Proteomic analysis of metabolic pathways supports chloroplast–mitochondria cross‐talk in a Cu‐limited diatom

Abstract

Diatoms are one of the most successful phytoplankton groups in our oceans, being responsible for over 20% of the Earth's photosynthetic productivity. Their chimeric genomes have genes derived from red algae, green algae, bacteria, and heterotrophs, resulting in multiple isoenzymes targeted to different cellular compartments with the potential for differential regulation under nutrient limitation. The resulting interactions between metabolic pathways are not yet fully understood. We previously showed how acclimation to Cu limitation enhanced susceptibility to overreduction of the photosynthetic electron transport chain and its reorganization to favor photoprotection over light harvesting in the oceanic diatom Thalassiosira oceanica (Hippmann et al., 2017, 10.1371/journal.pone.0181753). In order to gain a better understanding of the overall metabolic changes that help alleviate the stress of Cu limitation, we have further analyzed the comprehensive proteomic datasets generated in that study to identify differentially expressed proteins involved in carbon, nitrogen, and oxidative stress-related metabolic pathways. Metabolic pathway analysis showed integrated responses to Cu limitation. The upregulation of ferredoxin (Fdx) was correlated with upregulation of plastidial Fdx-dependent isoenzymes involved in nitrogen assimilation as well as enzymes involved in glutathione synthesis, thus suggesting an integration of nitrogen uptake and metabolism with photosynthesis and oxidative stress resistance. The differential expression of glycolytic isoenzymes located in the chloroplast and mitochondria may enable them to channel both excess electrons and/or ATP between these compartments. An additional support for chloroplast-mitochondrial cross-talk is the increased expression of chloroplast and mitochondrial proteins involved in the proposed malate shunt under Cu limitation.

Complementary environmental analysis and functional characterization of a plastid diatom lower glycolytic-gluconeogenesis pathway

“…A second, complete lower half of glycolysis-gluconeogenesis is predicted to occur in the diatom plastid, based on plastid-targeted ptEnolase and ptPGAM1A proteins identified in silico in multiple species (23, 34, 39, 40). Thus, diatom plastids possess independent and separate pathways for the conversion of glyceraldehyde-3-phosphate to pyruvate in plastid and for mitochondrial respiration (Fig.…”

“…Diatom ptEnolase and ptPGAM genes have further been shown to be transcriptionally co-regulated with photosynthetic carbon assimilation, suggesting metabolically important functions linked to photosynthetic activity (41). Finally, ptPGAM proteins have recently been shown to over-accumulate under copper starvation, in the open-water diatom Thalassiosira oceanica , suggesting a possible connection between its function and photo-stress (40).…”

“…1A ). The lower half of respiratory glycolysis-gluconeogenesis in diatoms occurs in the mitochondria, as opposed to the cytoplasm (Kroth, Chiovitti et al 2008, Río Bártulos, Rogers et al 2018); and a complete plastid lower half glycolysis-gluconeogenesis, including cpEnolase and cpPGAM proteins, has been inferred from sequenced diatom genomes (Kroth, Chiovitti et al 2008, Smith, Abbriano et al 2012, Hippmann, Schuback et al 2022) ( Fig. 1A ).…”

Differential Expression of Stress Adaptation Genes in a Diatom Ulnaria acus under Different Culture Conditions

“…The glutathione, involved in reducing oxidized proteins, is an important ADS component [49]. Glutathione requirement of a cell may be studied by analyzing glutathione synthetase (GSHS) expression [50,51]. The cell redox potential is supported with proline, which is capable of binding ROS and functioning as a molecular chaperone [52].…”

Recent Progress on Systems and Synthetic Biology of Diatoms for Improving Algal Productivity

“…Some green microalgae, such as C. reinhardtii, are model organisms for physiological study, but the difficulty and inefficiency in heterologous gene expression limit the research development. In that case, diatoms, as one of the most successful photosynthetic groups (Hippmann et al, 2022), have caught great attention from the science community in recent years for their genetic modification potential. Figure 1 summarizes the development of green microalgae and diatoms in PE enhancement.…”