Molecular analysis of physiological responses to changes in nitrogen in a marine macroalga, Porphyra yezoensis (Rhodophyta)

Heat stress memory differentially regulates the expression of nitrogen transporter genes in the filamentous red alga 'Bangia' sp. ESS1

Introduction

To withstand high temperatures that would be lethal to a plant in the naïve state, land plants must establish heat stress memory. The acquisition of heat stress tolerance via heat stress memory in algae has only been observed in the red alga 'Bangia' sp. ESS1.

Methods

In this study, we further evaluated the intrinsic ability of this alga to establish heat stress memory by monitoring hydrogen peroxide (H2O2) production and examining the relationship between heat stress memory and the expression of genes encoding nitrogen transporters, since heat stress generally reduces nitrogen absorption. Next, genes encoding nitrogen transporters were selected from our unpublished transcriptome data of 'Bangia' sp. ESS1.

Results

We observed a reduction in H2O2 content when heat stress memory was established in the alga. In addition, six ammonium transporter genes, a single-copy nitrate transporter gene and two urea transporter genes were identified. Two of these nitrogen transporter genes were induced by heat stress but not by heat stress memory, two genes showed heat stress memory-dependent expression, and one gene was induced by both treatments. Heat stress memory therefore differentially regulated the expression of the nitrogen transporter genes by reducing heat stress-inducible gene expression and inducing heat stress memory-dependent gene expression.

Discussion

These findings point to the functional diversity of nitrogen transporter genes, which play different roles under various heat stress conditions. The characteristic effects of heat stress memory on the expression of individual nitrogen transporter genes might represent an indispensable strategy for reducing the threshold of sensitivity to recurrent high-temperature conditions and for maintaining nitrogen absorption under such conditions in 'Bangia' sp. ESS1.

Diversity and ecological function of urease-producing bacteria in the cultivation environment of Gracilariopsis lemaneiformis

Urease-producing bacteria (UPB) provide inorganic nitrogen for primary producers by hydrolyzing urea, and play an important role in marine nitrogen cycle. However, there is still an incomplete understanding of UPB and their ecological functions in the cultivation environment of the red macroalgae Gracilariopsis lemaneiformis. This study comprehensively analyzed the diversity of culturable UPB and explored their effects on urea uptake by G. lemaneiformis. A total of 34 isolates belonging to four main bacterial phyla i.e. (Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria) were identified through 16S rRNA sequencing and were screened for UPB by urea agar chromogenic medium assay and ureC gene cloning. Our data revealed that only 8 strains contained urease. All of these UPB exhibited different urease activities, which were determined by the Berthelot reaction colorimetry assay. Additionally, the UPB strain (G13) isolated from G. lemaneiformis with higher urease activity was selected for co-culture with G. lemaneiformis to explore its role in promoting or inhibiting nitrogen uptake by macroalgae. The results showed a significant increase in urea consumption in the culture medium and the total cellular nitrogen in G. lemaneiformis in the UPB-co culture group compared to the sterile group. This suggests that the selected UPB strain positively influences nitrogen uptake by G. lemaneiformis. Similarly, isotopic assays revealed that the δ15N content of G. lemaneiformis was significantly higher in the UPB-co culture than in the control group, where δ15N-urea was the only nitrogen source in the culture medium. This indicates that the UPB helped G. lemaneiformis to absorb more nitrogen from urea. Moreover, the highest content of δ15N was found in G. lemaneiformis with epiphytic bacteria compared to sterilized (i.e. control), showing that epiphytic bacteria, along with UPB, have a compound effect in helping G. lemaneiformis absorb more nitrogen from urea. Taken together, these results provide unique insight into the ecological role of UPB and suggest that urease from macroalgae environment-associated bacteria might be an important player in marine nitrogen cycling.

Modified Atmosphere Packaging (MAP) for Seaweed Conservation: Impact on Physicochemical Characteristics and Microbiological Activity

Conventional conservation techniques such as drying, salting or freezing do not allow for preserving the original characteristics of seaweeds. The present work aims to study the impact of minimal processing, in particular "Modified Atmosphere Packaging" (MAP), on the physicochemical characteristics and food safety of two seaweed species, "laver" (Porphyra umbilicalis) and "sea-lettuce" (Ulva lactuca), stored at 6 °C for 15 days. Different parameters were evaluated using analytical methods, namely the composition of headspace gases, color, texture, microorganisms, and volatile organic compounds (VOCs). The main findings of this study were that the MAP treatment was able to inhibit the respiration rate of minimally processed seaweeds, also preserving their color and texture. There was a remarkable reduction in the microbial load for P. umbilicalis treated under modified and vacuum atmospheres, and U. lactuca exhibited relatively steady values with no notable differences between the treatments and the control. Therefore, during the 15-day study period, both seaweeds met the requirements for food safety. GC-TOF-MS allowed to conclude that both MAP and vacuum treatments were more efficient in maintaining the odor characteristics of U. lactuca compared to P. umbilicalis with no significant differences throughout the storage days. Metabolic responses to diverse sources of abiotic stress seemed to account for most of the changes observed.

A Preliminary Study on the Mechanisms of Growth and Physiological Changes in Response to Different Temperatures in Neopyropia yezoensis (Rhodophyta)

As an economically valuable red seaweed, Neopyropia yezoensis (Rhodophyta) is cultivated in intertidal areas, and its growth and development are greatly influenced by environmental factors such as temperature. Although much effort has been devoted to delineating the influence, the underlying cellular and molecular mechanisms remain elusive. In this study, the gametophyte blades and protoplasts were cultured at different temperatures (13 °C, 17 °C, 21 °C, 25 °C). Only blades cultured at 13 °C maintained a normal growth state (the relative growth rate of thalli was positive, and the content of phycobiliprotein and pigments changed little); the survival and division rates of protoplasts were high at 13 °C, but greatly decreased with the increase in temperature, suggesting that 13 °C is suitable for the growth of N. yezoensis. In our efforts to delineate the underlying mechanism, a partial coding sequence (CDS) of Cyclin B and the complete CDS of cyclin-dependent-kinase B (CDKB) in N. yezoensis were cloned. Since Cyclin B controls G2/M phase transition by activating CDK and regulates the progression of cell division, we then analyzed how Cyclin B expression in the gametophyte blades might change with temperatures by qPCR and Western blotting. The results showed that the expression of Cyclin B first increased and then decreased after transfer from 13 °C to higher temperatures, and the downregulation of Cyclin B was more obvious with the increase in temperature. The phosphorylation of extracellular signal-regulated kinase (ERK) decreased with the increase in temperature, suggesting inactivation of ERK at higher temperatures; inhibition of ERK by FR180204 significantly decreased the survival and division rates of protoplasts cultured at 13 °C. These results suggest that downregulation of Cyclin B and inactivation of ERK might be involved in negatively regulating the survival and division of protoplasts and the growth of gametophyte blades of N. yezoensis at high temperatures.

The function of high-affinity urea transporters in nitrogen-deficient conditions

Urea is the most used nitrogenous fertilizer worldwide and an important nitrogen-containing plant metabolite. Despite its major use as fertilizer, its direct uptake is limited due to the ubiquitous presence of bacterial urease, which leads to the formation of ammonium. In this review, we will focus mainly on the more recent research about the high-affinity urea transporter function in nitrogen-deficient conditions. The effective use of nitrogenous compounds is essential for plants to be able to deal with nitrogen-deficient conditions. Leaf senescence, either induced by development and/or by nitrogen deficiency, plays an important role in the efficient use of already assimilated nitrogen. Proteinaceous nitrogen is set free through catabolic reactions: the released amino acids from protein catabilization are in turn catabolized leading to an accumulation of ammonium and urea. The concentration and conversion to transportable forms of nitrogen, e.g. amino acids like glutamine and asparagine, are coordinated around the vascular tissue. Urea itself can be translocated directly over the phloem by a mechanism that involves DUR3, or it is converted by urease to ammonium and assimilated again into amino acids. The details of the high-affinity transporter function in this physiological context and the implications for crop yield are explained.

Low temperature causes discoloration by repressing growth and nitrogen transporter gene expression in the edible red alga Pyropia yezoensis

The reduced availability of nitrogen sources in seawater leads to discoloration of the edible red seaweed Pyropia yezoensis and induces the expression of genes encoding ammonium, nitrate and urea transporters. In the present study, we demonstrate that low temperatures can also cause discoloration of this economically important seaweed. Thus, we addressed regulatory mechanisms of cold-inducible discoloration. When P. yezoensis thalli were incubated at 0, 5 and 10°C, the thalli exhibited retarded growth and discoloration, along with reduced phycoerythrin contents. Fertilization with nitrogen sources did not recover this discoloration at 0°C, suggesting that defects in nitrogen absorption cause low temperature-induced discoloration. The expression levels of many nitrogen transporter genes were reduced at low temperature. We propose that low temperature-mediated repression of ammonium, nitrate and urea transporter gene expression promotes the reduced absorption of nitrogen sources in P. yezoensis, thereby leading to discoloration. This process is different from the well-known mechanism underlying discoloration in P. yezoensis under nitrogen-deficient conditions at normal culture temperature.

Discolored Red Seaweed Pyropia yezoensis with Low Commercial Value Is a Novel Resource for Production of Agar Polysaccharides

The red seaweed Pyropia yezoensis has been demonstrated to be a novel resource for the production of high-quality agar. P. yezoensis is grown for the food industry in large-scale Japanese mariculture operations. However, discolored P. yezoensis is mostly discarded as an industrial waste, although it has some kind of utility values. Here, we evaluated the utility of discolored P. yezoensis as a resource for agar production. The quality of agar from the discolored seaweed was comparable to that from normal seaweed. In addition, as a distinguishing characteristic, agar yield was higher from discolored seaweeds than from normal types. Moreover, we successfully used agar from discolored P. yezoensis for bacterial plate media and DNA electrophoresis gels without agarose purification. Thus, our results demonstrate that discolored P. yezoensis is suitable for agar production and use in life science research. Diverting discolored P. yezoensis from disposal to agar production provides a solution to the current industrial waste problem in mariculture, as well as a secure source of agar for research purposes.

Isolation and functional characterization of an ammonium transporter gene, PyAMT1, related to nitrogen assimilation in the marine macroalga Pyropia yezoensis (Rhodophyta)

Ammonium and nitrate are the primary nitrogen sources in natural environments, and are essential for growth and development in photosynthetic eukaryotes. In this study, we report on the isolation and characterization of an ammonium transporter gene (PyAMT1) which performs a key function in nitrogen (N) metabolism of Pyropia yezoensis thalli. The predicted length of PyAMT1 was 483 amino acids (AAs). The AA sequence included 11 putative transmembrane domains and showed approximately 33-44% identity to algal and plant AMT1 AA sequences. Functional complementation in an AMT-defective yeast mutant indicated that PyAMT1 mediated ammonium transport across the plasma membrane. Expression analysis showed that the PyAMT1 mRNA level was strongly induced by N-deficiency, and was more highly suppressed by resupply of inorganic-N than organic-N. These results suggest that PyAMT1 plays important roles in the ammonium transport system, and is highly regulated in response to external/internal N-status.

Characterization of the global transcriptome for Pyropia haitanensis (Bangiales, Rhodophyta) and development of cSSR markers

Background

Pyropia haitanensis is an economically important mariculture crop in China and is also valuable in life science research. However, the lack of genetic information of this organism hinders the understanding of the molecular mechanisms of specific traits. Thus, high-throughput sequencing is needed to generate a number of transcriptome sequences to be used for gene discovery and molecular marker development.

Results

In this study, high-throughput sequencing was used to analyze the global transcriptome of P. haitanensis. Approximately 103 million 90 bp paired-end reads were generated using an Illumina HiSeq 2000. De novo assembly with paired-end information yielded 24,575 unigenes with an average length of 645 bp. Based on sequence similarity searches with known proteins, a total of 16,377 (66.64%) genes were identified. Of these annotated unigenes, 5,471 and 9,168 unigenes were assigned to gene ontology and clusters of orthologous groups, respectively. Searching against the KEGG database indicated that 12,167 (49.51%) unigenes mapped to 124 KEGG pathways. Among the carbon fixation pathways, almost all the essential genes related to the C3- and C4-pathways for P. haitanensis were discovered. Significantly different expression levels of three key genes (Rubisco, PEPC and PEPCK) in different lifecycle stages of P. haitanensis indicated that the carbon fixation pathway in the conchocelis and thallus were different, and the C4-like pathway might play important roles in the conchocelis stage. In addition, 2,727 cSSRs loci were identified in the unigenes. Among them, trinucleotide SSRs were the dominant repeat motif (87.17%, 2,377) and GCC/CCG motifs were the most common repeats (60.07%, 1,638). High quality primers to 824 loci were designed and 100 primer pairs were randomly evaluated in six strains of P. haitanensis. Eighty-seven primer pairs successfully yielded amplicons.

Conclusion

This study generated a large number of putative P. haitanensis transcript sequences, which can be used for novel gene discovery and gene expression profiling analyses under different physiological conditions. A number of the cSSR markers identified can be used for molecular markers and will facilitate marker assisted selection in P. haitanensis breeding. These sequences and markers will provide valuable resources for further P. haitanensis studies.

Analysis of Porphyra membrane transporters demonstrates gene transfer among photosynthetic eukaryotes and numerous sodium-coupled transport systems

Membrane transporters play a central role in many cellular processes that rely on the movement of ions and organic molecules between the environment and the cell, and between cellular compartments. Transporters have been well characterized in plants and green algae, but little is known about transporters or their evolutionary histories in the red algae. Here we examined 482 expressed sequence tag contigs that encode putative membrane transporters in the economically important red seaweed Porphyra (Bangiophyceae, Rhodophyta). These contigs are part of a comprehensive transcriptome dataset from Porphyra umbilicalis and Porphyra purpurea. Using phylogenomics, we identified 30 trees that support the expected monophyly of red and green algae/plants (i.e. the Plantae hypothesis) and 19 expressed sequence tag contigs that show evidence of endosymbiotic/horizontal gene transfer involving stramenopiles. The majority (77%) of analyzed contigs encode transporters with unresolved phylogenies, demonstrating the difficulty in resolving the evolutionary history of genes. We observed molecular features of many sodium-coupled transport systems in marine algae, and the potential for coregulation of Porphyra transporter genes that are associated with fatty acid biosynthesis and intracellular lipid trafficking. Although both the tissue-specific and subcellular locations of the encoded proteins require further investigation, our study provides red algal gene candidates associated with transport functions and novel insights into the biology and evolution of these transporters.

Ammonium and urea transporter inventory of the selaginella and physcomitrella genomes

Ammonium and urea are important nitrogen sources for autotrophic organisms. Plant genomes encode several families of specific transporters for these molecules, plus other uptake mechanisms such as aquaporins and ABC transporters. Selaginella and Physcomitrella are representatives of lycophytes and bryophytes, respectively, and the recent completion of their genome sequences provided us with an opportunity for comparative genome studies, with special emphasis on the adaptive processes that accompanied the conquest of dry land and the evolution of a vascular system. Our phylogenetic analysis revealed that the number of genes encoding urea transporters underwent a progressive reduction during evolution, eventually down to a single copy in vascular plants. Conversely, no clear evolutionary pattern was found for ammonium transporters, and their number and distribution in families varies between species. In particular Selaginella, similar to rice, favors the AMT2/MEP family of ammonium transporters over the plant-specific AMT1 type. In comparison, Physcomitrella presents several members belonging to both families.

Ammonium and nitrate tolerance in lichens

Since lichens lack roots and take up water, solutes and gases over the entire thallus surface, these organisms respond more sensitively to changes in atmospheric purity than vascular plants. After centuries where effects of sulphur dioxide and acidity were in the focus of research on atmospheric chemistry and lichens, recently the globally increased levels of ammonia and nitrate increasingly affect lichen vegetation and gave rise to intense research on the tolerance of lichens to nitrogen pollution. The present paper discusses the main findings on the uptake of ammonia and nitrate in the lichen symbiosis and to the tolerance of lichens to eutrophication. Ammonia and nitrate are both efficiently taken up under ambient conditions. The tolerance to high nitrogen levels depends, among others, on the capability of the photobiont to provide sufficient amounts of carbon skeletons for ammonia assimilation. Lowly productive lichens are apparently predisposed to be sensitive to excess nitrogen.

Genome-wide transcriptome analyses of silicon metabolism in Phaeodactylum tricornutum reveal the multilevel regulation of silicic acid transporters

Background

Diatoms are largely responsible for production of biogenic silica in the global ocean. However, in surface seawater, Si(OH)₄ can be a major limiting factor for diatom productivity. Analyzing at the global scale the genes networks involved in Si transport and metabolism is critical in order to elucidate Si biomineralization, and to understand diatoms contribution to biogeochemical cycles.

Methodology/Principal Findings

Using whole genome expression analyses we evaluated the transcriptional response to Si availability for the model species Phaeodactylum tricornutum. Among the differentially regulated genes we found genes involved in glutamine-nitrogen pathways, encoding putative extracellular matrix components, or involved in iron regulation. Some of these compounds may be good candidates for intracellular intermediates involved in silicic acid storage and/or intracellular transport, which are very important processes that remain mysterious in diatoms. Expression analyses and localization studies gave the first picture of the spatial distribution of a silicic acid transporter in a diatom model species, and support the existence of transcriptional and post-transcriptional regulations.

Conclusions/Significance

Our global analyses revealed that about one fourth of the differentially expressed genes are organized in clusters, underlying a possible evolution of P. tricornutum genome, and perhaps other pennate diatoms, toward a better optimization of its response to variable environmental stimuli. High fitness and adaptation of diatoms to various Si levels in marine environments might arise in part by global regulations from gene (expression level) to genomic (organization in clusters, dosage compensation by gene duplication), and by post-transcriptional regulation and spatial distribution of SIT proteins.