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Title: Structural analysis of a new carotenoid-binding protein: the C-terminal domain homolog of the OCP

Abstract

The Orange Carotenoid Protein (OCP) is a water-soluble protein that governs photoprotection in many cyanobacteria. The 35 kDa OCP is structurally and functionally modular, consisting of an N-terminal effector domain (NTD) and a C-terminal regulatory domain (CTD); a carotenoid spans the two domains. The CTD is a member of the ubiquitous Nuclear Transport Factor-2 (NTF2) superfamily (pfam02136). With the increasing availability of cyanobacterial genomes, bioinformatic analysis has revealed the existence of a new family of proteins, homologs to the CTD, the C-terminal domain-like carotenoid proteins (CCPs). Here we purify holo-CCP2 directly from cyanobacteria and establish that it natively binds canthaxanthin (CAN). We use small-angle X-ray scattering (SAXS) to characterize the structure of this carotenoprotein in two distinct oligomeric states. A single carotenoid molecule spans the two CCPs in the dimer. Our analysis with X-ray footprinting-mass spectrometry (XFMS) identifies critical residues for carotenoid binding that likely contribute to the extreme red shift (ca. 80 nm) of the absorption maximum of the carotenoid bound by the CCP2 dimer and a further 10 nm shift in the tetramer form. These data provide the first structural description of carotenoid binding by a protein consisting of only an NTF2 domain.

Authors:
; ; ; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Michigan State Univ., East Lansing, MI (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES); USDOE Office of Science (SC), Biological and Environmental Research (BER); National Science Foundation (NSF); European Union (EU); Czech Science Foundation; National Institutes of Health (NIH)
OSTI Identifier:
1664560
Alternate Identifier(s):
OSTI ID: 1711416; OSTI ID: 1713256
Grant/Contract Number:  
SC0020606; AC02-05CH11231; FG02-91ER20021; IOS-1557324; 795070; 18-21631S; 1R01GM126218; P30-GM124169-01
Resource Type:
Published Article
Journal Name:
Scientific Reports
Additional Journal Information:
Journal Name: Scientific Reports Journal Volume: 10 Journal Issue: 1; Journal ID: ISSN 2045-2322
Publisher:
Nature Publishing Group
Country of Publication:
United Kingdom
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; biochemistry; biophysical chemistry; proteins; structural biology

Citation Formats

Dominguez-Martin, Maria Agustina, Hammel, Michal, Gupta, Sayan, Lechno-Yossef, Sigal, Sutter, Markus, Rosenberg, Daniel J., Chen, Yan, Petzold, Christopher J., Ralston, Corie Y., Polívka, Tomáš, and Kerfeld, Cheryl A. Structural analysis of a new carotenoid-binding protein: the C-terminal domain homolog of the OCP. United Kingdom: N. p., 2020. Web. https://doi.org/10.1038/s41598-020-72383-y.
Dominguez-Martin, Maria Agustina, Hammel, Michal, Gupta, Sayan, Lechno-Yossef, Sigal, Sutter, Markus, Rosenberg, Daniel J., Chen, Yan, Petzold, Christopher J., Ralston, Corie Y., Polívka, Tomáš, & Kerfeld, Cheryl A. Structural analysis of a new carotenoid-binding protein: the C-terminal domain homolog of the OCP. United Kingdom. https://doi.org/10.1038/s41598-020-72383-y
Dominguez-Martin, Maria Agustina, Hammel, Michal, Gupta, Sayan, Lechno-Yossef, Sigal, Sutter, Markus, Rosenberg, Daniel J., Chen, Yan, Petzold, Christopher J., Ralston, Corie Y., Polívka, Tomáš, and Kerfeld, Cheryl A. Wed . "Structural analysis of a new carotenoid-binding protein: the C-terminal domain homolog of the OCP". United Kingdom. https://doi.org/10.1038/s41598-020-72383-y.
@article{osti_1664560,
title = {Structural analysis of a new carotenoid-binding protein: the C-terminal domain homolog of the OCP},
author = {Dominguez-Martin, Maria Agustina and Hammel, Michal and Gupta, Sayan and Lechno-Yossef, Sigal and Sutter, Markus and Rosenberg, Daniel J. and Chen, Yan and Petzold, Christopher J. and Ralston, Corie Y. and Polívka, Tomáš and Kerfeld, Cheryl A.},
abstractNote = {The Orange Carotenoid Protein (OCP) is a water-soluble protein that governs photoprotection in many cyanobacteria. The 35 kDa OCP is structurally and functionally modular, consisting of an N-terminal effector domain (NTD) and a C-terminal regulatory domain (CTD); a carotenoid spans the two domains. The CTD is a member of the ubiquitous Nuclear Transport Factor-2 (NTF2) superfamily (pfam02136). With the increasing availability of cyanobacterial genomes, bioinformatic analysis has revealed the existence of a new family of proteins, homologs to the CTD, the C-terminal domain-like carotenoid proteins (CCPs). Here we purify holo-CCP2 directly from cyanobacteria and establish that it natively binds canthaxanthin (CAN). We use small-angle X-ray scattering (SAXS) to characterize the structure of this carotenoprotein in two distinct oligomeric states. A single carotenoid molecule spans the two CCPs in the dimer. Our analysis with X-ray footprinting-mass spectrometry (XFMS) identifies critical residues for carotenoid binding that likely contribute to the extreme red shift (ca. 80 nm) of the absorption maximum of the carotenoid bound by the CCP2 dimer and a further 10 nm shift in the tetramer form. These data provide the first structural description of carotenoid binding by a protein consisting of only an NTF2 domain.},
doi = {10.1038/s41598-020-72383-y},
journal = {Scientific Reports},
number = 1,
volume = 10,
place = {United Kingdom},
year = {2020},
month = {9}
}

Journal Article:
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https://doi.org/10.1038/s41598-020-72383-y

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Works referenced in this record:

Additional families of orange carotenoid proteins in the photoprotective system of cyanobacteria
journal, July 2017


Comparative Protein Modelling by Satisfaction of Spatial Restraints
journal, December 1993


SASBDB, a repository for biological small-angle scattering data
journal, October 2014

  • Valentini, Erica; Kikhney, Alexey G.; Previtali, Gianpietro
  • Nucleic Acids Research, Vol. 43, Issue D1
  • DOI: 10.1093/nar/gku1047

Cyanobacterial carboxysomes contain an unique rubisco‐activase‐like protein
journal, October 2019

  • Lechno‐Yossef, Sigal; Rohnke, Brandon A.; Belza, Ana C. O.
  • New Phytologist, Vol. 225, Issue 2
  • DOI: 10.1111/nph.16195

Different Functions of the Paralogs to the N-Terminal Domain of the Orange Carotenoid Protein in the Cyanobacterium Anabaena sp. PCC 7120
journal, May 2016

  • López-Igual, Rocío; Wilson, Adjélé; Leverenz, Ryan L.
  • Plant Physiology, Vol. 171, Issue 3
  • DOI: 10.1104/pp.16.00502

Light‐controlled carotenoid transfer between water‐soluble proteins related to cyanobacterial photoprotection
journal, March 2019

  • Slonimskiy, Yury B.; Muzzopappa, Fernando; Maksimov, Eugene G.
  • The FEBS Journal, Vol. 286, Issue 10
  • DOI: 10.1111/febs.14803

Paired cloning vectors for complementation of mutations in the cyanobacterium Anabaena sp. strain PCC 7120
journal, July 2007


The Multiple Roles of the Protein in the Photoactivation of Orange Carotenoid Protein
journal, January 2020


Assembly of photoactive orange carotenoid protein from its domains unravels a carotenoid shuttle mechanism
journal, February 2017

  • Moldenhauer, Marcus; Sluchanko, Nikolai N.; Buhrke, David
  • Photosynthesis Research, Vol. 133, Issue 1-3
  • DOI: 10.1007/s11120-017-0353-3

Structure, Diversity, and Evolution of a New Family of Soluble Carotenoid-Binding Proteins in Cyanobacteria
journal, October 2016


Structure and Function of the Water-Soluble Carotenoid-Binding Proteins of Cyanobacteria
journal, January 2004


Carotenoids in Photosynthesis
journal, March 1996


Structural basis for AcrVA4 inhibition of specific CRISPR-Cas12a
journal, August 2019


A 12 A carotenoid translocation in a photoswitch associated with cyanobacterial photoprotection
journal, June 2015


When There Is Too Much Light: Fig. 1.
journal, January 2001


Structure and functions of Orange Carotenoid Protein homologs in cyanobacteria
journal, June 2017

  • Bao, Han; Melnicki, Matthew R.; Kerfeld, Cheryl A.
  • Current Opinion in Plant Biology, Vol. 37
  • DOI: 10.1016/j.pbi.2017.03.010

Hydroxyl radical probe of protein surfaces using synchrotron X-ray radiolysis and mass spectrometry
journal, January 2002

  • Kiselar, J. G.; Maleknia, S. D.; Sullivan, M.
  • International Journal of Radiation Biology, Vol. 78, Issue 2
  • DOI: 10.1080/09553000110094805

FoXS: a web server for rapid computation and fitting of SAXS profiles
journal, May 2010

  • Schneidman-Duhovny, D.; Hammel, M.; Sali, A.
  • Nucleic Acids Research, Vol. 38, Issue Web Server
  • DOI: 10.1093/nar/gkq461

Carotenoids of blue-green algae—11. carotenoids of chromatically-adapted cyanobacteria
journal, January 1983

  • Fiksdahl, Anne; Foss, Per; Liaaen-Jensen, Synnøve
  • Comparative Biochemistry and Physiology Part B: Comparative Biochemistry, Vol. 76, Issue 3
  • DOI: 10.1016/0305-0491(83)90300-0

Versatility of carotenoids: An integrated view on diversity, evolution, functional roles and environmental interactions
journal, November 2015


Structure, function and evolution of the cyanobacterial orange carotenoid protein and its homologs
journal, July 2017

  • Kerfeld, Cheryl A.; Melnicki, Matthew R.; Sutter, Markus
  • New Phytologist, Vol. 215, Issue 3
  • DOI: 10.1111/nph.14670

Structural peculiarities of keto-carotenoids in water-soluble proteins revealed by simulation of linear absorption
journal, January 2019

  • Pishchalnikov, Roman Y.; Yaroshevich, Igor A.; Slastnikova, Tatiana A.
  • Physical Chemistry Chemical Physics, Vol. 21, Issue 46
  • DOI: 10.1039/c9cp04508b

Water-soluble carotenoid proteins of cyanobacteria
journal, October 2004


Structural and spectroscopic characterization of HCP2
journal, May 2019

  • Dominguez-Martin, Maria Agustina; Polívka, Tomáš; Sutter, Markus
  • Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1860, Issue 5
  • DOI: 10.1016/j.bbabio.2019.03.004

Structural dynamics in the C terminal domain homolog of orange carotenoid Protein reveals residues critical for carotenoid uptake
journal, August 2020

  • Harris, Dvir; Muzzopappa, Fernando; Glaser, Fabian
  • Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1861, Issue 8
  • DOI: 10.1016/j.bbabio.2020.148214

Filling out the structural map of the NTF2-like superfamily
journal, November 2013


Regulation of BolA abundance mediates morphogenesis in Fremyella diplosiphon
journal, November 2015


Local and global structural drivers for the photoactivation of the orange carotenoid protein
journal, September 2015

  • Gupta, Sayan; Guttman, Miklos; Leverenz, Ryan L.
  • Proceedings of the National Academy of Sciences, Vol. 112, Issue 41
  • DOI: 10.1073/pnas.1512240112

Accurate SAXS Profile Computation and its Assessment by Contrast Variation Experiments
journal, August 2013

  • Schneidman-Duhovny, Dina; Hammel, Michal; Tainer, John A.
  • Biophysical Journal, Vol. 105, Issue 4
  • DOI: 10.1016/j.bpj.2013.07.020

Comparative ultrafast spectroscopy and structural analysis of OCP1 and OCP2 from Tolypothrix
journal, February 2020

  • Kuznetsova, Valentyna; Dominguez-Martin, Maria Agustina; Bao, Han
  • Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1861, Issue 2
  • DOI: 10.1016/j.bbabio.2019.148120

Ring-to-chain conformation may be a determining factor in the ability of xanthophylls to bind to the bulk light-harvesting complex of plants
journal, December 2002


Structure and flexibility within proteins as identified through small angle X-ray scattering
journal, January 2009

  • Pelikan, M.; Hura, G.; Hammel, M.
  • General Physiology and Biophysics, Vol. 28, Issue 2
  • DOI: 10.4149/gpb_2009_02_174

The molecular basis of the coloration mechanism in lobster shell:  -Crustacyanin at 3.2-A resolution
journal, July 2002

  • Cianci, M.; Rizkallah, P. J.; Olczak, A.
  • Proceedings of the National Academy of Sciences, Vol. 99, Issue 15
  • DOI: 10.1073/pnas.152088999

The Crystal Structure of a Cyanobacterial Water-Soluble Carotenoid Binding Protein
journal, January 2003


Spectroscopic Properties of the Carotenoid 3‘-Hydroxyechinenone in the Orange Carotenoid Protein from the Cyanobacterium Arthrospira maxima
journal, March 2005

  • Polívka, Tomáš; Kerfeld, Cheryl A.; Pascher, Torbjörn
  • Biochemistry, Vol. 44, Issue 10
  • DOI: 10.1021/bi047473t

UCSF Chimera?A visualization system for exploratory research and analysis
journal, January 2004

  • Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C.
  • Journal of Computational Chemistry, Vol. 25, Issue 13
  • DOI: 10.1002/jcc.20084

Synthetic OCP heterodimers are photoactive and recapitulate the fusion of two primitive carotenoproteins in the evolution of cyanobacterial photoprotection
journal, June 2017

  • Lechno-Yossef, Sigal; Melnicki, Matthew R.; Bao, Han
  • The Plant Journal, Vol. 91, Issue 4
  • DOI: 10.1111/tpj.13593

Accurate assessment of mass, models and resolution by small-angle scattering
journal, April 2013


Structural rearrangements in the C-terminal domain homolog of Orange Carotenoid Protein are crucial for carotenoid transfer
journal, August 2018


Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS)
journal, July 2009

  • Hura, Greg L.; Menon, Angeli L.; Hammel, Michal
  • Nature Methods, Vol. 6, Issue 8
  • DOI: 10.1038/nmeth.1353

Characterization of Canthaxanthin Isomers Isolated from a New Soil Dietzia sp. and Their Antioxidant Activities
journal, February 2013

  • Venugopalan, Vijayalatha
  • Journal of Microbiology and Biotechnology, Vol. 23, Issue 2
  • DOI: 10.4014/jmb.1203.03032

A comparative study of three signaling forms of the orange carotenoid protein
journal, May 2016

  • Maksimov, E. G.; Moldenhauer, M.; Shirshin, E. A.
  • Photosynthesis Research, Vol. 130, Issue 1-3
  • DOI: 10.1007/s11120-016-0272-8

Effect of carotenoid structure on excited-state dynamics of carbonyl carotenoids
journal, January 2009

  • Chábera, Pavel; Fuciman, Marcel; Hříbek, Petr
  • Physical Chemistry Chemical Physics, Vol. 11, Issue 39
  • DOI: 10.1039/b909924g

Orange and red carotenoid proteins are involved in the adaptation of the terrestrial cyanobacterium Nostoc flagelliforme to desiccation
journal, March 2019