orange carotenoid protein
{{Infobox nonhuman protein
| Name = Orange carotenoid-binding protein (Kerfeld et al., Structure 2003)
| image = PDB 1m98 EBI.jpg
| width =
| caption = Crystal structure of orange carotenoid protein (Kerfeld et al., Structure 2003)
| Organism = Arthrospira maxima
| TaxID = 129910
| Symbol = Ocp
| AltSymbols = [https://www.ncbi.nlm.nih.gov/protein/WP_006625883 WP_006625883]
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| DrugBank =
| EntrezGene =
| HomoloGene =
| PDB = 1M98
| RefSeqmRNA =
| RefSeqProtein =
| UniProt = P83689
| ECnumber =
| Chromosome =
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| footnotes = Pfam domains [http://pfam.xfam.org/family/PF09150 Carot_N], [http://pfam.xfam.org/family/PF02136 NTF2]
}}
Orange carotenoid protein (OCP) is a water-soluble protein which plays a role in photoprotection in diverse cyanobacteria. It is the only photoactive protein known to use a carotenoid as the photoresponsive chromophore. The protein consists of two domains, with a single keto-carotenoid molecule non-covalently bound between the two domains. It is a very efficient quencher of excitation energy absorbed by the primary light-harvesting antenna complexes of cyanobacteria, the phycobilisomes. The quenching is induced by blue-green light. It is also capable of preventing oxidative damage by directly scavenging singlet oxygen (1O2).
History
OCP was first described in 1981 by Holt and Krogmann{{cite journal | vauthors = Brand JJ, Kerfeld CA, Cramer WA | title = David W. Krogmann, 1931-2016 | journal = Photosynthesis Research | volume = 132 | issue = 1 | pages = 1–12 | date = April 2017 | pmid = 28155215 | doi = 10.1007/s11120-016-0335-x | bibcode = 2017PhoRe.132....1B | s2cid = 30744637 }} who isolated it from the unicellular cyanobacterium Arthrospira maxima, although its function would remain obscure until 2006. The crystal structure of the OCP was reported in 2003.{{Cite journal| vauthors = Kerfeld CA, Sawaya MR, Brahmandam V, Cascio D, Ho KK, Trevithick-Sutton CC, Krogmann DW, Yeates TO | display-authors = 6 |date=January 2003|title=The Crystal Structure of a Cyanobacterial Water-Soluble Carotenoid Binding Protein |journal=Structure|language=en|volume=11|issue=1|pages=55–65|doi=10.1016/S0969-2126(02)00936-X| pmid = 12517340 |doi-access=free}} At the same time the protein was shown to be an effective quencher of singlet oxygen and was suggested to be involved in photoprotection, or carotenoid transport.{{Cite journal| vauthors = Kerfeld CA |date=2004|title=Structure and Function of the Water-Soluble Carotenoid-Binding Proteins of Cyanobacteria |journal=Photosynthesis Research|volume=81|issue=3|pages=215–225|doi=10.1023/b:pres.0000036886.60187.c8|pmid=16034528|bibcode=2004PhoRe..81..215K |s2cid=28232976|issn=0166-8595}}{{cite journal | vauthors = Kerfeld CA | title = Water-soluble carotenoid proteins of cyanobacteria | journal = Archives of Biochemistry and Biophysics | volume = 430 | issue = 1 | pages = 2–9 | date = October 2004 | pmid = 15325905 | doi = 10.1016/j.abb.2004.03.018 | s2cid = 25306222 | url = https://escholarship.org/content/qt3dm533x9/qt3dm533x9.pdf?t=lnoslm }} In 2000, it was demonstrated that cyanobacteria could perform photoprotective fluorescence quenching independent of lipid phase transitions, differential transmembrane pH, and inhibitors. The action spectrum for this quenching process suggested the involvement of carotenoids, and the specific involvement of the OCP was later demonstrated by Kirilovsky and coworkers in 2006. In 2008, OCP was shown to require photoactivation by strong blue-green light for its photoprotective quenching function. Photoactivation is accompanied by a pronounced color change, from orange to red, which had been previously observed by Kerfeld et al in the initial structural studies. In 2015 a combination of biophysical methods by researchers in Berkeley showed that the visible color change is the consequence of a 12Å translocation of the [https://today.lbl.gov/2015/07/01/protein-shifts-more-than-just-color-for-cyanobacterial-photoprotection/ carotenoid].{{cite journal | vauthors = Leverenz RL, Sutter M, Wilson A, Gupta S, Thurotte A, Bourcier de Carbon C, Petzold CJ, Ralston C, Perreau F, Kirilovsky D, Kerfeld CA | display-authors = 6 | title = PHOTOSYNTHESIS. A 12 Å carotenoid translocation in a photoswitch associated with cyanobacterial photoprotection | journal = Science | volume = 348 | issue = 6242 | pages = 1463–6 | date = June 2015 | pmid = 26113721 | doi = 10.1126/science.aaa7234 | s2cid = 37890881 | doi-access = free }}{{cite journal | vauthors = Gupta S, Guttman M, Leverenz RL, Zhumadilova K, Pawlowski EG, Petzold CJ, Lee KK, Ralston CY, Kerfeld CA | display-authors = 6 | title = Local and global structural drivers for the photoactivation of the orange carotenoid protein | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 112 | issue = 41 | pages = E5567-74 | date = October 2015 | pmid = 26385969 | doi = 10.1073/pnas.1512240112 | pmc = 4611662 | bibcode = 2015PNAS..112E5567G | doi-access = free }}{{Cite web|title=Orange is the New Red | work = Lawrence Berkeley National Laboratory Press release | publisher = LegiStorm |url=https://www.legistorm.com/stormfeed/view_rss/671624/organization/107078/title/orange-is-the-new-red-lawrence-berkeley-national-laboratory-press-release-legistorm.html|access-date=2021-09-19 |language=en}}
Physiological significance
For a long time, cyanobacteria were considered incapable of performing non-photochemical quenching (NPQ) as a photoprotective mechanism, relying instead on a mechanism of energy redistribution between the two photosynthetic reaction centers, PSII and PSI, known as "state transitions".
OCP is found in a majority of cyanobacterial genomes,{{cite journal | vauthors = Bao H, Melnicki MR, Pawlowski EG, Sutter M, Agostoni M, Lechno-Yossef S, Cai F, Montgomery BL, Kerfeld CA | display-authors = 6 | title = Additional families of orange carotenoid proteins in the photoprotective system of cyanobacteria | journal = Nature Plants | volume = 3 | issue = 8 | pages = 17089 | date = July 2017 | pmid = 28692021 | doi = 10.1038/nplants.2017.89 | bibcode = 2017NatPl...317089B | s2cid = 25263965 }} with remarkable conservation of its amino acid sequence, implying evolutionary constraints to preserve an important function. Mutant cells engineered to lack OCP photobleach under high light and become photoinhibited more rapidly under fluctuating light. Under nutrient stress conditions, which are expected to be norm in marine environments, photoprotective mechanisms such as OCP become important even at lower irradiances.
This protein is not found in chloroplasts, and appears to be specific to cyanobacteria.
Function
=Photoactivity=
File:Orange Carotenoid Protein spectra of orange vs red form.svg
Upon illumination with blue-green light, OCP switches from an orange form (OCPO) to a red form (OCPR). The reversion of OCPR to OCPO is light independent and occurs slowly in darkness. OCPO is considered the dark, stable form of the protein, and does not contribute to phycobilisome quenching. OCPR is considered to be essential for induction of the photoprotection mechanism. The photoconversion from the orange to red form has a poor light efficiency (very low quantum yield), which helps to ensure the protein's photoprotective role only functions during high light conditions; otherwise, the dissipative NPQ process could unproductively divert light energy away from photosynthesis under light-limiting conditions.
=Energy quenching=
As evidenced by a decreased fluorescence, OCP in its red form is capable of dissipating absorbed light energy from the phycobilisome antenna complex. According to Rakhimberdieva and coworkers, about 30-40% of the energy absorbed by phycobilisomes does not reach the reaction centers when the carotenoid-induced NPQ is active.
The exact mechanism and quenching site in both the carotenoid as well as the phycobilisome still remain uncertain. The linker polypeptide ApcE in the allophycocyanin (APC) core of the phycobilisomes is known to be important, but is not the site of quenching. Several lines of evidence suggest that it is the 660 nm fluorescence emission band of the APC core which is quenched by OCPR.
The temperature dependence of the rate of fluorescence quenching is similar to that of soluble protein folding, supporting the hypothesis that OCPO slightly unfolds when it converts to OCPR.
=Singlet oxygen quenching=
As first shown in 2003, the auxiliary function of carotenoids as quenchers of singlet oxygen contributes to the photoprotective role of OCP has also been demonstrated under strong orange-red light, which are conditions where OCP cannot be photoactivated for its energy-quenching role. This is significant because all oxygenic phototrophs have a particular risk of oxidative damage initiated by singlet oxygen (1O2), which is produced when their own light-harvesting pigments act as photosensitizers.
Structure
File:Ribbon view of the Orange Carotenoid Protein Structure 1M98.png (PDB code [https://pubmed.ncbi.nlm.nih.gov/12517340/ 1M98]).]]
=3D structure=
The three-dimensional protein structure of OCP (in the OCPO form) was solved in 2003, before its photoprotective role had been defined. The 35 kDa protein contains two structural domains: an all-α-helical N-terminal domain (NTD) consisting of two interleaved 4-helix bundles, and a mixed α/β C-terminal domain (CTD). The two domains are connected by an extended linker. In OCPO, the carotenoid spans both domains, which are tightly associated in this form of protein. In 2013 Kerfeld and co-workers showed that the NTD is the effector (quencher) domain of the protein while the CTD plays a regulatory role.{{cite journal | vauthors = Leverenz RL, Jallet D, Li MD, Mathies RA, Kirilovsky D, Kerfeld CA | title = Structural and functional modularity of the orange carotenoid protein: distinct roles for the N- and C-terminal domains in cyanobacterial photoprotection | journal = The Plant Cell | volume = 26 | issue = 1 | pages = 426–37 | date = January 2014 | pmid = 24399299 | doi = 10.1105/tpc.113.118588 | pmc = 3963587 | bibcode = 2014PlanC..26..426L }}
=Protein–protein interactions=
The OCP participates in key protein–protein interactions that are critical to its photoprotective function. The activated OCPR form binds to allophycocyanin in the core of the phycobilisome and initiates the OCP-dependent photoprotective quenching mechanism. Another protein, the fluorescence recovery protein (FRP), interacts with the CTD in OCPR and catalyzes the reaction which reverts it back to the OCPO form. Because OCPO cannot bind to the phycobilisome antenna, FRP effectively can detach OCP from the antenna and restore full light-harvesting capacity.
=Evolution=
The primary structure (amino acid sequence) is highly conserved among OCP sequences, and the full-length protein is usually co-located on the chromosome with a second open reading frame that was later characterized as the FRP. Often, biosynthetic genes for ketocarotenoid synthesis (e.g., CrtW) are nearby. These conserved functional linkages underscore the evolutionary importance of the OCP style of photoprotection for many cyanobacteria.
The first structure determination of the OCP coincided with the beginning of the genome sequencing era, and it was already apparent in 2003 that there is also a variety of evolutionarily related genes which encode proteins with only one of the two domains present in OCP. The N-terminal domain (NTD), "Carot_N", is found only in cyanobacteria, but exhibits a considerable amount of gene duplication. The C-terminal domain (CTD), however, is homologous with the widespread NTF2 superfamily, which shares a protein fold with its namesake, nuclear transport factor 2, as well as around 20 other subfamilies of proteins with functions as diverse as limonene-1,2-epoxide hydrolase, SnoaL polyketide cyclase, and delta-5-3-ketosteroid isomerase (KSI). Most, if not all, of the members of the NTF2 superfamily form oligomers, often using the surface of their beta sheet to interact with another monomer or other protein.
Bioinformatic analyses carried out over the past 15 years has resulted in the identification of new groups of carotenoid proteins:{{cite journal | vauthors = Bao H, Melnicki MR, Kerfeld CA | title = Structure and functions of Orange Carotenoid Protein homologs in cyanobacteria | journal = Current Opinion in Plant Biology | volume = 37 | pages = 1–9 | date = June 2017 | pmid = 28391046 | doi = 10.1016/j.pbi.2017.03.010 | doi-access = free | bibcode = 2017COPB...37....1B }} In addition to new families of the OCP, there are HCPs{{cite journal | vauthors = Melnicki MR, Leverenz RL, Sutter M, López-Igual R, Wilson A, Pawlowski EG, Perreau F, Kirilovsky D, Kerfeld CA | display-authors = 6 | title = Structure, Diversity, and Evolution of a New Family of Soluble Carotenoid-Binding Proteins in Cyanobacteria | journal = Molecular Plant | volume = 9 | issue = 10 | pages = 1379–1394 | date = October 2016 | pmid = 27392608 | doi = 10.1016/j.molp.2016.06.009 | s2cid = 3919204 | doi-access = free | bibcode = 2016MPlan...9.1379M }} and CCPs that correspond to the NTD and CTD of the OCP, respectively. Based on the primary structure, the HCPs can be subdivided into at least nine evolutionarily distinct clades, each binds carotenoid.{{cite journal | vauthors = Khan T, Dominguez-Martin MA, Šímová I, Fuciman M, Kerfeld CA, Polívka T | title = Excited-State Properties of Canthaxanthin in Cyanobacterial Carotenoid-Binding Proteins HCP2 and HCP3 | journal = The Journal of Physical Chemistry B | volume = 124 | issue = 24 | pages = 4896–4905 | date = June 2020 | pmid = 32437153 | doi = 10.1021/acs.jpcb.0c03137 | s2cid = 218837047 }}{{cite journal | vauthors = Dominguez-Martin MA, Polívka T, Sutter M, Ferlez B, Lechno-Yossef S, Montgomery BL, Kerfeld CA | title = Structural and spectroscopic characterization of HCP2 | journal = Biochimica et Biophysica Acta (BBA) - Bioenergetics| volume = 1860 | issue = 5 | pages = 414–424 | date = May 2019 | pmid = 30880081 | doi = 10.1016/j.bbabio.2019.03.004 | s2cid = 81983757 | doi-access = free | url = https://zenodo.org/records/3973524/files/Structural%20and%20Spectroscopic%20characterization%20of%20HCP2.pdf }} The CCPs resolve into 2 major groups, and these proteins also bind carotenoid.{{cite journal | vauthors = Dominguez-Martin MA, Hammel M, Gupta S, Lechno-Yossef S, Sutter M, Rosenberg DJ, Chen Y, Petzold CJ, Ralston CY, Polívka T, Kerfeld CA | display-authors = 6 | title = Structural analysis of a new carotenoid-binding protein: the C-terminal domain homolog of the OCP | journal = Scientific Reports | volume = 10 | issue = 1 | pages = 15564 | date = September 2020 | pmid = 32968135 | doi = 10.1038/s41598-020-72383-y | pmc = 7512017 | bibcode = 2020NatSR..1015564D }} Given these data, and the ability to devolve OCP into its two component domains while retaining function{{cite journal | vauthors = Lechno-Yossef S, Melnicki MR, Bao H, Montgomery BL, Kerfeld CA | title = Synthetic OCP heterodimers are photoactive and recapitulate the fusion of two primitive carotenoproteins in the evolution of cyanobacterial photoprotection | journal = The Plant Journal | volume = 91 | issue = 4 | pages = 646–656 | date = August 2017 | pmid = 28503830 | doi = 10.1111/tpj.13593 | s2cid = 206332517 | doi-access = free | url = https://www.biorxiv.org/content/biorxiv/early/2017/01/21/102160.full.pdf }} has led to a reconstruction of the evolution of the OCP.{{cite journal | vauthors = Kerfeld CA, Melnicki MR, Sutter M, Dominguez-Martin MA | title = Structure, function and evolution of the cyanobacterial orange carotenoid protein and its homologs | journal = The New Phytologist | volume = 215 | issue = 3 | pages = 937–951 | date = August 2017 | pmid = 28675536 | doi = 10.1111/nph.14670 | doi-access = free | bibcode = 2017NewPh.215..937K | osti = 1596267 }}
Applications
Its water-solubility, together with its status as the only known photoactive protein containing a carotenoid, makes the OCP a valuable model for studying solution-state energetic and photophysical properties of carotenoids, which are a diverse class of molecules found across all domains of life. Moreover, carotenoids are widely investigated for their properties as anti-oxidants, and thus the protein may serve as a template for delivery of carotenoids for therapeutic purposes in human medicine.
Because of its high efficiency of fluorescence quenching, coupled to its low quantum yield of photoactivation by specific wavelengths of light, OCP has ideal properties as a photoswitch and has been proposed as a novel system for developing optogenetics technologies and may have other applications in optofluidics and biophotonics.