Nitrogen Reallocation Research Articles

Salinity-Induced Photorespiration in Populus Vascular Tissues Facilitate Nitrogen Reallocation.

Adaptation to abiotic stress is critical for the survival of perennial tree species. Salinity affects plant growth and productivity by interfering with major biosynthetic processes. Detrimental effects of salinity may vary between different plant tissues and cell types. However, spatial molecular mechanisms controlling plant responses to salinity stress are not yet thoroughly understood in perennial trees. We used laser capture microdissection in clones of Populus tremula x alba to isolate palisade and vascular cells of intermediary leaf from plants exposed to 150 mM NaCl for 10 days, followed by a recovery period. Cell-specific changes in proteins and metabolites were determined. Salinity induced a vascular-specific accumulation of proteins associated with photorespiration, and the accumulation of serine, 3-phosphoglycerate and NH4 + suggesting changes in N metabolism. Accumulation of the GLUTAMINE SYNTHETASE 2 protein, and increased GS1.1 gene expression, indicated that NH4 + produced in photorespiration was assimilated to glutamine, the main amino acid translocated in Populus trees. Further analysis of total soluble proteins in stems and roots showed the accumulation of bark storage proteins induced by the salinity treatments. Collectively, our results suggest that the salt-induced photorespiration in vascular cells mediates N-reallocation in Populus, an essential process for the adaptation of trees to adverse conditions.

Multi-omics responses of barley seedlings to low and high linear energy transfer irradiation

Barley is a resilient crop with high nutritional value and adaptability, making it a promising candidate for phytoremediation and space agriculture. The study presents a comprehensive multi-omics analysis of the impact of ionising radiation (IR) on barley seedlings, intending to identify candidate pathways for creating radiation-resilient barley plants. We found that different IR treatments (gamma, electron, proton, neutron) increased the intensity of protein catabolism and led to the attenuation of translation. The impact of IRs on protein synthesis and degradation was accompanied by rearrangements in energy metabolism and reallocation of nitrogen, probably due to enhanced protein catabolism. At least partially, those changes seem to fuel secondary metabolites production, including riboflavin, various phytoalexins, phytosiderophores, ferulic and sinapic acids, kaempferol, quercetin, nictoflorin, gallate, and podophyllotoxin. Many of these compounds have antioxidant or radioprotective properties. To focus on possible targets for gene editing, we identified genes differentially regulated after all types of IR exposure and potential transcription factors regulating secondary metabolism, including AP2/ERF, WRKY, bHLH, bZIP, MYB, and NAC families.

Environmental irradiance and nitrogen source variability trigger the intracellular carbon and nitrogen reallocation of Gracilariopsis lemaneiformis (Rhodophyta)

A rhodophyte Gracilariopsis lemaneiformis is widely cultivated for food, carbon sequestration and bioproducts, and commonly experiences changing irradiance levels and nitrogen sources that might influence the productivity and biochemical composition of the alga. To explore optimal culture conditions or manipulations to gain best yield of carbohydrates and amino acids of G. lemaneiformis during mariculture, we cultured G. lemaneiformis in four conditions including high irradiance and low irradiance coupled with nitrate and ammonium (denoted as HI-NO3−, LI-NO3−, HI-NH4+ and LI-NH4+). The results showed that irradiance, nitrogen source and their interactions significantly regulated the intracellular carbon and nitrogen metabolism of G. lemaneiformis and the influence of irradiance was greater than of nitrogen source. High irradiance promoted more carbon accumulation of G. lemaneiformis, which was confirmed by higher growth rate, net photosynthesis rates and contents of soluble carbohydrate, carbon and C/N ratios. In contrast, low irradiance is conductive to nitrogen accumulation, as revealed by high contents of nitrogen, phycoerythrin, soluble protein and amino acids. Furthermore, we found nitrate coupled with high irradiance significantly promoted carbon sequestration of G. lemaneiformis, and the ammonium combined with low irradiance significantly promoted nitrogen assimilation and transformation. In addition, arginine exhibited a higher nitrogen storage capacity than phycoerythrin, as evidenced by the higher content of arginine and correspondingly higher nitrogen reserves in G. lemaneiformis under low light coupled with ammonium and nitrogen- enriched environments. Moreover, the content of proline was higher under low irradiance conditions, but its proportion among the eighteen free amino acids was upregulated by high irradiance, indicating its important role in responding to high-light aquaculture environments. These findings demonstrate that irradiance and nitrogen source influence the carbon and nitrogen reallocation of G. lemaneiformis and that the combination of these two variables can induce the production of chemical products for biotechnological, aquaculture, and nutraceutical industry.

Multi-Omics Analysis of Vicia cracca Responses to Chronic Radiation Exposure in the Chernobyl Exclusion Zone.

Our understanding of the long-term consequences of chronic ionising radiation for living organisms remains scarce. Modern molecular biology techniques are helpful tools for researching pollutant effects on biota. To reveal the molecular phenotype of plants growing under chronic radiation exposure, we sampled Vicia cracca L. plants in the Chernobyl exclusion zone and areas with normal radiation backgrounds. We performed a detailed analysis of soil and gene expression patterns and conducted coordinated multi-omics analyses of plant samples, including transcriptomics, proteomics, and metabolomics. Plants growing under chronic radiation exposure showed complex and multidirectional biological effects, including significant alterations in the metabolism and gene expression patterns of irradiated plants. We revealed profound changes in carbon metabolism, nitrogen reallocation, and photosynthesis. These plants showed signs of DNA damage, redox imbalance, and stress responses. The upregulation of histones, chaperones, peroxidases, and secondary metabolism was noted.

Nitrogen availability determines the vertical patterns of accumulation, partitioning, and reallocation of dry matter and nitrogen in maize

Nitrogen availability determines the vertical patterns of accumulation, partitioning, and reallocation of dry matter and nitrogen in maize

Knock out of amino acid transporter gene OsLHT1 accelerates leaf senescence and enhances resistance to rice blast fungus.

Plant amino acid transporters regulate not only long-distance transport and reallocation of nitrogen (N) from source to sink organs, but also the amount of amino acids in leaves hijacked by invading pathogens. However, the function of amino acid transporters in plant defense responses to pathogen infection remains unknown. In this study, we found that the rice amino acid transporter gene OsLHT1 was expressed in leaves and up-regulated by maturation, N starvation, and inoculation of the blast fungus Magnaporthe oryzae. Knock out of OsLHT1 resulted in development stage- and N supply-dependent premature senescence of leaves at the vegetative growth stage. In comparison with the wild type, Oslht1 mutant lines showed sustained rusty red spots on fully mature leaf blades irrespective of N supply levels. Notably, no relationship between the severity of leaf rusty red spots and concentration of total N or amino acids was found in Oslht1 mutants at different developmental stages. Disruption of OsLHT1 altered transport and metabolism of amino acids and biosynthesis of flavones and flavonoids, enhanced expression of jasmonic acid- and salicylic acid-related defense genes, production of jasmonic acid and salicylic acid, and accumulation of reactive oxygen species. OsLHT1 inactivation dramatically prevented the leaf invasion by M. oryzae, a hemi-biotrophic ascomycete fungus. Overall, these results establish a link connecting the activity of an amino acid transporter with leaf metabolism and defense against rice blast fungus.

Multigenerational elevated atmospheric CO2 concentration induced changes of wheat grain quality via altering nitrogen reallocation and starch catabolism

Previous studies indicated the grain yield and compositions of wheat (Triticum aestivum L.) were affected by long-term elevated atmospheric CO2 concentration conditions. However, the roles of protein expression in wheat grain quality changes under multigenerational elevated atmospheric CO2 concentration are still rarely known. This study explored that the changes of grain quality in wheat offspring induced by multigenerational elevated atmospheric CO2 concentration exposure and analyzed the roles of the differently expressed proteins using 4D proteomics in regulating the wheat grain quality. The changes of grain protein accumulation, gluten index and dough development time indicated that the nutritional and end-use quality of wheat grains were directly affected by elevated atmospheric CO2 concentration. This was mainly due to the changed expressions of α-amylase inhibitors, glutamine synthetase, glutamate dehydrogenase, formamidase and β-glucosidase, which regulated the starch accumulation and nitrogen metabolism in grains. This study elucidates the mechanisms underlying the effects of long-term elevated atmospheric CO2 concentration on wheat grain quality.

Reallocation of nitrogen and phosphorus from roots drives regrowth of grasses and sedges after defoliation under deficit irrigation and nitrogen enrichment

Abstract Reallocation of nutrients from roots to shoots is essential for plant regrowth in grasslands, particularly in nutrient‐poor conditions. However, the response of root nutrient reallocation to changes in nitrogen (N) and water availability remains largely unknown. Using a novel 15N and 32P labelling technique, we quantified the contribution of N and phosphorus (P) to shoot regrowth from either root reallocation or direct soil uptake for perennial grasses exposed to high‐frequency deficit irrigation (HFDI) and N addition. Without N addition, HFDI showed no impact on uptake and reallocation of N and P, likely due to unaffected soil N availability and a greater diffusion barrier offsetting increased accumulation in plant‐available soil P. With N addition, HFDI increased plant N rather than P uptake, because of increasing soil N availability instead of P under combined HFDI and N addition. The HFDI decreased both N and P reallocation with N addition, possibly due to exhaustion of nutrient reserves in roots that were re‐allocated above‐ground. Reallocation contributed 48%–97% of N and 58%–79% of P required during the first 2 weeks of shoot regrowth. Synthesis. Our results highlight the importance of N and P reallocation from roots to buffer against changes in soil N and P availability and to maintain N:P ratio in shoot regrowth.

Free Amino Acids and Methylglyoxal as Players in the Radiation Hormesis Effect after Low-Dose γ-Irradiation of Barley Seeds

Low-dose γ-irradiation can stimulate plant growth and development; however, the knowledge on the molecular mechanisms of such stimulation is yet fragmented. Irradiation of seeds leads to the mobilisation of endosperm resources and reallocation of available nitrogen to facilitate development. Based on the metabolomic analysis, several metabolites possibly involved in radiation stimulation were studied using the HPLC approach in barley cultivars after γ-irradiation of seeds. The comparison of changes in metabolite concentrations and changes in morphological traits after irradiation revealed seven metabolites that may be involved in the growth stimulation after γ-irradiation of barley seeds. Among them are free amino acids, such as γ-aminobutyric acid, β-alanine, arginine, lysine, glutamine, methionine, and a signalling compound methylglyoxal.

Symmetry between the anisotropic N behavior in the lattice under high pressures and the formation of expanded austenite

The nitrogen expanded austenite (γN or the S-phase), easily attainable by nitriding processes of FCC chromium-containing materials such as stainless steel (SS), Ni-based superalloys and CoCr alloys, discloses singular properties such as strong anisotropic expansion and crystal direction-dependent diffusion. These fundamental aspects were undertaken here from an experimental-theoretical approach. The S-phase was produced by plasma nitriding on SS 316L powder grains, and the material was submitted to quasi-hydrostatic compression-decompression experiments up to 30 GPa with in situ structural analyses. The experimental results agreed very well with a solid mechanics-based analysis. With this methodology – that was effective for modified surfaces – the anisotropic nitrogen reallocation in the lattice was found to obey a same linear relation during both compression (the S-phase decay) and nitriding (the S-phase formation). The transition from austenite with low nitrogen content – CN (the first-order expansion) to the S-phase (colossal saturated second-order) was featured by inversion of relative magnitudes, between 111 and 100, of the K〈ϕ〉=E〈ϕ〉31−2ν〈ϕ〉, elastic moduli E〈ϕ〉 and Poisson's ratios ν〈ϕ〉 (ϕ=hkl), all of them dependent on the orientation factor Γ[ϕ]. Rates of compression/expansion between 111 and 100 were affected accordingly. Such phenomena was concluded to arise from the inversion of the anisotropy factor, from Aγ>1 to AγN<1, which is an intrinsic property of the nitrided austenite and rules the aforementioned anisotropy inversions. Stress-induced nitrogen redistribution among crystal directions (at constant temperature) promoted changes in CN and affected elastic constants (Sij). It let the elastic modulus evolve with stresses applied on the solid. The elastic properties Sij and E〈ϕ〉 of the S-phase were determined at different pressure ranges, including pressures close to the atmospheric condition.

Sargassum stenophyllum (Fucales, Ochrophyta) responses to temperature short-term exposure: photosynthesis and chemical composition

Sargassum species form extensive benthic beds in tropical and subtropical low intertidal and subtidal zones, acting as important drivers for marine community structure. Temperature, as one of the most important abiotic factor, affects seaweed performance and triggers changes in metabolic responses; therefore, laboratory experiments involving temperature ranges are tools for understanding seaweed engineering. The aim of this study was to assess the physiological vulnerability and sensitivity of Sargassum stenophyllum C. Martius exposed to five different temperatures by analyzing photosynthetic performance and chemical composition related to carbon and nitrogen metabolism. There were no significant differences in energy quenching between treatments, except at 35 °C, which showed decreased photochemical quenching and increased non-regulated non-photochemical quenching. Chlorophyll a and chlorophyll c at 15 °C and 35 °C exhibited lower amounts at the end of experiment. Protein content showed progressive diminution in the treatments. Total soluble carbohydrates content showed higher concentration as temperature increased. After 7 days, total amino acid content showed increase from 15 °C to 30 °C. No generalization between the amino acid patterns, although glutamine and glutamate content at 15 °C and 35 °C were reduced; and the highest values of isoleucine and leucine were detected at 35 °C. We postulated that accumulation of certain chemical compounds in S. stenophyllum results from a reallocation of carbon and nitrogen, osmoregulation responses and protection against oxidative stress. Results suggest this species’ tolerance ranges between 15 °C and 30 °C and sensitivity at 35 °C.

APSIM-Tropical Pasture: A model for simulating perennial tropical grass growth and its parameterisation for palisade grass (Brachiaria brizantha)

Tropical grasses are used as forage, to produce energy from biomass, for land restoration and carbon sequestration, among other applications. Many modelling approaches have been employed to simulate tropical grasses growth, but these have several limitations that must be solved by adapting them or creating new models. This study aimed to develop a tropical pasture model in the Agricultural Production Systems Simulator (APSIM) modelling framework, and to parameterise it to simulate Brachiaria brizantha ‘BRS Piatã’ growth, under grazing and cut-and-carry management. For this, three field experiments were conducted in the South-east of Brazil where pasture growth was measured in a cut-and-carry system, with irrigated and rainfed treatments, and in a rainfed grazing system. Model evaluation was performed through precision and accuracy indices and simulation errors. Under cut-and-carry management, forage productivity was estimated with R2 values from 0.89 to 0.94, Willmott agreement indices between 0.97 and 0.98, and Nash-Sutcliffe Efficiency values of 0.88 to up to 0.92. This demonstrates the capacity of the APSIM-Tropical Pasture model to simulate tropical pastures. Simulation of phenology, early growth after sowing, partitioning and senescence during flowering, and reallocation and retranslocation of plant dry matter and nitrogen were important aspects for this capacity. Then, APSIM-Tropical Pasture can be used to simulate tropical pastures, but several requirements for further improvements have been identified, such as to improve the simulations of flowering for palisade grass, N effects on pasture yield, reallocation and retranslocation processes. Under grazing management, forage productivity was estimated with R2 = 0.80, Willmott agreement index of 0.91, and Nash-Sutcliffe Efficiency value of 0.62. Despite these reasonable results, simulations presented problems, since does not take into account the effect of grazing animals on pastures. This indicates that, in its current form, APSIM-Tropical Pasture is not able to simulate pastures under grazing effectively. However, this simulation of grazed system was important to identify main modelling constraints and direct future research to improve knowledge of processes and interactions needed for pasture model development.

Alteration of local and systemic amino acids metabolism for the inducible defense in tea plant (Camellia sinensis) in response to leaf herbivory by Ectropis oblique

Leaf herbivory on tea plants (Camellia sinensis) by tea geometrids (Ectropis oblique) can cause severe yield loss and quality damage for tea. In previous work, we discovered that leaf herbivory triggered systemic carbon depletion in undamaged roots to enhance resource investment for local defense induced in damaged leaves. Here, we investigated the dynamics of amino acids in the local and systemic responses and the roles of nitrogen resource reallocation for the inducible defense in tea plants in response to leaf herbivory. The comparative analysis of the dynamics of flavonoids, caffeine, theanine and basic amino acids at metabolic and transcriptome levels revealed that leaf herbivory triggered the differential reconfiguration of these amino acid-derived defensive metabolites and nitrogenous primary metabolism between the local and systemic responses. The tight association of the metabolism and reallocation of amino acids with the activation of defensive secondary metabolism indicated that the systemic nitrogen reallocation played a potentially important role for the resource investment in tea plant resistance against leaf herbivory. This study provided an extended understanding of the role of systemic nitrogen reallocation for the interaction of tea plants and geometrids and the root-mediated resource-based resistance strategy employed by tea plants in response to leaf herbivory.

C4 photosynthesis and climate through the lens of optimality

CO2, temperature, water availability, and light intensity were all potential selective pressures that determined the competitive advantage and expansion of the C4 photosynthetic carbon-concentrating mechanism over the last ∼30 My. To tease apart how selective pressures varied along the ecological trajectory of C4 expansion and dominance, we coupled hydraulics to photosynthesis models while optimizing photosynthesis over stomatal resistance and leaf/fine-root allocation. We further examined the importance of nitrogen reallocation from the dark to the light reactions. We show here that the primary selective pressures favoring C4 dominance changed through the course of C4 evolution. The higher stomatal resistance and leaf-to-root ratios enabled by C4 led to an advantage without any initial difference in hydraulic properties. We further predict a reorganization of the hydraulic system leading to higher turgor-loss points and possibly lower hydraulic conductance. Selection on nitrogen reallocation varied with CO2 concentration. Through paleoclimate model simulations, we find that water limitation was the primary driver for a C4 advantage, with atmospheric CO2 as high as 600 ppm, thus confirming molecular-based estimates for C4 evolution in the Oligocene. Under these high-CO2 conditions, nitrogen reallocation was necessary. Low CO2 and high light, but not nitrogen reallocation, were the primary drivers for the mid- to late-Miocene global expansion of C4 We also predicted the timing and spatial distribution for origins of C4 ecological dominance. The predicted origins are broadly consistent with prior estimates, but expand upon them to include a center of origin in northwest Africa and a Miocene-long origin in Australia.

Coordinated Expression of Cytosolic and Chloroplastic Glutamine Synthetase During Reproductive Stage and Its Impact in GS1 RNAi Transgenic Rice

To understand the reallocation of organic nitrogen from leaf to the flower head of rice, the role of glutamine synthetase (GS) was investigated by characterizing GS1 RNAi transgenic rice, which revealed a significant reduction in panicle number and number of seeds per panicle. We observed the expression of GS isotypes at transcriptional and protein levels in flag leaves, leaf sheaths and panicles at three different flower development stages. The mRNA expression of GS1;1 was clearly suppressed in flag leaves, especially at the flowering stage. GS1 protein was barely detectable in flag leaves until the flowering stage, while GS1 protein was compromised in the leaf sheath and panicle, with transient expression of GS2 protein at the flowering stage. The glutamine level in transgenic plants was significantly reduced in both flag leaves and panicles, but ammonium was highly accumulated. The level of other amino acids, including aspartate and asparagine, tended to be higher in RNAi transgenic plants than the wild type plants during the reproductive stage. In addition, accumulation of toxic ammonium in panicles with low glutamine level might have caused low seed-setting in the transgenic rice. These results indicated that nitrogen reallocation was critical for panicle development, and that multiple GS isotypes functioned cooperatively to complete the rice life cycle when leaf nitrogen was remobilized to the developing reproductive organs.

New insight into the mechanism underlying the silk gland biological process by knocking out fibroin heavy chain in the silkworm

BackgroundExploring whether and how mutation of silk protein contributes to subsequent re-allocation of nitrogen, and impacts on the timing of silk gland degradation, is important to understand silk gland biology. Rapid development and wide application of genome editing approach in the silkworm provide us an opportunity to address these issues.ResultsUsing CRISPR/Cas9 system, we successfully performed genome editing of Bmfib-H. The loss-of-function mutations caused naked pupa and thin cocoon mutant phenotypes. Compared with the wild type, the posterior silk gland of mutant showed obviously degraded into fragments in advance of programmed cell death of silk gland cells. Comparative transcriptomic analyses of silk gland at the fourth day of the fifth instar larval stage(L5D4)identified 1456 differential expressed genes (DEGs) between posterior silk gland (PSG) and mid silk gland (MSG) and 1388 DEGs between the mutant and the wild type. Hierarchical clustering of all the DEGs indicated a remarkable down-regulated and an up-regulated gene clade in the mutant silk glands, respectively. Down-regulated genes were overrepresented in the pathways involved in cancer, DNA replication and cell proliferation. Intriguingly, up-regulated DEGs are significantly enriched in the proteasome. By further comparison on the transcriptome of MSG and PSG between the wild type and the mutant, we consistently observed that up-regulated DEGs in the mutant PSG were enriched in protein degrading activity and proteasome. Meantime, we observed a series of up-regulated genes involved in autophagy. Since these protein degradation processes would be normally occur after the spinning time, the results suggesting that these progresses were activated remarkably ahead of schedule in the mutant.ConclusionsAccumulation of abnormal fib-H protein might arouse the activation of proteasomes as well as autophagy process, to promote the rapid degradation of such abnormal proteins and the silk gland cells. Our study therefore proposes a subsequent process of protein and partial cellular degradation caused by mutation of silk protein, which might be helpful for understanding its impact of the silk gland biological process, and further exploration the re-allocation of nitrogen in the silkworm.

Two Splicing Variants of OsNPF7.7 Regulate Shoot Branching and Nitrogen Utilization Efficiency in Rice.

Rice includes 93 nitrate and peptide transporters family (NPF) members that facilitate the soil uptake and internal reallocation of nitrogen for growth and development. This study demonstrated that OsNPF7.7 had two splicing variants, and altered expression of each variant could regulate shoot branching and nitrogen utilization efficiency (NUtE) in rice. The expression of both variants was down-regulated in the buds by increased nitrogen level in the Japonica rice variety ZH11. The expression level of long-variant OsNPF7.7-1 was higher in panicles at reproductive stage, however, the expression level of short-variant OsNPF7.7-2 was higher in buds and leaves at vegetative stage compared to each other in ZH11. OsNPF7.7-1 was localized in the plasma membrane, whereas OsNPF7.7-2 was localized in the vacuole membrane. Furthermore, the results indicated that the expression level of each variant for OsNPF7.7 determined axillary bud outgrowth, and then influenced the rice tiller number. Overexpression of OsNPF7.7-1 could promote nitrate influx and concentration in root, whereas overexpression of OsNPF7.7-2 could improve ammonium influx and concentration in root. RNAi and osnpf7.7 lines of OsNPF7.7 showed an increased amount of amino acids in leaf sheaths, but a decreased amount in leaf blades, which affected nitrogen allocation and plant growth. The elevated expression of each variant for OsNPF7.7 in ZH11 enhanced NUtE using certain fertilization regimes under paddy field conditions. Moreover, overexpression of each variant for OsNPF7.7 in KY131 increased significantly the filled grain number per plant. Thus, increased each variant of OsNPF7.7 has the potential to improve grain yield and NUtE in rice.

The study of a determinate growth orchid highlights the role of new leaf production in photosynthetic light acclimation

Plants usually respond to the changes of growth irradiance by a combination of the physiological modifications in their preexisting leaves and the production of new leaves. However, those with a determinate growth habit produce certain number of leaves in a growing season and cannot produce new leaves when light condition changes. We used an epiphytic orchid with only one leaf produced every growing season to examine whether and how determinate growth species adapt to changing environments after their preexisting leaves mature. Leaf photosynthesis and anatomy of Pleione aurita were investigated at full expansion and at 40 days after the fully expanded leaves were transferred from high to low light or from low to high light. Leaves show large physiological and morphological plasticity to light gradients at full expansion and the transferred leaves exhibited multiple physiological modifications, including reallocation of nitrogen between light harvesting and carbon fixation, and enhancement of thermal dissipation in their new environments, to optimize carbon assimilation and avoid photoinhibition. Irrespective of the various changes either to shade or sun, the sole preexisting leaf could not fully acclimate to new light environments due to the mesophyll thickness constraint. This leads to the consequence that only plants exposed to high light throughout the experiment had a positive annual biomass gain. Our results highlighted the importance of new leaf production in the carbon accumulation during photosynthetic light acclimation, and contribute new insights of epiphytes physiological responses to their highly dynamic arboreal habitat.

Transcriptomic analyses of nitrogen assimilation processes in a Chinese strain of Aureococcus anophagefferens.

Aureococcus anophagefferens is a harmful alga that dominates plankton communities during brown tides in North America, Africa, and Asia. In order to figure out the processes of nitrogen assimilation in a Chinese strain of A. anophagefferens, RNA-seq technology was used to examine transcriptomic differences in A. anophagefferens that was grown on urea, nitrate, or a mixture of urea and nitrate, and that was under N-replete, limited and recovery conditions. We noted that transcripts upregulated by nitrate and N-limitation included those encoding proteins involved in amino acid, nucleotide and aminosugar transport, degradation of amides and cyanates, and nitrate assimilation pathway. The data suggest that A. anophagefferens possesses an ability to utilize a variety of dissolved organic nitrogen. Moreover, transcripts for synthesis of proteins, glutamate-derived amino acids, spermines and sterols were upregulated by urea. Transcripts encoding key enzymes that are involved in the ornithine–urea cycle (OUC) and TCA cycle were differentially regulated by urea and nitrogen concentration, which suggests that the OUC may be linked to the TCA cycle and involved in reallocation of intracellular carbon and nitrogen. These genes regulated by urea may be crucial for the rapid proliferation of A. anophagefferens when urea is provided as the N source. Here, we provide the experimental procedures and analytical processes in detail. The data set is deposited in GEO with the accession number GSE60576.

Cellular responses associated with ROS production and cell fate decision in early stress response to iron limitation in the diatom Thalassiosira pseudonana.

Investigation of how diatoms cope with the rapid fluctuations in iron bioavailability in marine environments may facilitate a better understanding of the mechanisms underlying their ecological success, in particular their ability to proliferate rapidly during favorable conditions. In this study, using in vivo biochemical markers and whole-cell iTRAQ-based proteomics analysis, we explored the cellular responses associated with reactive oxygen species (ROS) production and cell fate decision during the early response to Fe limitation in the centric diatom Thalassiosira pseudonana. Fe limitation caused a significant decrease in Photosystem (PS) II photosynthetic efficiency, damage to the photosynthetic electron transport chain in PS I, and blockage of the respiratory chain in complexes III and IV, which could all result in excess ROS accumulation. The increase in ROS likely triggered programmed cell death (PCD) in some of the Fe-limited cells through synthesis of a series of proteins involved in the delicate balance between pro-survival and pro-PCD factors. The results provide molecular-level insights into the major strategies that may be employed by T. pseudonana in response to Fe-limitation: the reduction of cell population density through PCD to reduce competition for available Fe, the reallocation of intracellular nitrogen and Fe to ensure survival, and an increase in expression of antioxidant and anti-PCD proteins to cope with stress.