Specialized proteomic responses and an ancient photoprotection mechanism sustain marine green algal growth during phosphate limitation

Abstract

Marine algae perform approximately half of global carbon fixation, but their growth is often limited by the availability of phosphate or other nutrients. As oceans warm, the area of phosphate-limited surface waters is predicted to increase, resulting in ocean desertification. Understanding the responses of key eukaryotic phytoplankton to nutrient limitation is therefore critical. We used advanced photo-bioreactors to investigate how the widespread marine green alga Micromonas commoda grows under transitions from replete nutrients to chronic phosphate limitation and subsequent relief, analysing photosystem changes and broad cellular responses using proteomics, transcriptomics and biophysical measurements. We find that physiological and protein expression responses previously attributed to stress are critical to supporting stable exponential growth when phosphate is limiting. Unexpectedly, the abundance of most proteins involved in light harvesting does not change, but an ancient light-harvesting-related protein, LHCSR, is induced and dissipates damaging excess absorbed light as heat throughout phosphate limitation. Concurrently, a suite of uncharacterized proteins with narrow phylogenetic distributions increase multifold. Notably, of the proteins that exhibit significant changes, 70% are not differentially expressed at the mRNA transcript level, highlighting the importance of post-transcriptional processes in microbial eukaryotes. Nevertheless, transcript-protein pairs with concordant changes were identified that will enable more robust interpretation of eukaryotic phytoplankton responses in the field from metatranscriptomic studies. Our results show that P-limited Micromonas responds quickly to a fresh pulse of phosphate by rapidly increasing replication, and that the protein network associated with this ability is composed of both conserved and phylogenetically recent proteome systems that promote dynamic phosphate homeostasis. That an ancient mechanism for mitigating light stress is central to sustaining growth during extended phosphate limitation highlights the possibility of interactive effects arising from combined stressors under ocean change, which could reduce the efficacy of algal strategies for optimizing marine photosynthesis.

A phosphate starvation response gene (psr1-like) is present and expressed in Micromonas pusilla and other marine algae

“…While both intracellular and extracellular metabolites were quantified in our 175 experiment, the results and discussion will focus primarily on changes in the intracellular 176 metabolite profile in response to P-deficiency, highlighting compounds that were most 177 relevant to the discovery of the psr1-like gene. We further focus the intracellular 178 metabolite comparison on the exponential growth phase (T 1 ) to capture clear changes in 179 metabolite profiles between treatments and facilitate comparison to previous studies 180 (Whitney & Lomas, 2016;Bachy et al, 2018). R statistical software (v3.0.2; R Core 181 Team) was used for statistical analyses.…”

“…The psr1-like gene in M. commoda and M. pusilla was one of the highest DE 496 genes in each experiment (Whitney & Lomas, 2016;Bachy et al, 2018), suggesting that 497 this potential TF plays a critical role in the P-deficiency response of Micromonas. 498…”

“…Micromonas species (Bachy et al, 2018;Whitney & Lomas, 2016), suggesting that these 476 genes could be co-regulated. In bacteria, for example, genes within the well-characterized 477…”

“…Here, we use a combined metabolomic and comparative genomic approach to 100 investigate the impact of P-deficiency on the physiology of Micromonas pusilla 101 CCMP1545. Many metabolites are produced by metabolic pathways under genetic 102 regulatory control (e.g., de Carvalho & Fernandes, 2010; Markou & Nerantzis, 2013); 103 thus, our approach complements recent physiological, transcriptional, and proteomic 104 work (Hoppe et al, 2018;Guo et al, 2018) and provides mechanistic insight into the 105 physiological response to P-deficiency and its underlying genetic regulation. We used a 106 targeted metabolomics approach to analyze the suite of intracellular and extracellular 107 molecules produced by M. pusilla.…”

“…59 Interestingly, P. donghaiense increased nitrate assimilation under P-deficiency (Shi et al, 60 2017), whereas E. huxleyi reduced nitrate uptake with a tight coupling between P and 61 nitrogen (N) pools (Rokitta et al, 2016). These varied strategies all minimize non-critical 62 P utilization and maximize P uptake, and thus play important roles in structuring 63 phytoplankton assemblages in the oceans (Dyhrman et al, 2006;Dyhrman et al, 2009;64 Martin et al, 2011;Rokitta et al, 2016;Guo et al, 2018). 65…”