Proteomic analysis provides new insights into the adaptive response of a dinoflagellate Prorocentrum donghaiense to changing ambient nitrogen

Utilizing proteomics to identify and optimize microalgae strains for high-quality dietary protein: a review

Algae-derived protein has immense potential to provide high-quality protein foods for the expanding human population. To meet its potential, a broad range of scientific tools are required to identify optimal algal strains from the hundreds of thousands available and identify ideal growing conditions for strains that produce high-quality protein with functional benefits. A research pipeline that includes proteomics can provide a deeper interpretation of microalgal composition and biochemistry in the pursuit of these goals. To date, proteomic investigations have largely focused on pathways that involve lipid production in selected microalgae species. Herein, we report the current state of microalgal proteome measurement and discuss promising approaches for the development of protein-containing food products derived from algae.

OMICS Approaches to Assess Dinoflagellate Responses to Chemical Stressors

Dinoflagellates are important primary producers known to form Harmful Algae Blooms (HABs). In water, nutrient availability, pH, salinity and anthropogenic contamination constitute chemical stressors for them. The emergence of OMICs approaches propelled our understanding of dinoflagellates' responses to stressors. However, in dinoflagellates, these approaches are still biased, as transcriptomic approaches are largely conducted compared to proteomic and metabolomic approaches. Furthermore, integrated OMICs approaches are just emerging. Here, we report recent contributions of the different OMICs approaches to the investigation of dinoflagellates' responses to chemical stressors and discuss the current challenges we need to face to push studies further despite the lack of genomic resources available for dinoflagellates.

Transcriptomic analysis provides insights into the algicidal mechanism of cocamidopropyl betaine against the red tide microalgae Skeletonema costatum

This study investigated the effect of the surfactant cocamidopropyl betaine (CAB) on the growth of red tide microalgae Skeletonema costatum. It was found that CAB caused cell lysis in a time- and dose-dependent manner and significantly inhibited the growth of S. costatum. Additionally, the transcriptomic approach was coupled with physiological analysis to elucidate the inhibitory mechanism of CAB on S. costatum. Among the 30726 genes identified, 17720 and 20583 genes were differentially expressed after treatment for 3 h and 6 h, respectively, which revealed that CAB redirected metabolic pathways, of which the expressions of genes related to the proteasome, ABC transporters, and amino acid-related metabolism were significantly upregulated, while genes involved in photosynthesis, biofilm and cell wall synthesis, mitogen-activated protein kinase (MAPK) cascades and antioxidant system were downregulated. The results above corresponded to the decreasing antioxidant enzymes activities, protein and photosynthetic pigments contents, as well as the increasing malondialdehyde (MDA) content. Our study presented herein shed light on the algicidal mechanism of CAB at the transcriptome level and was useful to red tide control, and marine environmental protection.

An overview of Prorocentrum donghaiense blooms in China: Species identification, occurrences, ecological consequences, and factors regulating prevalence

Prorocentrum donghaiense Lu (also identified as Prorocentrum shikokuense Hada and Prorocentrum obtusidens Schiller) is a bloom-forming dinoflagellate species distributed worldwide. Blooms of P. donghaiense occur annually in adjacent waters of the East China Sea (ECS), especially in the waters near the Changjiang River Estuary. Blooms of this species have also been reported in nearby Japanese and Korean waters. There has been an apparent bloom-forming species succession pattern in the ECS since 2000, with diatom blooms in the early spring, shifting to long-lasting and large-scale dinoflagellate blooms dominated by P. donghaiense during the spring, and finally ended by diatom and/or Noctiluca scintillans blooms in summer. These bloom succession patterns were closely correlated with changes in environmental factors, such as temperature increase and anthropogenic eutrophication. Decreasing silicate by the construction of the Three Gorges Dam and increasing dissolved inorganic nitrogen flux were mainly influenced by high intensity human activities in the Changjiang River watershed, resulting in low Si/N ratio and high N/P ratios, possibly accelerating outbreak of P. donghaiense blooms. Phosphorous deficiency might be the most critical factor controlling the succession of microalgal blooms from diatoms to dinoflagellates. Prorocentrum donghaiense is a nontoxic species, but it can disrupt marine ecosystem by decreasing phytoplankton biodiversity and changing the structure of the food chain. Prorocentrum donghaiense blooms in the ECS have been intensively studied during the last two decades. Several possible mechanisms that contribute or trigger the annual blooms of this species have been proposed, but further research is required particularly on the aspect of nutrient budget, ecosystem impacts, as well as social-economic impact assessment.

Omics study of harmful algal blooms in China: Current status, challenges, and future perspectives

In the past two decades, the frequency, scale, and scope of harmful algal blooms (HABs) have increased significantly in the coastal waters of China. HABs have become a major ecological and environmental problem in China that seriously threatens the structure and function of marine ecosystems, the sustainable development of mariculture, and the health of human beings. Much effort has been devoted to studying HABs in China, and great achievements have been made in understanding the oceanographic and ecological mechanisms of HABs as well as the biology and physiological ecology of HAB-causing species. Furthermore, state-of-the-art omics technologies, such as transcriptomics and proteomics, have been used to elucidate the physiological responses of HAB-causing species to environmental changes, the biosynthesis of paralytic shellfish toxin, and the mechanisms underlying the formation of HABs. This review summarizes omics studies of HABs in China over the past few years and discusses challenges and future perspectives of HAB research.

Transcriptome responses of the dinoflagellate Karenia mikimotoi driven by nitrogen deficiency

The availability of ambient N nutrient is often correlated with the occurrences of harmful algal bloom formed by certain dinoflagellates, making it important to understand how these species might be responding to such conditions. Here, transcriptome sequencing of Karenia mikimotoi was conducted to understand the underlying molecular mechanisms by which this dinoflagellate copes with nitrogen (N) deficiency. Transcriptomic analysis revealed 8802 unigenes (3.56%) that were differentially expressed with ≥ 2-fold change. Under N-depleted conditions, genes involved in glycolysis, fatty acid metabolism, and the tricarboxylic acid (TCA) cycle as well as lipid accumulation were significantly upregulated. The elevated expression of enzymes used in protein degradation and turnover suggests possible metabolic reconfiguration towards accelerated N recycling. Moreover, a significant increase in urea transporter was observed, indicating increased assimilation of organic nitrogen resources as an alternative in N-depleted cultures of K. mikimotoi. The down-regulated glutamate synthase genes were also identified under N deficiency, suggesting suppression of primary amino acid synthesis to save N resource. Taken together, results of this study show enhanced multiple N resource acquisition and reuse of multiple N resources constitute a comprehensive strategy to cope with N deficiency in a dinoflagellate.

Integrated effects of Ulva prolifera bloom and decay on nutrients inventory and cycling in marginal sea of China

Ulva prolifera blooms occur annually in the Yellow Sea. Most studies focus on how U. prolifera blooming is influenced by nitrogen chemical forms and concentrations, while little concern goes to how U. prolifera bloom-decay cycle would impact local seawater nutrients structure. Therefore, we use ¹⁵N-labeled NO₃ tracers and transcriptome analysis to determine N uptake, metabolism, and interconversion during U. prolifera growth and decay, so that we can quantify the conversions rate and fluxes of different nitrogen chemical forms. U. prolifera absorbes 17.37 μmol g^-1·d^-1 NO₃-N during growth. NO₃-N predominates (73.75-92.15%) in the dissolved inorganic nitrogen (DIN) in U. prolifera. During decay, NH₄-N accountes for 60.87-92.13% of the in-cell DIN. The decomposing U. prolifera releases considerable amounts of NH₄-N and dissolved organic nitrogen (DON) (63.8-98.2% < 1 kDa fraction and 1.8-36.2% is > 1 kDa fraction) into the ambient environment. The high DON release rate (59.57 μmol g^-1 d^-1) indicates active DON biosynthesis in U. prolifera. The isotope ¹⁵NO₃-N tracer showes that 73.6% of the ¹⁵NO₃-N is transformed to DON. The <1 kDa and the >1 kDa fractions account for 67.46-90.86% and 9.14-32.54% of the DON, respectively. The high efficiency of U. prolifera in utilizing NO₃-N is explained by the responsive nitrate/nitrite transporter in cell membrane, and the DON biosynthesized capability is attributed to the up-regulated glutamine synthetase. Our study highlights the unique role of U. prolifera as a "Nitrogen-Pump" in converting nitrogen chemical forms during its bloom-decay cycle and quantifies its impacts on local N-nutrients inventory.

Quantitative proteomic analysis provides insights into the algicidal mechanism of Halobacillus sp. P1 against the marine diatom Skeletonema costatum

Algicidal behavior is a common interaction between marine microalgae and bacteria, especially in the dissipation phase of algal blooms. The marine bacterium Halobacillus sp. P1 was previously isolated and exhibits high algicidal activity against the diatom Skeletonema costatum. However, little is known about the mechanism underlying this algicidal process. Here, a tandem mass tag (TMT)-based proteomic approach was coupled with physiological analysis to investigate the cellular responses of S. costatum when treated with P1 culture supernatant. Among the 4582 proteins identified, 82 and 437 proteins were differentially expressed after treatment for 12 and 24 h, respectively. The proteomic results were in accordance with the results of verification by parallel reaction monitoring (PRM) assays. Proteins involved in reactive oxygen species scavenging, protein degradation and transport were upregulated, while proteins participating in nitrogen metabolism, protein translation, photosynthetic pigment biosynthesis and cell cycle regulation were significantly downregulated (p-value ≤0.05), corresponding to the increasing malondialdehyde content and the decreasing nitrogen, protein and chlorophyll a contents. A nutrient competitive relationship might exist between the bacterium P1 and S. costatum, and the inhibition of nitrogen metabolism by the P1 culture supernatant might be the key lethal factor that results in the dysfunction of S. costatum metabolism. Our study sheds light on the algicidal mechanism of P1 at the molecular level and provides new insights into algae-bacteria interactions.

Transcriptomic response to changing ambient phosphorus in the marine dinoflagellate Prorocentrum donghaiense

Dinoflagellates represent major contributors to the harmful algal blooms in the oceans. Phosphorus (P) is an essential macronutrient that limits the growth and proliferation of dinoflagellates. However, the specific molecular mechanisms involved in the P acclimation of dinoflagellates remain poorly understood. Here, the transcriptomes of a dinoflagellate Prorocentrum donghaiense grown under inorganic P-replete, P-deficient, and inorganic- and organic P-resupplied conditions were compared. Genes encoding low- and high-affinity P transporters were significantly down-regulated in the P-deficient cells, while organic P utilization genes were significantly up-regulated, indicating strong ability of P. donghaiense to utilize organic P. Up-regulation of membrane phospholipid catabolism and endocytosis provided intracellular and extracellular organic P for the P-deficient cells. Physiological responses of P. donghaiense to dissolved inorganic P (DIP) or dissolved organic P (DOP) resupply exhibited insignificant differences. However, the corresponding transcriptomic responses significantly differed. Although the expression of multiple genes was significantly altered after DIP resupplementation, few biological processes varied. In contrast, various metabolic processes associated with cell growth, such as translation, transport, nucleotide, carbohydrate and lipid metabolisms, were significantly altered in the DOP-resupplied cells. Our results indicated that P. donghaiense evolved diverse DOP utilization strategies to adapt to low P environments, and that DOPs might play critical roles in the P. donghaiense bloom formation.

Algicidal Activity of Novel Marine Bacterium Paracoccus sp. Strain Y42 against a Harmful Algal-Bloom-Causing Dinoflagellate, Prorocentrum donghaiense

Prorocentrum donghaiense blooms occur frequently in the Yangtze River estuary and the adjacent East China Sea. These blooms have damaged marine ecosystems and caused enormous economic losses over the past 2 decades. Thus, highly efficient, low-cost, ecofriendly approaches must be developed to control P. donghaiense blooms. In this study, a bacterial strain (strain Y42) was identified as Paracoccus sp. and was used to lyse P. donghaiense The supernatant of the strain Y42 culture was able to lyse P. donghaiense, and the algicidal activity of this Y42 supernatant was stable with different temperatures and durations of light exposure and over a wide pH range. In addition to P. donghaiense, Y42 showed high algicidal activity against Alexandrium minutum, Scrippsiella trochoidea, and Skeletonema costatum, suggesting that it targets primarily Pyrrophyta. To clarify the algicidal effects of Y42, we assessed algal lysis and determined the chlorophyll a contents, photosynthetic activity, and malondialdehyde contents of P. donghaiense after exposure to the Y42 supernatant. Scanning electron microscopy and transmission electron microscopy analyses showed that the Y42 supernatant disrupted membrane integrity and caused algal cell breakage at the megacytic zone. Photosynthetic pigment loss and significant declines in both photosynthetic efficiency and the electron transport rate indicated that the Y42 supernatant damaged the photosynthetic system of P. donghaiense Malondialdehyde overproduction indicated that the Y42 supernatant caused lipid peroxidation and oxidative damage to membrane systems in the algal cell, ultimately leading to death. The findings of this study reveal the potential of Y42 to remove algal cells from P. donghaiense blooms.IMPORTANCEP. donghaiense is one of the most common dinoflagellate species that form harmful algal blooms, which frequently cause serious ecological pollution and pose health hazards to humans and other animals. Screening for bacteria with high algicidal activity against P. donghaiense and studying their algicidal processes and characteristics will contribute to an understanding of their algicidal effects and provide a theoretical basis for preventing algal blooms and reducing their harm to the environment. This study reports the algicidal activity and characteristics of Paracoccus against P. donghaiense The stability of the algicidal activity of Paracoccus in different environments (including different temperature, pH, and sunlight conditions) indicates its potential for use in the control of P. donghaiense blooms.

Exploring dinoflagellate biology with high-throughput proteomics

Dinoflagellates are notorious for their ability to form the harmful algal blooms known as "red tides," yet the mechanisms underlying bloom formation remain poorly understood. Despite recent advances in nucleic acid sequencing, which have generated transcriptomes from a wide range of species exposed to a variety of different conditions, measuring changes in RNA levels have not generally produced great insight into dinoflagellate cell biology or environmental physiology, nor do we have a thorough grasp on the molecular events underpinning bloom formation. Not only is the transcriptomic response of dinoflagellates to environmental change generally muted, but there is a markedly low degree of congruency between mRNA expression and protein expression in dinoflagellates. Herein we discuss the application of high-throughput proteomics to the study of dinoflagellate biology. By profiling the cellular protein complement (the proteome) instead of mRNA (the transcriptome), the biomolecular events that underlie the changes of phenotypes can be more readily evaluated, as proteins directly determine the structure and the function of the cell. Recent advances in proteomics have seen this technique become a high-throughput method that is now able to provide a perspective different from the more commonly employed nucleic acid sequencing. We suggest that the time is ripe to exploit these new technologies in addressing the many mysteries of dinoflagellate biology, such as how the symbiotic dinoflagellate inhabiting reef corals acclimate to increases in temperature, as well as how harmful algal blooms are initiated at the sub-cellular level. Furthermore, as dinoflagellates are not the only eukaryotes that demonstrate muted transcriptional responses, the techniques addressed within this review are amenable to a wide array of organisms.

Circadian and irradiance effects on expression of antenna protein genes and pigment contents in dinoflagellate Prorocentrum donghaiense (Dinophycae)

PCP and acpPC are the two major antennae proteins that bind pigments in peridinin-containing dinoflagellates. The relationship between antennae proteins and cellular pigments at molecular level is still poorly understood. Here we identified and characterized the two antennae protein genes in dinoflagellate Prorocentrum donghaiense under different light conditions. The mature PCP protein was 32 kDa, while acpPC was a polyprotein each of 19 kDa. Both genes showed higher expression under low light than under high light, suggesting their possible role in a low light adaptation mechanism. The two genes showed differential diel expression rhythm, with PCP being more highly expressed in the dark than in the light period and acpPC the other way around. HPLC analysis of cellular pigments indicated a diel change of chlorophyll c2, but invariability of other pigments. A stable peridinin: chlorophyll a pigment ratio was detected under different light intensities and over the diel cycle, although the diadinoxanthin:chlorophyll a ratio increased significantly with light intensity. The results suggest that 1) PCP and acpPC genes are functionally distinct, 2) PCP and acpPC can function under low light as an adaptive mechanism in P. donghaiense, 3). the ratios of diadinoxanthin:chlorophyll a and peridinin: chlorophyll a can potentially be used as an indicator of algal photophysiological status and a pigment signature respectively under different light conditions in P. donghaiense.

Comparative proteomic studies of a Scrippsiella acuminata bloom with its laboratory-grown culture using a 15N-metabolic labeling approach

Comparative proteomic analysis was carried out using cells isolated from a natural bloom of Scrippsiella acuminata (formerly Scrippsiella trochoidea) in the early bloom (EB) and late bloom (LB) stages as well as with laboratory-grown cultures of cells isolated from the bloom in early growth (EG) and late growth (LG) stages. For quantitative proteomics, LG cells were grown for 20 generations in the presence of ¹⁵N as a reference (i.e. common denominator) for all comparison. In comparisons with early growth laboratory grown cells (EG/LG), nearly 64% of proteins identified had similar abundance levels, with the remaining 36% mostly more abundant in EG cells. Calvin cycle, amino acid metabolism, chlorophyll biosynthesis and transcription/translation were among the up-regulated processes. Cells from the early bloom (EB/LG) had a greater abundance of transporters and enzymes related to light harvesting and oxidative phosphorylation, while the abundance of these proteins decreased in late bloom cells (LB/LG). All natural bloom samples showed either constant or lower abundance levels of enzymes involved in sugar synthesis and glycolytic pathways compared to laboratory grown cells. Our results represent the first examination of the proteomic changes in the development of a natural dinoflagellate bloom. Importantly, our results demonstrate that the proteome of cells grown in the laboratory is distinctively different from cells in a natural bloom.

Cell Cycle-Dependent Expression Dynamics of G1/S Specific Cyclin, Cellulose Synthase and Cellulase in the Dinoflagellate Prorocentrum donghaiense

Dinoflagellates undergo a typical eukaryotic cell cycle consisting of G1, S, G2, and M phases and some of the typical cell cycle related genes have been computationally identified. However, very few of these genes have been experimentally linked to the cell cycle phases. Besides, although thecate dinoflagellates are known to possess theca composed of cellulose, information on cellulose synthesis and degradation associated with the cell cycle is also limited. In this study, we isolated G1/S cyclin, cellulose synthase and cellulase encoding genes in dinoflagellate Prorocentrum donghaiense. Further, using reverse transcription quantitative PCR (RT-qPCR), we characterized the expression profiles of the three genes throughout the cell cycle. All three showed clear expression dynamics throughout the cell cycle, with fold changes of 26, 2.4 and 9.3 for G1/S cyclin, cellulose synthase and cellulase gene, respectively. The transcript abundance of G1/S cyclin increased in late G1 phase and dropped in early S phase, indicating that this protein is involved in the G1/S transition. Throughout the cell cycle, the average transcript level of cellulose synthase was 4.5-fold higher than that of cellulase. Cellulose synthase and cellulase gene expressions showed peak transcript abundances at middle G1 phase and G2M phase, respectively, indicating the respective roles of these enzymes in the growth of newly divided cells and in cytokinesis. Our results suggest that G1/S cyclin, cellulase, and cellulose synthase genes associated with G1/S transition, G2M, and G1 phases of the cell cycle and are candidates of biomarkers for assessing growth status of P. donghaiense.

Comparative Transcriptomic Analysis Reveals Novel Insights into the Adaptive Response of Skeletonema costatum to Changing Ambient Phosphorus

Phosphorus (P) is a limiting macronutrient for diatom growth and productivity in the ocean. Much effort has been devoted to the physiological response of marine diatoms to ambient P change, however, the whole-genome molecular mechanisms are poorly understood. Here, we utilized RNA-Seq to compare the global gene expression patterns of a marine diatom Skeletonema costatum grown in inorganic P-replete, P-deficient, and inorganic- and organic-P resupplied conditions. In total 34,942 unique genes were assembled and 20.8% of them altered significantly in abundance under different P conditions. Genes encoding key enzymes/proteins involved in P utilization, nucleotide metabolism, photosynthesis, glycolysis, and cell cycle regulation were significantly up-regulated in P-deficient cells. Genes participating in circadian rhythm regulation, such as circadian clock associated 1, were also up-regulated in P-deficient cells. The response of S. costatum to ambient P deficiency shows several similarities to the well-described responses of other marine diatom species, but also has its unique features. S. costatum has evolved the ability to re-program its circadian clock and intracellular biological processes in response to ambient P deficiency. This study provides new insights into the adaptive mechanisms to ambient P deficiency in marine diatoms.

Transcriptome Analysis of Scrippsiella trochoidea CCMP 3099 Reveals Physiological Changes Related to Nitrate Depletion

Dinoflagellates are a major component of marine phytoplankton and many species are recognized for their ability to produce harmful algal blooms (HABs). Scrippsiella trochoidea is a non-toxic, marine dinoflagellate that can be found in both cold and tropic waters where it is known to produce “red tide” events. Little is known about the genomic makeup of S. trochoidea and a transcriptome study was conducted to shed light on the biochemical and physiological adaptations related to nutrient depletion. Cultures were grown under N and P limiting conditions and transcriptomes were generated via RNAseq technology. De novo assembly reconstructed 107,415 putative transcripts of which only 41% could be annotated. No significant transcriptomic response was observed in response to initial P depletion, however, a strong transcriptional response to N depletion was detected. Among the down-regulated pathways were those for glutamine/glutamate metabolism as well as urea and nitrate/nitrite transporters. Transcripts for ammonia transporters displayed both up- and down-regulation, perhaps related to a shift to higher affinity transporters. Genes for the utilization of DON compounds were up-regulated. These included transcripts for amino acids transporters, polyamine oxidase, and extracellular proteinase and peptidases. N depletion also triggered down regulation of transcripts related to the production of Photosystems I & II and related proteins. These data are consistent with a metabolic strategy that conserves N while maximizing sustained metabolism by emphasizing the relative contribution of organic N sources. Surprisingly, the transcriptome also contained transcripts potentially related to secondary metabolite production, including a homolog to the Short Isoform Saxitoxin gene (sxtA) from Alexandrium fundyense, which was significantly up-regulated under N-depletion. A total of 113 unique hits to Sxt genes, covering 17 of the 34 genes found in C. raciborskii were detected, indicating that S. trochoidea has previously unrecognized potential for the production of secondary metabolites with potential toxicity.