to phosphorous limitation and elucidating the formation mechanism of algal blooms.

A Novel Cyclophilin B Gene in the Red Tide Dinoflagellate Cochlodinium polykrikoides: Molecular Characterizations and Transcriptional Responses to Environmental Stresses

The marine dinoflagellate Cochlodinium polykrikoides is one of the most common ichthyotoxic species that causes harmful algal blooms (HABs), which leads to ecological damage and huge economic loss in aquaculture industries. Cyclophilins (CYPs) belong to the immunophilin superfamily, and they may play a role in the survival mechanisms of the dinoflagellate in stress environments. In the present study, we identified a novel cyclophilin gene from C. polykrikoides and examined physiological and gene transcriptional responses to biocides copper sulphate (CuSO₄) and sodium hypochlorite (NaOCl). The full length of CpCYP was 903 bp, ranging from the dinoflagellate splice leader (DinoSL) sequence to the polyA tail, comprising a 639 bp ORF, a 117 bp 5′-UTR, and a 147 bp 3′-UTR. Motif and phylogenetic comparisons showed that CpCYP was affiliated to group B of CYP. In biocide stressors, cell counts, chlorophyll a, and photosynthetic efficiency (Fv/Fm) of C. polykrikoides were considerably decreased in both exposure time- and dose-dependent manners. In addition, CpCYP gene expression was significantly induced after 24 h exposure to the biocide-treated stress conditions. These results indicate an effect of the biocides on the cell physiology and expression profile of CpCYP, suggesting that the gene may play a role in environmental stress responses.

Microbial cyclophilins: specialized functions in virulence and beyond

Cyclophilins belong to the superfamily of peptidyl-prolyl cis/trans isomerases (PPIases, EC: 5.2.1.8), the enzymes that catalyze the cis/trans isomerization of peptidyl-prolyl peptide bonds in unfolded and partially folded polypeptide chains and native state proteins. Cyclophilins have been extensively studied, since they are involved in multiple cellular processes related to human pathologies, such as neurodegenerative disorders, infectious diseases, and cancer. However, the presence of cyclophilins in all domains of life indicates a broader biological importance. In this mini-review, we summarize current advances in the study of microbial cyclophilins. Apart from their anticipated role in protein folding and chaperoning, cyclophilins are involved in several other biological processes, such as cellular signal transduction, adaptation to stress, control of pathogens virulence, and modulation of host immune response. Since many existing family members do not have well-defined functions and novel ones are being characterized, the requirement for further studies on their biological role and molecular mechanism of action is apparent.

Physiological and biochemical responses of the freshwater green algae Closterium ehrenbergii to the common disinfectant chlorine

Chlorine (Cl2) is widely used as a disinfectant in water treatment plants and for cleaning swimming pools; it is finally discharged into aquatic environments, possibly causing damage to the non-target organisms in the receiving water bodies. Present study evaluated the effects of the biocide Cl2 to the green alga Closterium ehrenbergii (C. ehrenbergii). Growth rate, chlorophyll a levels, carotenoids, chlorophyll autofluorescence, and antioxidant enzymes were monitored up to 72-h after Cl2 exposure. C. ehrenbergii showed dose-dependent decrease in growth rate and cell division after exposure to Cl2. By using cell counts, the median effective concentration (EC50)-72-h was calculated to be 0.071mgL(-1). Cl2 significantly decreased the pigment levels and chlorophyll autofluorescence intensity, indicating that the photosystem was damaged in C. ehrenbergii. In addition, it increased the production of reactive oxygen species (ROS) in the cells. This stressor significantly increased the activities of antioxidant enzymes, including superoxide dismutase (SOD), catalase, and glutathione, and affected the physiology of the cells. These results indicate that Cl2 induces oxidative stress in the cellular metabolic process and leads to physiological and biochemical damages in the green algae. Cl2 discharged in industrial effluents and from water treatment plants may cause harmful effects to the C. ehrenbergii a common freshwater microalgae and other non-target organisms.