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De novo transcriptome analysis of the red seaweed Gracilaria chilensis and identification of linkers associated with phycobilisomes. Mar Genomics 2017; 31:17-19. [DOI: 10.1016/j.margen.2016.11.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 10/29/2016] [Accepted: 11/07/2016] [Indexed: 11/22/2022]
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Boekema EJ, Scheffers DJ, van Bezouwen LS, Bolhuis H, Folea IM. Focus on membrane differentiation and membrane domains in the prokaryotic cell. J Mol Microbiol Biotechnol 2013; 23:345-56. [PMID: 23920497 DOI: 10.1159/000351361] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
A summary is presented of membrane differentiation in the prokaryotic cell, with an emphasis on the organization of proteins in the plasma/cell membrane. Many species belonging to the Eubacteria and Archaea have special membrane domains and/or membrane proliferation, which are vital for different cellular processes. Typical membrane domains are found in bacteria where a specific membrane protein is abundantly expressed. Lipid rafts form another example. Despite the rareness of conventional organelles as found in eukaryotes, some bacteria are known to have an intricate internal cell membrane organization. Membrane proliferation can be divided into curvature and invaginations which can lead to internal compartmentalization. This study discusses some of the clearest examples of bacteria with such domains and internal membranes. The need for membrane specialization is highest among the heterogeneous group of bacteria which harvest light energy, such as photosynthetic bacteria and halophilic archaea. Most of the highly specialized membranes and domains, such as the purple membrane, chromatophore and chlorosome, are found in these autotrophic organisms. Otherwise the need for membrane differentiation is lower and variable, except for those structures involved in cell division. Microscopy techniques have given essential insight into bacterial membrane morphology. As microscopy will further contribute to the unraveling of membrane organization in the years to come, past and present technology in electron microscopy and light microscopy is discussed. Electron microscopy was the first to unravel bacterial morphology because it can directly visualize membranes with inserted proteins, which no other technique can do. Electron microscopy techniques developed in the 1950s and perfected in the following decades involve the thin sectioning and freeze fractioning of cells. Several studies from the golden age of these techniques show amazing examples of cell membrane morphology. More recently, light microscopy in combination with the use of fluorescent dyes has become an attractive technique for protein localization with the natural membrane. However, the resolution problem in light microscopy remains and overinterpretation of observed phenomena is a pitfall. Thus, light microscopy as a stand-alone technique is not sufficient to prove, for instance, the long-range helical distribution of proteins in membrane such as MinD spirals in Bacillus subtilis. Electron tomography is an emerging electron microscopy technique that can provide three-dimensional reconstructions of small, nonchemically fixed bacteria. It will become a useful tool for studying prokaryotic membranes in more detail and is expected to collect information complementary to those of advanced light microscopy. Together, microscopy techniques can meet the challenge of the coming years: to specify membrane structures in more detail and to bring them to the level of specific protein-protein interactions.
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Affiliation(s)
- Egbert J Boekema
- Department of Electron Microscopy, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, NL–9747 AG Groningen, The Netherlands.
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Krupnik T, Kotabová E, van Bezouwen LS, Mazur R, Garstka M, Nixon PJ, Barber J, Kaňa R, Boekema EJ, Kargul J. A reaction center-dependent photoprotection mechanism in a highly robust photosystem II from an extremophilic red alga, Cyanidioschyzon merolae. J Biol Chem 2013; 288:23529-42. [PMID: 23775073 DOI: 10.1074/jbc.m113.484659] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Members of the rhodophytan order Cyanidiales are unique among phototrophs in their ability to live in extremely low pH levels and moderately high temperatures. The photosynthetic apparatus of the red alga Cyanidioschyzon merolae represents an intermediate type between cyanobacteria and higher plants, suggesting that this alga may provide the evolutionary link between prokaryotic and eukaryotic phototrophs. Although we now have a detailed structural model of photosystem II (PSII) from cyanobacteria at an atomic resolution, no corresponding structure of the eukaryotic PSII complex has been published to date. Here we report the isolation and characterization of a highly active and robust dimeric PSII complex from C. merolae. We show that this complex is highly stable across a range of extreme light, temperature, and pH conditions. By measuring fluorescence quenching properties of the isolated C. merolae PSII complex, we provide the first direct evidence of pH-dependent non-photochemical quenching in the red algal PSII reaction center. This type of quenching, together with high zeaxanthin content, appears to underlie photoprotection mechanisms that are efficiently employed by this robust natural water-splitting complex under excess irradiance. In order to provide structural details of this eukaryotic form of PSII, we have employed electron microscopy and single particle analyses to obtain a 17 Å map of the C. merolae PSII dimer in which we locate the position of the protein mass corresponding to the additional extrinsic protein stabilizing the oxygen-evolving complex, PsbQ'. We conclude that this lumenal subunit is present in the vicinity of the CP43 protein, close to the membrane plane.
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Affiliation(s)
- Tomasz Krupnik
- Department of Plant Molecular Physiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
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Bernát G, Schreiber U, Sendtko E, Stadnichuk IN, Rexroth S, Rögner M, Koenig F. Unique properties vs. common themes: the atypical cyanobacterium Gloeobacter violaceus PCC 7421 is capable of state transitions and blue-light-induced fluorescence quenching. PLANT & CELL PHYSIOLOGY 2012; 53:528-542. [PMID: 22302714 DOI: 10.1093/pcp/pcs009] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The atypical unicellular cyanobacterium Gloeobacter violaceus PCC 7421, which diverged very early during the evolution of cyanobacteria, can be regarded as a key organism for understanding many structural, functional, regulatory and evolutionary aspects of oxygenic photosynthesis. In the present work, the performance of two basic photosynthetic adaptation/protection mechanisms, common to all other oxygenic photoautrophs, had been challenged in this ancient cyanobacterium which lacks thylakoid membranes: state transitions and non-photochemical fluorescence quenching. Both low temperature fluorescence spectra and room temperature fluorescence transients show that G. violaceus is capable of performing state transitions similar to evolutionarily more recent cyanobacteria, being in state 2 in darkness and in state 1 upon illumination by weak blue or far-red light. Compared with state 2, variable fluorescence yield in state 1 is strongly enhanced (almost 80%), while the functional absorption cross-section of PSII is only increased by 8%. In contrast to weak blue light, which enhances fluorescence yield via state 1 formation, strong blue light reversibly quenches Chl fluorescence in G. violaceus. This strongly suggests regulated heat dissipation which is triggered by the orange carotenoid protein whose presence was directly proven by immunoblotting and mass spectrometry in this primordial cyanobacterium. The results are discussed in the framework of cyanobacterial evolution.
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Affiliation(s)
- Gábor Bernát
- Plant Biochemistry, Ruhr-University Bochum, D-44801 Bochum, Germany.
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Battchikova N, Eisenhut M, Aro EM. Cyanobacterial NDH-1 complexes: novel insights and remaining puzzles. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1807:935-44. [PMID: 21035426 DOI: 10.1016/j.bbabio.2010.10.017] [Citation(s) in RCA: 174] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Revised: 10/21/2010] [Accepted: 10/22/2010] [Indexed: 11/18/2022]
Abstract
Cyanobacterial NDH-1 complexes belong to a family of energy converting NAD(P)H:Quinone oxidoreductases that includes bacterial type-I NADH dehydrogenase and mitochondrial Complex I. Several distinct NDH-1 complexes may coexist in cyanobacterial cells and thus be responsible for a variety of functions including respiration, cyclic electron flow around PSI and CO(2) uptake. The present review is focused on specific features that allow to regard the cyanobacterial NDH-1 complexes, together with NDH complexes from chloroplasts, as a separate sub-class of the Complex I family of enzymes. Here, we summarize our current knowledge about structure of functionally different NDH-1 complexes in cyanobacteria and consider implications for a functional mechanism. This article is part of a Special Issue entitled: Regulation of Electron Transport in Chloroplasts.
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Affiliation(s)
- Natalia Battchikova
- Department of Biochemistry and Food Chemistry, Molecular Plant Biology, University of Turku, FI-20014 Turku, Finland
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Boekema EJ, Folea M, Kouřil R. Single particle electron microscopy. PHOTOSYNTHESIS RESEARCH 2009; 102:189-96. [PMID: 19513809 PMCID: PMC2777225 DOI: 10.1007/s11120-009-9443-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2008] [Accepted: 05/19/2009] [Indexed: 05/07/2023]
Abstract
Electron microscopy (EM) in combination with image analysis is a powerful technique to study protein structures at low, medium, and high resolution. Since electron micrographs of biological objects are very noisy, improvement of the signal-to-noise ratio by image processing is an integral part of EM, and this is performed by averaging large numbers of individual projections. Averaging procedures can be divided into crystallographic and non-crystallographic methods. The crystallographic averaging method, based on two-dimensional (2D) crystals of (membrane) proteins, yielded in solving atomic protein structures in the last century. More recently, single particle analysis could be extended to solve atomic structures as well. It is a suitable method for large proteins, viruses, and proteins that are difficult to crystallize. Because it is also a fast method to reveal the low-to-medium resolution structures, the impact of its application is growing rapidly. Technical aspects, results, and possibilities are presented.
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Affiliation(s)
- Egbert J Boekema
- Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
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Structural organisation of phycobilisomes from Synechocystis sp. strain PCC6803 and their interaction with the membrane. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2009; 1787:272-9. [DOI: 10.1016/j.bbabio.2009.01.009] [Citation(s) in RCA: 163] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2008] [Revised: 01/14/2009] [Accepted: 01/15/2009] [Indexed: 11/20/2022]
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Kereïche S, Kouřil R, Oostergetel GT, Fusetti F, Boekema EJ, Doust AB, van der Weij-de Wit CD, Dekker JP. Association of chlorophyll a/c2 complexes to photosystem I and photosystem II in the cryptophyte Rhodomonas CS24. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2008; 1777:1122-8. [DOI: 10.1016/j.bbabio.2008.04.045] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2007] [Revised: 04/10/2008] [Accepted: 04/22/2008] [Indexed: 11/25/2022]
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Folea IM, Zhang P, Aro EM, Boekema EJ. Domain organization of photosystem II in membranes of the cyanobacteriumSynechocystisPCC6803 investigated by electron microscopy. FEBS Lett 2008; 582:1749-54. [DOI: 10.1016/j.febslet.2008.04.044] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2008] [Revised: 04/18/2008] [Accepted: 04/21/2008] [Indexed: 10/22/2022]
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Single particle analysis of thylakoid proteins from Thermosynechococcus elongatus and Synechocystis 6803: localization of the CupA subunit of NDH-1. FEBS Lett 2007; 582:249-54. [PMID: 18083126 DOI: 10.1016/j.febslet.2007.12.012] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2007] [Revised: 12/05/2007] [Accepted: 12/06/2007] [Indexed: 11/20/2022]
Abstract
The larger protein complexes of the cyanobacterial photosynthetic membrane of Thermosynechoccus elongatus and Synechocystis 6803 were studied by single particle electron microscopy after detergent solubilization, without any purification steps. Besides the "standard" L-shaped NDH-1L complex, related to complex I, large numbers of a U-shaped NDH-1MS complex were found in both cyanobacteria. In membranes from Synechocystis DeltacupA and DeltacupA/cupB mutants the U-shaped complexes were absent, indicating that CupA is responsible for the U-shape by binding at the tip of the membrane-bound arm of NDH-1MS. Comparison of membranes grown under air levels of CO(2) or 3% CO(2) indicates that the number of NDH-1MS particles is 30-fold higher under low-CO(2).
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Bishop CL, Ulas S, Baena-Gonzalez E, Aro EM, Purton S, Nugent JHA, Mäenpää P. The PsbZ subunit of Photosystem II in Synechocystis sp. PCC 6803 modulates electron flow through the photosynthetic electron transfer chain. PHOTOSYNTHESIS RESEARCH 2007; 93:139-47. [PMID: 17516144 DOI: 10.1007/s11120-007-9182-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2006] [Accepted: 04/19/2007] [Indexed: 05/15/2023]
Abstract
The psbZ gene of Synechocystis sp. PCC 6803 encodes the approximately 6.6 kDa photosystem II (PSII) subunit. We here report biophysical, biochemical and in vivo characterization of Synechocystis sp. PCC 6803 mutants lacking psbZ. We show that these mutants are able to perform wild-type levels of light-harvesting, energy transfer, PSII oxygen evolution, state transitions and non-photochemical quenching (NPQ) under standard growth conditions. The mutants grow photoautotrophically; however, their growth rate is clearly retarded under low-light conditions and they are not capable of photomixotrophic growth. Further differences exist in the electron transfer properties between the mutants and wild type. In the absence of PsbZ, electron flow potentially increased through photosystem I (PSI) without a change in the maximum electron transfer capacity of PSII. Further, rereduction of P700(+) is much faster, suggesting faster cyclic electron flow around PSI. This implies a role for PsbZ in the regulation of electron transfer, with implication for photoprotection.
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Affiliation(s)
- Cleo L Bishop
- Photosynthesis Research Group, Department of Biology, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK
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Lax JEM, Arteni AA, Boekema EJ, Pistorius EK, Michel KP, Rögner M. Structural response of Photosystem 2 to iron deficiency: Characterization of a new Photosystem 2–IdiA complex from the cyanobacterium Thermosynechococcus elongatus BP-1. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2007; 1767:528-34. [PMID: 17316552 DOI: 10.1016/j.bbabio.2007.01.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2006] [Revised: 12/12/2006] [Accepted: 01/04/2007] [Indexed: 11/17/2022]
Abstract
Iron deficiency triggers various processes in cyanobacterial cells of which the synthesis of an additional antenna system (IsiA) around photosystem (PS) 1 is well documented [T.S. Bibby, J. Nield, J. Barber, Iron deficiency induces the formation of an antenna ring around trimeric photosystem I in cyanobacteria, Nature 412 (2001) 743-745, E.J. Boekema, A. Hifney, A.E. Yakushevska, M. Piotrowski, W. Keegstra, S. Berry, K.P. Michel, E.K. Pistorius, J. Kruip, A giant chlorophyll-protein complex induced by iron deficiency in cyanobacteria, Nature 412 (2001) 745-748]. Here we show that PS2 also undergoes prominent structural changes upon iron deficiency: Prerequisite is the isolation and purification of a PS2-IdiA complex which is exclusively synthesized under these conditions. Immunoblotting in combination with size exclusion chromatography shows that IdiA is only bound to dimeric PS2. Using single particle analysis of negatively stained specimens, IdiA can be localized in averaged electron micrographs on top of the CP43 subunit facing the cytoplasmic side in a model derived from the known 3D structure of PS2 [B. Loll, J. Kern, W. Saenger, A. Zouni, J. Biesiadka, Towards complete cofactor arrangement in the 3.0 A resolution structure of photosystem II, Nature 438 (2005) 1040-4]. The presence of IdiA as integral part of PS2 is the first example of a new PS2 protein being expressed under stress conditions, which is missing in highly purified PS2 complexes isolated from iron-sufficient cells.
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Affiliation(s)
- Julia E-M Lax
- Plant Biochemistry, Faculty of Biology, Ruhr-University Bochum, 44780 Bochum, Germany
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Arteni AA, Zhang P, Battchikova N, Ogawa T, Aro EM, Boekema EJ. Structural characterization of NDH-1 complexes of Thermosynechococcus elongatus by single particle electron microscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2006; 1757:1469-75. [PMID: 16844076 DOI: 10.1016/j.bbabio.2006.05.042] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2005] [Revised: 05/23/2006] [Accepted: 05/25/2006] [Indexed: 11/28/2022]
Abstract
The structure of the multifunctional NAD(P)H dehydrogenase type 1 (NDH-1) complexes from cyanobacteria was investigated by growing the wild type and specific ndh His-tag mutants of Thermosynechococcus elongatus BP-1 under different CO(2) conditions, followed by an electron microscopy (EM) analysis of their purified membrane protein complexes. Single particle averaging showed that the complete NDH-1 complex (NDH-1L) is L-shaped, with a relatively short hydrophilic arm. Two smaller complexes were observed, differing only at the tip of the membrane-embedded arm. The smallest one is considered to be similar to NDH-1M, lacking the NdhD1 and NdhF1 subunits. The other fragment, named NDH-1I, is intermediate between NDH-1L and NDH-1M and only lacks a mass compatible with the size of the NdhF1 subunit. Both smaller complexes were observed under low- and high-CO(2) growth conditions, but were much more abundant under the latter conditions. EM characterization of cyanobacterial NDH-1 further showed small numbers of NDH-1 complexes with additional masses. One type of particle has a much longer peripheral arm, similar to the one of NADH: ubiquinone oxidoreductase (complex I) in E. coli and other organisms. This indicates that Thermosynechococcus elongatus must have protein(s) which are structurally homologous to the E. coli NuoE, -F, and -G subunits. Another low-abundance type of particle (NDH-1U) has a second labile hydrophilic arm at the tip of the membrane-embedded arm. This U-shaped particle has not been observed before by EM in a NDH-I preparation.
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Affiliation(s)
- Ana A Arteni
- Department of Biophysical Chemistry, GBB, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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Dudkina NV, Heinemeyer J, Sunderhaus S, Boekema EJ, Braun HP. Respiratory chain supercomplexes in the plant mitochondrial membrane. TRENDS IN PLANT SCIENCE 2006; 11:232-40. [PMID: 16616870 DOI: 10.1016/j.tplants.2006.03.007] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2006] [Revised: 02/20/2006] [Accepted: 03/27/2006] [Indexed: 05/08/2023]
Abstract
The intricate, heavily folded inner membrane of mitochondria houses the respiratory chain complexes. These complexes, together with the ATP synthase complex, are responsible for energy production, which is stored as ATP. The structure of the individual membrane-bound protein components has been well characterized. In particular, the use of Blue-native polyacrylamide gel electrophoresis has been instrumental in recent years in providing evidence that these components are organized into supercomplexes. Single particle electron microscopy studies have enabled a structural characterization of some of the mitochondrial supercomplexes. This has provided the opportunity to define a functional role for these supercomplexes for the first time, in particular for the dimeric ATP synthase complex, which appears to be responsible for the folding of the inner mitochondrial membrane.
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Affiliation(s)
- Natalya V Dudkina
- Department of Biophysical Chemistry, GBB, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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Current literature in mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2005; 40:1390-401. [PMID: 16237664 DOI: 10.1002/jms.811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
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