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

Nature Microbiology volume 3, pages 781–790 (2018)Cite this article

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Abstract

Marine algae perform approximately half of global carbon fixation, but their growth is often limited by the availability of phosphate or other nutrients1,2. As oceans warm, the area of phosphate-limited surface waters is predicted to increase, resulting in ocean desertification3,4. Understanding the responses of key eukaryotic phytoplankton to nutrient limitation is therefore critical5,6. 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.

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Fig. 1: Algal relationships and Micromonas growth under changes in phosphate availability.
Fig. 2: Proteomic changes under acclimated P-limited growth.
Fig. 3: Relationships between transcript fold change and protein fold change for differentially expressed transcripts encoding proteins that changed significantly between Plimited and Preplete.
Fig. 4: Non-photochemical quenching as a strategy for sustained growth potential during P limitation.

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Acknowledgements

We thank D. Au, L. Bird, Z. Kolber, R. Thompson and S. Tozzi for contributions to photo-bioreactor design, construction and refinement. We thank M. Ares, K. Halsey, K. Hoadley and J. Barry for helpful discussions and S. Sudek for data deposition. Proteomics was performed at EMSL, a PNNL facility sponsored by DOE’s Office of Biological and Environmental Research. This research was supported by the Packard Foundation, Gordon and Betty Moore Foundation Award GBMF3788 (A.Z.W.), National Science Foundation NSF-IOS0843119 (A.Z.W. and U.G.) and US Department of Energy DOE-DE-SC0004765 (A.Z.W., S.J.C. and R.D.S.).

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Author notes

  1. Susanne Wilken

    Present address: Department of Freshwater and Marine Ecology, University of Amsterdam, Amsterdam, the Netherlands

  2. Govindarajan Kunde-Ramamoorthy

    Present address: The Jackson Laboratory, Farmington, CT, USA

Authors and Affiliations

  1. Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA

    Jian Guo, Susanne Wilken, Valeria Jimenez, Chang Jae Choi, Richard Dannebaum, Lisa Sudek, Charles Bachy, Emily Nahas Reistetter, Virginia A. Elrod, Denis Klimov & Alexandra Z. Worden

  2. Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, CA, USA

    Valeria Jimenez & Alexandra Z. Worden

  3. Pacific Northwest National Laboratory, Richland, WA, USA

    Charles Ansong, Samuel O. Purvine, Richard D. Smith & Stephen J. Callister

  4. Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, CA, USA

    Richard Dannebaum, Chia-Lin Wei & Govindarajan Kunde-Ramamoorthy

  5. University of Exeter, Exeter, UK

    David S. Milner & Thomas A. Richards

  6. Department of Biology, Washington University, St Louis, MO, USA

    Ursula Goodenough

  7. The Jackson Laboratory, Farmington, CT, USA

    Chia-Lin Wei

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Contributions

A.Z.W., E.N.R., J.G. and V.J. designed the experiments, E.N.R., J.G. and V.J. performed the experiments, flow cytometry and nutrient measurements with contributions from L.S. and V.A.E. S.W. performed NPQ and pigment analyses. C.K.A., S.O.P., R.D.S., S.J.C. performed proteomic analyses and J.G. and S.J.C. further analysed proteomics data with input from A.Z.W. R.D., G.K-R. and C-L.W. performed RNA-seq. R.D. and V.J. analysed RNA-seq with input from A.Z.W. and U.G., C.J.C. performed protein taxonomic distribution studies, C.B. performed phylogenetic analysis and T.A.R. and D.S.M. performed yeast complementation. D.K. was responsible for all technical aspects of the photo-bioreactors. J.G., S.W., U.G. and A.Z.W. wrote the manuscript and all authors read or edited the manuscript.

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Correspondence to Alexandra Z. Worden.

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Supplementary information

Supplementary Information

Supplementary Figures 1–13 and Supplementary Figure References.

Reporting Summary

Supplementary Data 1

P values associated with various tests.

Supplementary Data 2

(A) Proteins that changed (Q < 0.05) or (B) exhibited significant fold changes (Q < 0.05, fold change ≥2) in relative abundance between phases, as computed from average protein abundances from biological duplicates (technical triplicate) over sampled time points. (C) Presence of UP cluster proteins exhibiting ≥3 fold change (Q < 0.05) and lacking known domains, in other taxa, and those ≥2 fold change. (D) MMETSP organisms and peptide files analysed.

Supplementary Data 3

Fold changes of transcripts and protein pairs with significant changes (significance as specified in file) between the PLIMITED and PREPLETE phases. (B) Concordant transcript protein pairs from P-bioreactor experiment and corresponding transcript fold change under N deprivation.

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Guo, J., Wilken, S., Jimenez, V. et al. Specialized proteomic responses and an ancient photoprotection mechanism sustain marine green algal growth during phosphate limitation. Nat Microbiol 3, 781–790 (2018). https://doi.org/10.1038/s41564-018-0178-7

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