Quantitative Proteomics Reveals Common and Specific Responses of a Marine Diatom Thalassiosira pseudonana to Different Macronutrient Deficiencies

Abstract

Macronutrients such as nitrogen (N), phosphorus (P), and silicon (Si) are essential for the productivity and distribution of diatoms in the ocean. Responses of diatoms to a particular macronutrient deficiency have been investigated, however, we know little about their common or specific responses to different macronutrients. Here, we investigated the physiology and quantitative proteomics of a diatom Thalassiosira pseudonana grown in nutrient-replete, N-, P-, and Si-deficient conditions. Cell growth was ceased in all macronutrient deficient conditions while cell volume and cellular C content under P- and Si-deficiencies increased. Contents of chlorophyll a, protein and cellular N decreased in both N- and P-deficient cells but chlorophyll a and cellular N increased in the Si-deficient cells. Cellular P content increased under N- and Si-deficiencies. Proteins involved in carbon fixation and photorespiration were down-regulated under all macronutrient deficiencies while neutral lipid synthesis and carbohydrate accumulation were enhanced. Photosynthesis, chlorophyll biosynthesis, and protein biosynthesis were down-regulated in both N- and P-deficient cells, while Si transporters, light-harvesting complex proteins, chloroplastic ATP synthase, plastid transcription and protein synthesis were up-regulated in the Si-deficient cells. Our results provided insights into the common and specific responses of T. pseudonana to different macronutrient deficiencies and identified specific proteins potentially indicating a particular macronutrient deficiency.

Comparative Proteomic Analysis Reveals New Insights Into the Common and Specific Metabolic Regulation of the Diatom Skeletonema dohrnii to the Silicate and Temperature Availability

“…The mitochondrial AOX protein used for removing an excess electron in the nutrient-limited diatom (Allen et al, 2008) and upregulation of this protein could be involved in the mitigation of mitochondrial ROS production (Lin et al, 2017) in temperature-limited cells, whereas downregulation of this AOX protein and many other essential enzymes of the FoF1-type proteins in S. dohrnii suggests the regulation of ATP production with a coincident blockage of the respiratory chain under Si limitation. Consistent proteomic regulation was seen earlier on diatoms and cyanobacteria responding to a lower temperature (Mackey et al, 2013;Dong et al, 2016) and Si concentration (Chen et al, 2018;Thangaraj et al, 2019). Taken together, in S. dohrnii PSII, linear electron flow (grana) to NADPH mechanisms could be regulated by (Si) concentration, whereas PSI, LHC, and cyclic electron flow (stroma) to ATP metabolisms could be modulated by temperature limitation.…”

“…Nitrate is often mentioned to limit diatom growth in the ocean because of its contribution to binding chlorophyll, amino acids, and nucleic acids. Earlier proteomic observation on diatoms showed that limitation of iron, phosphate, and silicate has a coupling effect with N transporters, leading to downregulated nitrate transporters and their assimilation (Nunn et al, 2013;Chen et al, 2018). Similarly, many downregulations of nitrate transporters observed in this study responded to Si deficiency (Table 1), indicating lower nitrate assimilation (Figure 1) and cellular N quota (Figure 1).…”

“…To determine the cellular elements (C, N, P, and Si), culture aliquots containing about 2 × 10 7 cells were collected and dried in an oven at 65 • C for 2 days, prior to pulverization in a tissue layer (Elementar, Germany). For N, P, and Si, the pulverized samples were transferred into a tinfoil cup and analyzed with a photometric auto-analyzer (CFASAN Plus/Skalar Analytic, Germany) and EL cube (Elementar, Germany) following the protocol described by Boyd et al (2015); Chen et al (2018). For cellular elements, the total carbohydrate was analyzed using the anthrone method (Guerra et al, 2013); total lipids were measured according to protocol described by Yoneda et al (2018) and determined gravimetrically using a microanalytical balance.…”

“…Nutrient limitation could suppress the photosynthesis mechanism of phytoplankton depending on temperature (Maranon et al, 2018), showing that photosynthesis proteins and associated electron transport in diatom could change their nature with Si bioavailability (Thangaraj et al, 2019). In addition, transcriptome (Brembu et al, 2017) and proteome studies (Chen et al, 2018) on diatom's carbon metabolism have shown that changes in Si availability could decrease carbon fixation with simulation increase in the lipid accumulation for the acclimation process (Smith et al, 2016). The interrelation between amino acid biosynthesis and associated protein processing of ribosomal assembly in eukaryotes has been demonstrated (Lott et al, 2013) to alter the growth rate and cellular development (Zhou et al, 2015) under stressful conditions.…”

Regulation of Carbon Metabolism by Environmental Conditions: A Perspective From Diatoms and Other Chromalveolates

“…There are a growing number of studies taking advantage of proteomics to study diatom responses to stress, e.g. Muhseen et al (2015) or Chen et al (2018). Proteomics approaches have been used successfully in Viridiplantae to identify candidates for thioredoxin interactions (Montrichard et al, 2009;Perez-Perez et al, 2017).…”