1
|
Nagy G, Garab G. Neutron scattering in photosynthesis research: recent advances and perspectives for testing crop plants. PHOTOSYNTHESIS RESEARCH 2021; 150:41-49. [PMID: 32488447 PMCID: PMC8556207 DOI: 10.1007/s11120-020-00763-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 05/25/2020] [Indexed: 05/05/2023]
Abstract
The photosynthetic performance of crop plants under a variety of environmental factors and stress conditions, at the fundamental level, depends largely on the organization and structural flexibility of thylakoid membranes. These highly organized membranes accommodate virtually all protein complexes and additional compounds carrying out the light reactions of photosynthesis. Most regulatory mechanisms fine-tuning the photosynthetic functions affect the organization of thylakoid membranes at different levels of the structural complexity. In order to monitor these reorganizations, non-invasive techniques are of special value. On the mesoscopic scale, small-angle neutron scattering (SANS) has been shown to deliver statistically and spatially averaged information on the periodic organization of the thylakoid membranes in vivo and/or, in isolated thylakoids, under physiologically relevant conditions, without fixation or staining. More importantly, SANS investigations have revealed rapid reversible reorganizations on the timescale of several seconds and minutes. In this paper, we give a short introduction into the basics of SANS technique, advantages and limitations, and briefly overview recent advances and potential applications of this technique in the physiology and biotechnology of crop plants. We also discuss future perspectives of neutron crystallography and different neutron scattering techniques, which are anticipated to become more accessible and of more use in photosynthesis research at new facilities with higher fluxes and innovative instrumentation.
Collapse
Affiliation(s)
- Gergely Nagy
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA.
- Institute for Solid State Physics and Optics, Wigner Research Centre for Physics, POB 49, 1525, Budapest, Hungary.
| | - Győző Garab
- Institute of Plant Biology, Biological Research Centre, POB 521, 6701, Szeged, Hungary.
- Department of Physics, Faculty of Science, Ostrava University, Chittussiho 10, Ostrava - Slezská, 710 0, Ostrava, Czech Republic.
| |
Collapse
|
2
|
Tani K, Kanno R, Ji XC, Hall M, Yu LJ, Kimura Y, Madigan MT, Mizoguchi A, Humbel BM, Wang-Otomo ZY. Cryo-EM Structure of the Photosynthetic LH1-RC Complex from Rhodospirillum rubrum. Biochemistry 2021; 60:2483-2491. [PMID: 34323477 DOI: 10.1021/acs.biochem.1c00360] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Rhodospirillum (Rsp.) rubrum is one of the most widely used model organisms in bacterial photosynthesis. This purple phototroph is characterized by the presence of both rhodoquinone (RQ) and ubiquinone as electron carriers and bacteriochlorophyll (BChl) a esterified at the propionic acid side chain by geranylgeraniol (BChl aG) instead of phytol. Despite intensive efforts, the structure of the light-harvesting-reaction center (LH1-RC) core complex from Rsp. rubrum remains at low resolutions. Using cryo-EM, here we present a robust new view of the Rsp. rubrum LH1-RC at 2.76 Å resolution. The LH1 complex forms a closed, slightly elliptical ring structure with 16 αβ-polypeptides surrounding the RC. Our biochemical analysis detected RQ molecules in the purified LH1-RC, and the cryo-EM density map specifically positions RQ at the QA site in the RC. The geranylgeraniol side chains of BChl aG coordinated by LH1 β-polypeptides exhibit a highly homologous tail-up conformation that allows for interactions with the bacteriochlorin rings of nearby LH1 α-associated BChls aG. The structure also revealed key protein-protein interactions in both N- and C-terminal regions of the LH1 αβ-polypeptides, mainly within a face-to-face structural subunit. Our high-resolution Rsp. rubrum LH1-RC structure provides new insight for evaluating past experimental and computational results obtained with this old organism over many decades and lays the foundation for more detailed exploration of light-energy conversion, quinone transport, and structure-function relationships in this pigment-protein complex.
Collapse
Affiliation(s)
- Kazutoshi Tani
- Graduate School of Medicine, Mie University, Tsu, Mie 514-8507, Japan
| | - Ryo Kanno
- Imaging Section, Research Support Division, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1, Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| | - Xuan-Cheng Ji
- Faculty of Science, Ibaraki University, Mito, Ibaraki 310-8512, Japan
| | - Malgorzata Hall
- Imaging Section, Research Support Division, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1, Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| | - Long-Jiang Yu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yukihiro Kimura
- Department of Agrobioscience, Graduate School of Agriculture, Kobe University, Nada, Kobe, Hyogo 657-8501, Japan
| | - Michael T Madigan
- School of Biological Sciences, Southern Illinois University, Carbondale, Illinois 62901, United States
| | - Akira Mizoguchi
- Graduate School of Medicine, Mie University, Tsu, Mie 514-8507, Japan
| | - Bruno M Humbel
- Imaging Section, Research Support Division, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1, Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| | | |
Collapse
|
3
|
Midtgaard SR, Darwish TA, Pedersen MC, Huda P, Larsen AH, Jensen GV, Kynde SAR, Skar‐Gislinge N, Nielsen AJZ, Olesen C, Blaise M, Dorosz JJ, Thorsen TS, Venskutonytė R, Krintel C, Møller JV, Frielinghaus H, Gilbert EP, Martel A, Kastrup JS, Jensen PE, Nissen P, Arleth L. Invisible detergents for structure determination of membrane proteins by small‐angle neutron scattering. FEBS J 2017; 285:357-371. [DOI: 10.1111/febs.14345] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 10/20/2017] [Accepted: 11/21/2017] [Indexed: 12/23/2022]
Affiliation(s)
- Søren Roi Midtgaard
- Structural Biophysics X‐ray and Neutron Science The Niels Bohr Institute University of Copenhagen Denmark
| | - Tamim A. Darwish
- National Deuteration Facility Australian Nuclear Science and Technology Organization Lucas Heights Australia
| | - Martin Cramer Pedersen
- Structural Biophysics X‐ray and Neutron Science The Niels Bohr Institute University of Copenhagen Denmark
- Department of Applied Mathematics Research School of Physics and Engineering Australian National University Canberra Australia
| | - Pie Huda
- Structural Biophysics X‐ray and Neutron Science The Niels Bohr Institute University of Copenhagen Denmark
| | - Andreas Haahr Larsen
- Structural Biophysics X‐ray and Neutron Science The Niels Bohr Institute University of Copenhagen Denmark
| | - Grethe Vestergaard Jensen
- Structural Biophysics X‐ray and Neutron Science The Niels Bohr Institute University of Copenhagen Denmark
| | | | - Nicholas Skar‐Gislinge
- Structural Biophysics X‐ray and Neutron Science The Niels Bohr Institute University of Copenhagen Denmark
| | | | - Claus Olesen
- Department of Biomedicine Aarhus University Denmark
| | - Mickael Blaise
- Institut de Recherche en Infectiologie de Montpellier CNRS Université de Montpellier France
- Centre for Carbohydrate Recognition and Signaling Department of Molecular Biology Aarhus University Denmark
| | - Jerzy Józef Dorosz
- Department of Drug Design and Pharmacology Faculty of Health and Medical Sciences University of Copenhagen Denmark
| | - Thor Seneca Thorsen
- Department of Drug Design and Pharmacology Faculty of Health and Medical Sciences University of Copenhagen Denmark
| | - Raminta Venskutonytė
- Department of Drug Design and Pharmacology Faculty of Health and Medical Sciences University of Copenhagen Denmark
| | - Christian Krintel
- Department of Drug Design and Pharmacology Faculty of Health and Medical Sciences University of Copenhagen Denmark
| | - Jesper V. Møller
- Department of Biomedicine Aarhus University Denmark
- Department of Molecular Biology and Genetics Centre for Membrane Pumps in Cells and Disease – PUMPkin Danish National Research Foundation Aarhus University Denmark
| | | | - Elliot Paul Gilbert
- Australian Centre for Neutron Scattering Australian Nuclear Science and Technology Organization Lucas Heights Australia
| | | | - Jette Sandholm Kastrup
- Department of Drug Design and Pharmacology Faculty of Health and Medical Sciences University of Copenhagen Denmark
| | - Poul Erik Jensen
- Copenhagen Plant Science Center University of Copenhagen Denmark
| | - Poul Nissen
- Department of Molecular Biology and Genetics Centre for Membrane Pumps in Cells and Disease – PUMPkin Danish National Research Foundation Aarhus University Denmark
- DANDRITE Nordic‐EMBL Partnership for Molecular Medicine Aarhus University Denmark
| | - Lise Arleth
- Structural Biophysics X‐ray and Neutron Science The Niels Bohr Institute University of Copenhagen Denmark
| |
Collapse
|
4
|
Jiang J, Zhang H, Lu X, Lu Y, Cuneo MJ, O'Neill HM, Urban V, Lo CS, Blankenship RE. Oligomerization state and pigment binding strength of the peridinin-Chl a-protein. FEBS Lett 2015; 589:2713-9. [PMID: 26241331 DOI: 10.1016/j.febslet.2015.07.039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Revised: 07/13/2015] [Accepted: 07/20/2015] [Indexed: 11/28/2022]
Abstract
The peridinin-chlorophyll a-protein (PCP) is one of the major light harvesting complexes (LHCs) in photosynthetic dinoflagellates. We analyzed the oligomeric state of PCP isolated from the dinoflagellate Symbiodinium, which has received increasing attention in recent years because of its role in coral bleaching. Size-exclusion chromatography (SEC) and small angle neutron scattering (SANS) analysis indicated PCP exists as monomers. Native mass spectrometry (native MS) demonstrated two oligomeric states of PCP, with the monomeric PCP being dominant. The trimerization may not be necessary for PCP to function as a light-harvesting complex.
Collapse
Affiliation(s)
- Jing Jiang
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Hao Zhang
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Xun Lu
- Center for Structural Molecular Biology, Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Yue Lu
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Matthew J Cuneo
- Center for Structural Molecular Biology, Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Hugh M O'Neill
- Center for Structural Molecular Biology, Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Volker Urban
- Center for Structural Molecular Biology, Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Cynthia S Lo
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Robert E Blankenship
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA; Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA.
| |
Collapse
|
5
|
Twenty years of gas phase structural biology. Structure 2014; 21:1541-50. [PMID: 24010713 DOI: 10.1016/j.str.2013.08.002] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 08/06/2013] [Accepted: 08/06/2013] [Indexed: 01/01/2023]
Abstract
Over the past two decades, mass spectrometry (MS) of protein complexes from their native state has made inroads into structural biology. To coincide with the 20(th) anniversary of Structure, and given that it is now approximately 20 years since the first mass spectra of noncovalent protein complexes were reported, it is timely to consider progress of MS as a structural biology tool. Early reports focused on soluble complexes, contributing to ligand binding studies, subunit interaction maps, and topological models. Recent discoveries have enabled delivery of membrane complexes, encapsulated in detergent micelles, prompting new opportunities. By maintaining interactions between membrane and cytoplasmic subunits in the gas phase, it is now possible to investigate the effects of lipids, nucleotides, and drugs on intact membrane assemblies. These investigations reveal allosteric and synergistic effects of small molecule binding and expose the consequences of posttranslational modifications. In this review, we consider recent progress in the study of protein complexes, focusing particularly on complexes extracted from membranes, and outline future prospects for gas phase structural biology.
Collapse
|
6
|
Tang KH, Blankenship RE. Neutron and light scattering studies of light-harvesting photosynthetic antenna complexes. PHOTOSYNTHESIS RESEARCH 2012; 111:205-217. [PMID: 21710338 DOI: 10.1007/s11120-011-9665-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Accepted: 06/02/2011] [Indexed: 05/31/2023]
Abstract
Small-angle neutron scattering (SANS) and dynamic light scattering (DLS) have been employed in studying the structural information of various biological systems, particularly in systems without high-resolution structural information available. In this report, we briefly present some principles and biological applications of neutron scattering and DLS, compare the differences in information that can be obtained with small-angle X-ray scattering (SAXS), and then report recent studies of SANS and DLS, together with other biophysical approaches, for light-harvesting antenna complexes and reaction centers of purple and green phototrophic bacteria.
Collapse
Affiliation(s)
- Kuo-Hsiang Tang
- Department of Biology and Department of Chemistry, Washington University in St. Louis, Campus Box 1137, St. Louis, MO 63130, USA
| | | |
Collapse
|
7
|
Tang KH, Urban VS, Wen J, Xin Y, Blankenship RE. SANS investigation of the photosynthetic machinery of Chloroflexus aurantiacus. Biophys J 2011; 99:2398-407. [PMID: 20959079 DOI: 10.1016/j.bpj.2010.07.068] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2010] [Revised: 07/18/2010] [Accepted: 07/27/2010] [Indexed: 11/30/2022] Open
Abstract
Green photosynthetic bacteria harvest light and perform photosynthesis in low-light environments, and contain specialized antenna complexes to adapt to this condition. We performed small-angle neutron scattering (SANS) studies to obtain structural information about the photosynthetic apparatus, including the peripheral light-harvesting chlorosome complex, the integral membrane light-harvesting B808-866 complex, and the reaction center (RC) in the thermophilic green phototrophic bacterium Chloroflexus aurantiacus. Using contrast variation in SANS measurements, we found that the B808-866 complex is wrapped around the RC in Cfx. aurantiacus, and the overall size and conformation of the B808-866 complex of Cfx. aurantiacus is roughly comparable to the LH1 antenna complex of the purple bacteria. A similar size of the isolated B808-866 complex was suggested by dynamic light scattering measurements, and a smaller size of the RC of Cfx. aurantiacus compared to the RC of the purple bacteria was observed. Further, our SANS measurements indicate that the chlorosome is a lipid body with a rod-like shape, and that the self-assembly of bacteriochlorophylls, the major component of the chlorosome, is lipid-like. Finally, two populations of chlorosome particles are suggested in our SANS measurements.
Collapse
Affiliation(s)
- Kuo-Hsiang Tang
- Department of Biology, Washington University in St. Louis, Missouri, USA
| | | | | | | | | |
Collapse
|
8
|
Palazzo G, Lopez F, Mallardi A. Effect of detergent concentration on the thermal stability of a membrane protein: The case study of bacterial reaction center solubilized by N,N-dimethyldodecylamine-N-oxide. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1804:137-46. [DOI: 10.1016/j.bbapap.2009.09.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2009] [Revised: 09/17/2009] [Accepted: 09/21/2009] [Indexed: 11/29/2022]
|
9
|
Nakagawa K, Suzuki S, Fujii R, Gardiner AT, Cogdell RJ, Nango M, Hashimoto H. Probing the effect of the binding site on the electrostatic behavior of a series of carotenoids reconstituted into the light-harvesting 1 complex from purple photosynthetic bacterium Rhodospirillum rubrum detected by stark spectroscopy. J Phys Chem B 2008; 112:9467-75. [PMID: 18613723 DOI: 10.1021/jp801773j] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Reconstitutions of the LH1 complexes from the purple photosynthetic bacterium Rhodospirillum rubrum S1 were performed with a range of carotenoid molecules having different numbers of C=C conjugated double bonds. Since, as we showed previously, some of the added carotenoids tended to aggregate and then to remain with the reconstituted LH1 complexes (Nakagawa, K.; Suzuki, S.; Fujii, R.; Gardiner, A.T.; Cogdell, R.J.; Nango, M.; Hashimoto, H. Photosynth. Res. 2008, 95, 339-344), a further purification step using a sucrose density gradient centrifugation was introduced to improve purity of the final reconstituted sample. The measured absorption, fluorescence-excitation, and Stark spectra of the LH1 complex reconstituted with spirilloxanthin were identical with those obtained with the native, spirilloxanthin-containing, LH1 complex of Rs. rubrum S1. This shows that the electrostatic environments surrounding the carotenoid and bacteriochlorophyll a (BChl a) molecules in both of these LH1 complexes were essentially the same. In the LH1 complexes reconstituted with either rhodopin or spheroidene, however, the wavelength maximum at the BChl a Qy absorption band was slightly different to that of the native LH1 complexes. These differences in the transition energy of the BChl a Qy absorption band can be explained using the values of the nonlinear optical parameters of this absorption band, i.e., the polarizability change Tr(Deltaalpha) and the static dipole-moment change |Deltamu| upon photoexcitation, as determined using Stark spectroscopy. The local electric field around the BChl a in the native LH1 complex (ES) was determined to be approximately 3.0x10(6) V/cm. Furthermore, on the basis of the values of the nonlinear optical parameters of the carotenoids in the reconstituted LH1 complexes, it is possible to suggest that the conformations of carotenoids, anhydrorhodovibrin and spheroidene, in the LH1 complex were similar to that of rhodopin glucoside in crystal structure of the LH2 complex from Rhodopseudomonas acidophila 10050.
Collapse
Affiliation(s)
- Katsunori Nakagawa
- Department of Life and Materials Engineering, Graduate School of Engineering, Nagoya Institute of Technology, Nagoya, Japan
| | | | | | | | | | | | | |
Collapse
|
10
|
Wang ZY, Gokan K, Kobayashi M, Nozawa T. Solution Structures of the Core Light-harvesting α and β Polypeptides from Rhodospirillum rubrum: Implications for the Pigment–Protein and Protein–Protein Interactions. J Mol Biol 2005; 347:465-77. [PMID: 15740753 DOI: 10.1016/j.jmb.2005.01.017] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2004] [Revised: 12/21/2004] [Accepted: 01/04/2005] [Indexed: 11/25/2022]
Abstract
We have determined the solution structures of the core light-harvesting (LH1) alpha and beta-polypeptides from wild-type purple photosynthetic bacterium Rhodospirillum rubrum using multidimensional NMR spectroscopy. The two polypeptides form stable alpha helices in organic solution. The structure of alpha-polypeptide consists of a long helix of 32 amino acid residues over the central transmembrane domain and a short helical segment at the N terminus that is followed by a three-residue loop. Pigment-coordinating histidine residue (His29) in the alpha-polypeptide is located near the middle of the central helix. The structure of beta-polypeptide shows a single helix of 32 amino acid residues in the membrane-spanning region with the pigment-coordinating histidine residue (His38) at a position close to the C-terminal end of the helix. Strong hydrogen bonds have been identified for the backbone amide protons over the central helical regions, indicating a rigid property of the two polypeptides. The overall structures of the R.rubrum LH1 alpha and beta-polypeptides are different from those previously reported for the LH1 beta-polypeptide of Rhodobacter sphaeroides, but are very similar to the structures of the corresponding LH2 alpha and beta-polypeptides determined by X-ray crystallography. A model constructed for the structural subunit (B820) of LH1 complex using the solution structures reveals several important features on the interactions between the LH1 alpha and beta-polypeptides. The significance of the N-terminal regions of the two polypeptides for stabilizing both B820 and LH1 complexes, as clarified by many experiments, may be attributed to the interactions between the short N-terminal helix (Trp2-Gln6) of alpha-polypeptide and a GxxxG motif in the beta-polypeptide.
Collapse
Affiliation(s)
- Zheng-Yu Wang
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aramaki-aza, Aoba, Aoba-ku, Sendai 980-8579, Japan.
| | | | | | | |
Collapse
|