Article | Published:

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

Nature Plants volume 3, Article number: 17089 (2017) | Download Citation


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.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.


  1. 1.

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

  2. 2.

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

  3. 3.

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

  4. 4.

    , , , & Light-induced energy dissipation in iron-starved cyanobacteria: roles of OCP and IsiA proteins. Plant Cell 19, 656–672 (2007).

  5. 5.

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

  6. 6.

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

  7. 7.

    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).

  8. 8.

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

  9. 9.

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

  10. 10.

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

  11. 11.

    , , , & Essential role of two tyrosines and two tryptophans on the photoprotection activity of the Orange Carotenoid Protein. Biochim. Biophys. Acta 1807, 293–301 (2011).

  12. 12.

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

  13. 13.

    , & Interrelated modules in cyanobacterial photosynthesis: the carbon-concentrating mechanism, photorespiration, and light perception. J. Exp. Bot. 67, 2931–2940 (2016).

  14. 14.

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

  15. 15.

    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).

  16. 16.

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

  17. 17.

    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).

  18. 18.

    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).

  19. 19.

    , , , & 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).

  20. 20.

    , , , & Biosynthesis of soluble carotenoid holoproteins in Escherichia coli. Sci. Rep. 5, 9085 (2015).

  21. 21.

    , , & Phycobilisomes from blue-green and red algae: isolation criteria and dissociation characteristics. Plant Physiol. 63, 615–620 (1979).

  22. 22.

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

  23. 23.

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

  24. 24.

    , & Global transcription profiles of the nitrogen stress response resulting in heterocyst or hormogonium development in Nostoc punctiforme. J. Bacteriol. 193, 6874–6886 (2011).

  25. 25.

    , , & 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).

  26. 26.

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

  27. 27.

    (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).

  28. 28.

    , & 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).

  29. 29.

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

  30. 30.

    , , & 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).

  31. 31.

    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).

  32. 32.

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

  33. 33.

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

  34. 34.

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

  35. 35.

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

  36. 36.

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

  37. 37.

    , & trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972–1973 (2009).

  38. 38.

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

  39. 39.

    & phyloXML: XML for evolutionary biology and comparative genomics. BMC Bioinformatics 10, 356 (2009).

  40. 40.

    , & Skylign: a tool for creating informative, interactive logos representing sequence alignments and profile hidden Markov models. BMC Bioinformatics 15, 7 (2014).

  41. 41.

    Profile hidden Markov models. Bioinformatics 14, 755–763 (1998).

  42. 42.

    , , & The plastid ancestor originated among one of the major cyanobacterial lineages. Nat. Commun. 5, 4937 (2014).

  43. 43.

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

  44. 44.

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

  45. 45.

    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).

  46. 46.

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

  47. 47.

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

  48. 48.

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

  49. 49.

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

  50. 50.

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

  51. 51.

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

  52. 52.

    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).

  53. 53.

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

  54. 54.

    , , , & Generic assignments, strain histories and properties of pure cultures of cyanobacteria. J. Gen. Microbiol. 111, 1–61 (1979).

Download references


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.

Author information


  1. MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824, 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, California 94720, USA

    • Matthew R. Melnicki
    • , Markus Sutter
    • , Fei Cai
    •  & Cheryl A. Kerfeld
  3. Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA

    • Beronda L. Montgomery
    •  & Cheryl A. Kerfeld
  4. Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, USA

    • Beronda L. Montgomery
  5. Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA

    • Cheryl A. Kerfeld


  1. Search for Han Bao in:

  2. Search for Matthew R. Melnicki in:

  3. Search for Emily G. Pawlowski in:

  4. Search for Markus Sutter in:

  5. Search for Marco Agostoni in:

  6. Search for Sigal Lechno-Yossef in:

  7. Search for Fei Cai in:

  8. Search for Beronda L. Montgomery in:

  9. Search for Cheryl A. Kerfeld in:


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.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Cheryl A. Kerfeld.

Supplementary information

PDF files

  1. 1.

    Supplementary Information

    Supplementary Figures 1-8, Supplementary Tables 1-2, Supplementary References.

Excel files

  1. 1.

    Supplementary File 1

    Annotated gene and taxon IDs for OCPs, FRPs and cyanobacterial genomes used in bioinformatic analyses.

XML files

  1. 1.

    Supplementary File 2

    Phylogenetic tree of OCP sequences, with embedded metadata.

  2. 2.

    Supplementary File 3

    Phylogenetic tree of RpoC1 sequences, with embedded metadata.

About this article

Publication history





Further reading