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Additional families of orange carotenoid proteins in the photoprotective system of cyanobacteria

Nature Plants volume 3, Article number: 17089 (2017) Cite this article

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Abstract

The orange carotenoid protein (OCP) is a structurally and functionally modular photoactive protein involved in cyanobacterial photoprotection. Using phylogenomic analysis, we have revealed two new paralogous OCP families, each distributed among taxonomically diverse cyanobacterial genomes. Based on bioinformatic properties and phylogenetic relationships, we named the new families OCP2 and OCPx to distinguish them from the canonical OCP that has been well characterized in Synechocystis, denoted hereafter as OCP1. We report the first characterization of a carotenoprotein photoprotective system in the chromatically acclimating cyanobacterium Tolypothrix sp. PCC 7601, which encodes both OCP1 and OCP2 as well as the regulatory fluorescence recovery protein (FRP). OCP2 expression could only be detected in cultures grown under high irradiance, surpassing expression levels of OCP1, which appears to be constitutive; under low irradiance, OCP2 expression was only detectable in a Tolypothrix mutant lacking the RcaE photoreceptor required for complementary chromatic acclimation. In vitro studies show that Tolypothrix OCP1 is functionally equivalent to Synechocystis OCP1, including its regulation by Tolypothrix FRP, which we show is structurally similar to the dimeric form of Synechocystis FRP. In contrast, Tolypothrix OCP2 shows both faster photoconversion and faster back-conversion, lack of regulation by the FRP, a different oligomeric state (monomer compared to dimer for OCP1) and lower fluorescence quenching of the phycobilisome. Collectively, these findings support our hypothesis that the OCP2 is relatively primitive. The OCP2 is transcriptionally regulated and may have evolved to respond to distinct photoprotective needs under particular environmental conditions such as high irradiance of a particular light quality, whereas the OCP1 is constitutively expressed and is regulated at the post-translational level by FRP and/or oligomerization.

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Figure 1: Phylogenetic distribution of OCP paralogues.
Figure 2: Sequence conservation of OCP1 and OCP2.
Figure 3: Absorption spectra and kinetics of photoconversion and dark recovery of OCPs.
Figure 4: Structure and function of the Tolypothrix FRP.
Figure 5: Comparison of OCP quaternary structures.
Figure 6: PBS fluorescence quenching induced by OCPs and NTDs.

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References

  1. Kirilovsky, D. & Kerfeld, C. A. The Orange Carotenoid Protein: a blue-green light photoactive protein. Photochem. Photobiol. Sci. 12, 1135–1143 (2013).

    Article  CAS  Google Scholar 

  2. Wilson, A. et al. A soluble carotenoid protein involved in phycobilisome-related energy dissipation in cyanobacteria. Plant Cell 18, 992–1007 (2006).

    Article  CAS  Google Scholar 

  3. Wilson, A. et al. A photoactive carotenoid protein acting as light intensity sensor. Proc. Natl Acad. Sci. USA 105, 12075–12080 (2008).

    Article  CAS  Google Scholar 

  4. Wilson, A., Boulay, C., Wilde, A., Kerfeld, C. A. & Kirilovsky, D. Light-induced energy dissipation in iron-starved cyanobacteria: roles of OCP and IsiA proteins. Plant Cell 19, 656–672 (2007).

    Article  CAS  Google Scholar 

  5. Gwizdala, M., Wilson, A. & Kirilovsky, D. In vitro reconstitution of the cyanobacterial photoprotective mechanism mediated by the Orange Carotenoid Protein in Synechocystis PCC 6803. Plant Cell 23, 2631–2643 (2011).

    Article  CAS  Google Scholar 

  6. Scott, M. et al. Mechanism of the down regulation of photosynthesis by blue light in the Cyanobacterium Synechocystis sp. PCC 6803. Biochemistry 45, 8952–8958 (2006).

    Article  CAS  Google Scholar 

  7. Sutter, M. et al. Crystal structure of the FRP and identification of the active site for modulation of OCP-mediated photoprotection in cyanobacteria. Proc. Natl Acad. Sci. USA 110, 10022–10027 (2013).

    Article  CAS  Google Scholar 

  8. Melnicki, M. R. et al. Structure, diversity, and evolution of a new family of soluble carotenoid-binding proteins in cyanobacteria. Mol. Plant 9, 1379–1394 (2016).

    Article  CAS  Google Scholar 

  9. Leverenz, R. L. et al. A 12 Å carotenoid translocation in a photoswitch associated with cyanobacterial photoprotection. Science 348, 1463–1466 (2015).

    Article  CAS  Google Scholar 

  10. Kerfeld, C. A. et al. The crystal structure of a cyanobacterial water-soluble carotenoid binding protein. Structure 11, 55–65 (2003).

    Article  CAS  Google Scholar 

  11. Wilson, A., Punginelli, C., Couturier, M., Perreau, F. & Kirilovsky, D. Essential role of two tyrosines and two tryptophans on the photoprotection activity of the Orange Carotenoid Protein. Biochim. Biophys. Acta 1807, 293–301 (2011).

    Article  CAS  Google Scholar 

  12. Sedoud, A. et al. The cyanobacterial photoactive orange carotenoid protein is an excellent singlet oxygen quencher. Plant Cell 26, 1781–1791 (2014).

    Article  CAS  Google Scholar 

  13. Montgomery, B. L., Lechno-Yossef, S. & Kerfeld, C. A. Interrelated modules in cyanobacterial photosynthesis: the carbon-concentrating mechanism, photorespiration, and light perception. J. Exp. Bot. 67, 2931–2940 (2016).

    Article  CAS  Google Scholar 

  14. Gupta, S. et al. Local and global structural drivers for the photoactivation of the orange carotenoid protein. Proc. Natl Acad. Sci. USA 112, E5567–E5574 (2015).

    Article  CAS  Google Scholar 

  15. Leverenz, R. L. et al. Structural and functional modularity of the orange carotenoid protein: distinct roles for the N- and C-terminal domains in cyanobacterial photoprotection. Plant Cell 26, 426–437 (2014).

    Article  CAS  Google Scholar 

  16. Shih, P. M. et al. Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing. Proc. Natl Acad. Sci. USA 110, 1053–1058 (2013).

    Article  CAS  Google Scholar 

  17. Lopez-Igual, R. et al. Different functions of the paralogs to the N-terminal domain of the orange carotenoid protein in the cyanobacterium Anabaena sp. PCC 7120. Plant Physiol. 171, 1852–1866 (2016).

    Article  Google Scholar 

  18. Wilson, A. et al. The essential role of the N-terminal domain of the orange carotenoid protein in cyanobacterial photoprotection: importance of a positive charge for phycobilisome binding. Plant Cell 24, 1972–1983 (2012).

    Article  CAS  Google Scholar 

  19. Pattanaik, B., Busch, A. W., Hu, P., Chen, J. & Montgomery, B. L. Responses to iron limitation are impacted by light quality and regulated by RcaE in the chromatically acclimating cyanobacterium Fremyella diplosiphon. Microbiology 160, 992–1005 (2014).

    Article  CAS  Google Scholar 

  20. Bourcier de Carbon, C., Thurotte, A., Wilson, A., Perreau, F. & Kirilovsky, D. Biosynthesis of soluble carotenoid holoproteins in Escherichia coli. Sci. Rep. 5, 9085 (2015).

    Article  CAS  Google Scholar 

  21. Gantt, E., Lipschultz, C. A., Grabowski, J. & Zimmerman, B. K. Phycobilisomes from blue-green and red algae: isolation criteria and dissociation characteristics. Plant Physiol. 63, 615–620 (1979).

    Article  CAS  Google Scholar 

  22. Montgomery, B. L. Mechanisms and fitness implications of photomorphogenesis during chromatic acclimation in cyanobacteria. J. Exp. Bot. 67, 4079–4090 (2016).

    Article  CAS  Google Scholar 

  23. Criscuolo, A . & Gribaldo, S. Large-scale phylogenomic analyses indicate a deep origin of primary plastids within cyanobacteria. Mol. Biol. Evol. 28, 3019–3032 (2011).

    Article  CAS  Google Scholar 

  24. Christman, H. D., Campbell, E. L. & Meeks, J. C. Global transcription profiles of the nitrogen stress response resulting in heterocyst or hormogonium development in Nostoc punctiforme. J. Bacteriol. 193, 6874–6886 (2011).

    Article  CAS  Google Scholar 

  25. D'Agostino, P. M., Song, X., Neilan, B. A. & Moffitt, M. C. Comparative proteomics reveals that a saxitoxin-producing and a nontoxic strain of Anabaena circinalis are two different ecotypes. J. Proteome. Res. 13, 1474–1484 (2014).

    Article  CAS  Google Scholar 

  26. Wilson, A. et al. Structural determinants underlying photoprotection in the photoactive orange carotenoid protein of cyanobacteria. J. Biol. Chem. 285, 18364–18375 (2010).

    Article  CAS  Google Scholar 

  27. Polívka, T. (2014) in Non-Photochemical Quenching and Energy Dissipation in Plants, Algae and Cyanobacteria (eds Demmig-Adams, B., Garab, G., Adams III, W. W. & Govindjee ) 203–227 (Springer, 2014).

    Google Scholar 

  28. Niedzwiedzki, D. M., Liu, H. & Blankenship, R. E. Excited state properties of 3'-hydroxyechinenone in solvents and in the orange carotenoid protein from Synechocystis sp. PCC 6803. J. Phys. Chem.. B 118, 6141–6149 (2014).

    Article  CAS  Google Scholar 

  29. Kerfeld, C. A. Structure and function of the water-soluble carotenoid-binding proteins of cyanobacteria. Photosyn. Res. 81, 215–225 (2004).

    Article  CAS  Google Scholar 

  30. Boulay, C., Wilson, A., D'Haene, S. & Kirilovsky, D. Identification of a protein required for recovery of full antenna capacity in OCP-related photoprotective mechanism in cyanobacteria. Proc. Natl Acad. Sci. USA 107, 11620–11625 (2010).

    Article  CAS  Google Scholar 

  31. Sluchanko, N. N. et al. The purple Trp288Ala mutant of Synechocystis OCP persistently quenches phycobilisome fluorescence and tightly interacts with FRP. Biochim. Biophys. Acta 1858, 1–11 (2017).

    Article  CAS  Google Scholar 

  32. D'Alessio, G. The evolutionary transition from monomeric to oligomeric proteins: tools, the environment, hypotheses. Prog. Biophys. Mol. Biol. 72, 271–298 (1999).

    Article  CAS  Google Scholar 

  33. Zhang, H. et al. Molecular mechanism of photoactivation and structural location of the cyanobacterial orange carotenoid protein. Biochemistry 53, 13–19 (2014).

    Article  Google Scholar 

  34. Harris, D. et al. Orange carotenoid protein burrows into the phycobilisome to provide photoprotection. Proc. Natl Acad. Sci. USA 113, E1655–E1662 (2016).

    Article  CAS  Google Scholar 

  35. Markowitz, V. M. et al. IMG: the integrated microbial genomes database and comparative analysis system. Nucleic Acids Res. 40, D115–D122 (2012).

    Article  CAS  Google Scholar 

  36. Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013).

    Article  CAS  Google Scholar 

  37. Capella-Gutierrez, S., Silla-Martinez, J. M. & Gabaldon, T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972–1973 (2009).

    Article  CAS  Google Scholar 

  38. Guindon, S. et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 59, 307–321 (2010).

    Article  CAS  Google Scholar 

  39. Han, M. V. & Zmasek, C. M. phyloXML: XML for evolutionary biology and comparative genomics. BMC Bioinformatics 10, 356 (2009).

    Article  Google Scholar 

  40. Wheeler, T. J., Clements, J. & Finn, R. D. Skylign: a tool for creating informative, interactive logos representing sequence alignments and profile hidden Markov models. BMC Bioinformatics 15, 7 (2014).

    Article  Google Scholar 

  41. Eddy, S. R. Profile hidden Markov models. Bioinformatics 14, 755–763 (1998).

    Article  CAS  Google Scholar 

  42. Ochoa de Alda, J. A., Esteban, R., Diago, M. L. & Houmard, J. The plastid ancestor originated among one of the major cyanobacterial lineages. Nat. Commun. 5, 4937 (2014).

    Article  CAS  Google Scholar 

  43. McKinney, W. in 9th Python in Science Conference Proceedings (eds van der Walt, S. & Millman, J.) 51–56 (SciPy, 2010).

  44. Kestler, H. A. et al. Vennmaster: area-proportional Euler diagrams for functional GO analysis of microarrays. BMC Bioinformatics 9, 67 (2008).

    Article  Google Scholar 

  45. Agostoni, M. et al. Competition-based phenotyping reveals a fitness cost for maintaining phycobilisomes under fluctuating light in the cyanobacterium Fremyella diplosiphon. Algal Res. 15, 110–119 (2016).

    Article  Google Scholar 

  46. Cunningham, F. X. & Gantt, E. A portfolio of plasmids for identification and analysis of carotenoid pathway enzymes: Adonis aestivalis as a case study. Photosynth Res. 92, 245–259 (2007).

    Article  CAS  Google Scholar 

  47. Britton, G. in UV/visible spectroscopy. Carotenoids, Spectroscopy (eds Britton, G., Liaaen-Jensen, S. & Pfander, H. ), Vol 1B, 13 (Birkhäuser, 1995).

    Google Scholar 

  48. Kabsch, W. XDS. Acta Crystallogr. D Biol. Crystallogr. 66, 125–132 (2010).

    Article  CAS  Google Scholar 

  49. Winn, M. D. et al. Overview of the CCP4 suite and current developments. Acta Crystallogr. D Biol. Crystallogr. 67, 235–242 (2011).

    Article  CAS  Google Scholar 

  50. Afonine, P. V. et al. Towards automated crystallographic structure refinement with phenix.refine. Acta Crystallogr. D Biol. Crystallogr. 68, 352–367 (2012).

    Article  CAS  Google Scholar 

  51. Emsley, P. et al. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126–2132 (2004).

    Article  Google Scholar 

  52. Cobley, J. G. et al. Construction of shuttle plasmids which can be efficiently mobilized from Escherichia coli into the chromatically adapting cyanobacterium, Fremyella diplosiphon. Plasmid 30, 90–105 (1993).

    Article  CAS  Google Scholar 

  53. Aráoz, R . & Häder, D.-P. Ultraviolet radiation induces both degradation and synthesis of phycobilisomes in Nostoc sp.: a spectroscopic and biochemical approach. FEMS Microbiol. Ecol. 23, 301–313 (1997).

    Article  Google Scholar 

  54. Rippka, R., Deruelles, J., Waterbury, J. B., Herdman, M. & Stanier, R. Y. Generic assignments, strain histories and properties of pure cultures of cyanobacteria. J. Gen. Microbiol. 111, 1–61 (1979).

    Google Scholar 

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Acknowledgements

This work was supported by the National Science Foundation (IOS 1557324). The authors thank W.F. Beck of Michigan State University for valuable discussions about the spectroscopic properties of carotenoids. The authors thank R. Burton for assistance in the DLS measurement. The Advanced Light Source is supported by the Director, Office of Science, Office of Basic Energy Sciences, of the US Department of Energy under Contract No. DE-AC02-05CH11231.

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Authors and Affiliations

  1. MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, 48824, Michigan, USA

    Han Bao, Matthew R. Melnicki, Emily G. Pawlowski, Markus Sutter, Marco Agostoni, Sigal Lechno-Yossef, Beronda L. Montgomery & Cheryl A. Kerfeld

  2. Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, 94720, California, USA

    Matthew R. Melnicki, Markus Sutter, Fei Cai & Cheryl A. Kerfeld

  3. Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, 48824, Michigan, USA

    Beronda L. Montgomery & Cheryl A. Kerfeld

  4. Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, 48824, Michigan, USA

    Beronda L. Montgomery

  5. Department of Plant and Microbial Biology, University of California, Berkeley, 94720, California, USA

    Cheryl A. Kerfeld

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Contributions

H.B. designed and performed the research, analysed and interpreted data, and wrote the article. C.A.K. designed the research, analysed and interpreted the data, and wrote the article. M.R.M. performed the bioinformatics and wrote the article. E.G.P., M.S., M.A., S.L.-Y., F.C. and B.L.M. performed the research and contributed to the analysis and interpretation of the data.

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Correspondence to Cheryl A. Kerfeld.

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Supplementary information

Supplementary Information

Supplementary Figures 1-8, Supplementary Tables 1-2, Supplementary References. (PDF 32136 kb)

Supplementary File 1

Annotated gene and taxon IDs for OCPs, FRPs and cyanobacterial genomes used in bioinformatic analyses. (XLS 172 kb)

Supplementary File 2

Phylogenetic tree of OCP sequences, with embedded metadata. (XM 589 kb)

Supplementary File 3

Phylogenetic tree of RpoC1 sequences, with embedded metadata. (XM 224 kb)

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Bao, H., Melnicki, M., Pawlowski, E. et al. Additional families of orange carotenoid proteins in the photoprotective system of cyanobacteria. Nature Plants 3, 17089 (2017). https://doi.org/10.1038/nplants.2017.89

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