Transcriptional Orchestration of the Global Cellular Response of a Model Pennate Diatom to Diel Light Cycling under Iron Limitation

Abstract

Environmental fluctuations affect distribution, growth and abundance of diatoms in nature, with iron (Fe) availability playing a central role. Studies on the response of diatoms to low Fe have either utilized continuous (24 hr) illumination or sampled a single time of day, missing any temporal dynamics. We profiled the physiology, metabolite composition, and global transcripts of the pennate diatom Phaeodactylum tricornutum during steady-state growth at low, intermediate, and high levels of dissolved Fe over light:dark cycles, to better understand fundamental aspects of genetic control of physiological acclimation to growth under Fe-limitation. We greatly expand the catalog of genes involved in the low Fe response, highlighting the importance of intracellular trafficking in Fe-limited diatoms. P. tricornutum exhibited transcriptomic hallmarks of slowed growth leading to prolonged periods of cell division/silica deposition, which could impact biogeochemical carbon sequestration in Fe-limited regions. Light harvesting and ribosome biogenesis transcripts were generally reduced under low Fe while transcript levels for genes putatively involved in the acquisition and recycling of Fe were increased. We also noted shifts in expression towards increased synthesis and catabolism of branched chain amino acids in P. tricornutum grown at low Fe whereas expression of genes involved in central core metabolism were relatively unaffected, indicating that essential cellular function is protected. Beyond the response of P. tricornutum to low Fe, we observed major coordinated shifts in transcript control of primary and intermediate metabolism over light:dark cycles which contribute to a new view of the significance of distinctive diatom pathways, such as mitochondrial glycolysis and the ornithine-urea cycle. This study provides new insight into transcriptional modulation of diatom physiology and metabolism across light:dark cycles in response to Fe availability, providing mechanistic understanding for the ability of diatoms to remain metabolically poised to respond quickly to Fe input and revealing strategies underlying their ecological success.

Cross‐compartment metabolic coupling enables flexible photoprotective mechanisms in the diatomPhaeodactylum tricornutum

“…In plants, glycolate oxidation occurs in the peroxisome (Bauwe et al ., ); however, there is recent evidence that the mitochondrial GOX participates in the photorespiratory cycle in P. tricornutum despite the presence of a peroxisomal glycolate oxidase (GOX_x) (Schmitz et al ., ). Transcript‐level expression of both GOX enzymes in P. tricornutum using published data (Smith et al ., ) provided further evidence for this mitochondrial pathway. The transcript abundance of GOX_m was 40 times higher than GOX_x on average, and GOX_m was coexpressed with known photorespiration genes, including glycine decarboxylase and phosphoglycolate phosphatase (Figs , S8).…”

“…These results highlight significant differences in biomass allocation dynamics between light regimes and irradiances. Predicted storage C allocation was consistent with the patterns of gene expression for fatty acid beta‐oxidation and biosynthesis as reported in a previous investigation into diel gene expression in P. tricornutum (Smith et al ., ) (Fig. f).…”

“…(f) Mean transcript abundance, relative to maximum, for genes associated with fatty acid biosynthesis (open circles) and fatty acid degradation (closed squares) from P. tricornutum as reported in Smith et al . (). Maximum was T = 0 for biosynthesis genes and T = 17 for beta‐oxidation genes.…”

“…Maximum was T = 0 for biosynthesis genes and T = 17 for beta‐oxidation genes. Error bars are the standard deviation of at least three biological replicates as reported (Smith et al ., ) of three representative genes for each pathway. FA biosynthesis‐Phatr3_Jdraft1143: 3‐hydroxyacyl‐[acyl‐carrier‐protein] dehydratase, Phatr3_J37367: 3‐oxoacyl‐[acyl‐carrier‐protein] synthase, Phatr3_J10068: enoyl‐[acyl‐carrier‐protein] reductase; FA degradation‐Phatr3_J11014: Acyl‐CoA dehydrogenase, Phatr3_J35240: 3‐hydroxacyl‐CoA dehydrogenase, Phatr3_J55192: Enoyl‐CoA hydratase.…”

Mitochondrial Energy Signaling and Its Role in the Low-Oxygen Stress Response of Plants

“…Most of the underlying genes were later shown to possess specific site II elements in their promoter region that bind to the TEOSINTE BRANCHED 1, CYCLOIDEA, PCF1 (TCP) family of transcription factors (Giraud et al, 2010), which are conserved among plants and control a wide range of developmental programs (Martín-Trillo and Cubas, 2010). Diurnal regulation of TCA cycle transcripts has also been demonstrated in unicellular photosynthetic diatoms (Chauton et al, 2013;Smith et al, 2016;Matthijs et al, 2017), green algae (Zones et al, 2015), and prokaryotic cyanobacteria (Stöckel et al, 2008;Welkie et al, 2014), suggesting conservation across photosynthetic organisms. The synthesis rates of mitochondrially encoded transcripts also show diurnal patterns, with lowest rates of transcription observed in Arabidopsis at the end of the day and early in the dark (Okada and Brennicke, 2006).…”