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Nishihara A, Tsukatani Y, Azai C, Nobu MK. Illuminating the coevolution of photosynthesis and Bacteria. Proc Natl Acad Sci U S A 2024; 121:e2322120121. [PMID: 38875151 PMCID: PMC11194577 DOI: 10.1073/pnas.2322120121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 05/06/2024] [Indexed: 06/16/2024] Open
Abstract
Life harnessing light energy transformed the relationship between biology and Earth-bringing a massive flux of organic carbon and oxidants to Earth's surface that gave way to today's organotrophy- and respiration-dominated biosphere. However, our understanding of how life drove this transition has largely relied on the geological record; much remains unresolved due to the complexity and paucity of the genetic record tied to photosynthesis. Here, through holistic phylogenetic comparison of the bacterial domain and all photosynthetic machinery (totally spanning >10,000 genomes), we identify evolutionary congruence between three independent biological systems-bacteria, (bacterio)chlorophyll-mediated light metabolism (chlorophototrophy), and carbon fixation-and uncover their intertwined history. Our analyses uniformly mapped progenitors of extant light-metabolizing machinery (reaction centers, [bacterio]chlorophyll synthases, and magnesium-chelatases) and enzymes facilitating the Calvin-Benson-Bassham cycle (form I RuBisCO and phosphoribulokinase) to the same ancient Terrabacteria organism near the base of the bacterial domain. These phylogenies consistently showed that extant phototrophs ultimately derived light metabolism from this bacterium, the last phototroph common ancestor (LPCA). LPCA was a non-oxygen-generating (anoxygenic) phototroph that already possessed carbon fixation and two reaction centers, a type I analogous to extant forms and a primitive type II. Analyses also indicate chlorophototrophy originated before LPCA. We further reconstructed evolution of chlorophototrophs/chlorophototrophy post-LPCA, including vertical inheritance in Terrabacteria, the rise of oxygen-generating chlorophototrophy in one descendant branch near the Great Oxidation Event, and subsequent emergence of Cyanobacteria. These collectively unveil a detailed view of the coevolution of light metabolism and Bacteria having clear congruence with the geological record.
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Affiliation(s)
- Arisa Nishihara
- Department of Life Science and Biotechnology, The National Institute of Advanced Industrial Science and Technology, Ibaraki305-0817, Japan
| | - Yusuke Tsukatani
- Biogeochemistry Research Center, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Kanagawa237-0061, Japan
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Kanagawa237-0061, Japan
| | - Chihiro Azai
- College of Life Sciences, Ritsumeikan University, Shiga525-8577, Japan
- Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, Tokyo112-8551, Japan
| | - Masaru K. Nobu
- Department of Life Science and Biotechnology, The National Institute of Advanced Industrial Science and Technology, Ibaraki305-0817, Japan
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Kanagawa237-0061, Japan
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2
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A phylogenetically novel cyanobacterium most closely related to Gloeobacter. ISME JOURNAL 2020; 14:2142-2152. [PMID: 32424249 PMCID: PMC7368068 DOI: 10.1038/s41396-020-0668-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 04/09/2020] [Accepted: 04/24/2020] [Indexed: 01/01/2023]
Abstract
Clues to the evolutionary steps producing innovations in oxygenic photosynthesis may be preserved in the genomes of organisms phylogenetically placed between non-photosynthetic Vampirovibrionia (formerly Melainabacteria) and the thylakoid-containing Cyanobacteria. However, only two species with published genomes are known to occupy this phylogenetic space, both within the genus Gloeobacter. Here, we describe nearly complete, metagenome-assembled genomes (MAGs) of an uncultured organism phylogenetically placed near Gloeobacter, for which we propose the name Candidatus Aurora vandensis {Au’ro.ra. L. fem. n. aurora, the goddess of the dawn in Roman mythology; van.de’nsis. N.L. fem. adj. vandensis of Lake Vanda, Antarctica}. The MAG of A. vandensis contains homologs of most genes necessary for oxygenic photosynthesis including key reaction center proteins. Many accessory subunits associated with the photosystems in other species either are missing from the MAG or are poorly conserved. The MAG also lacks homologs of genes associated with the pigments phycocyanoerethrin, phycoeretherin and several structural parts of the phycobilisome. Additional characterization of this organism is expected to inform models of the evolution of oxygenic photosynthesis.
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3
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Demoulin CF, Lara YJ, Cornet L, François C, Baurain D, Wilmotte A, Javaux EJ. Cyanobacteria evolution: Insight from the fossil record. Free Radic Biol Med 2019; 140:206-223. [PMID: 31078731 PMCID: PMC6880289 DOI: 10.1016/j.freeradbiomed.2019.05.007] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 03/13/2019] [Accepted: 05/05/2019] [Indexed: 11/07/2022]
Abstract
Cyanobacteria played an important role in the evolution of Early Earth and the biosphere. They are responsible for the oxygenation of the atmosphere and oceans since the Great Oxidation Event around 2.4 Ga, debatably earlier. They are also major primary producers in past and present oceans, and the ancestors of the chloroplast. Nevertheless, the identification of cyanobacteria in the early fossil record remains ambiguous because the morphological criteria commonly used are not always reliable for microfossil interpretation. Recently, new biosignatures specific to cyanobacteria were proposed. Here, we review the classic and new cyanobacterial biosignatures. We also assess the reliability of the previously described cyanobacteria fossil record and the challenges of molecular approaches on modern cyanobacteria. Finally, we suggest possible new calibration points for molecular clocks, and strategies to improve our understanding of the timing and pattern of the evolution of cyanobacteria and oxygenic photosynthesis.
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Affiliation(s)
- Catherine F Demoulin
- Early Life Traces & Evolution - Astrobiology, UR ASTROBIOLOGY, Geology Department, University of Liège, Liège, Belgium.
| | - Yannick J Lara
- Early Life Traces & Evolution - Astrobiology, UR ASTROBIOLOGY, Geology Department, University of Liège, Liège, Belgium
| | - Luc Cornet
- Early Life Traces & Evolution - Astrobiology, UR ASTROBIOLOGY, Geology Department, University of Liège, Liège, Belgium; Eukaryotic Phylogenomics, InBioS-PhytoSYSTEMS, University of Liège, Liège, Belgium
| | - Camille François
- Early Life Traces & Evolution - Astrobiology, UR ASTROBIOLOGY, Geology Department, University of Liège, Liège, Belgium
| | - Denis Baurain
- Eukaryotic Phylogenomics, InBioS-PhytoSYSTEMS, University of Liège, Liège, Belgium
| | - Annick Wilmotte
- BCCM/ULC Cyanobacteria Collection, InBioS-CIP, Centre for Protein Engineering, University of Liège, Liège, Belgium
| | - Emmanuelle J Javaux
- Early Life Traces & Evolution - Astrobiology, UR ASTROBIOLOGY, Geology Department, University of Liège, Liège, Belgium
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4
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Soo RM, Hemp J, Hugenholtz P. Evolution of photosynthesis and aerobic respiration in the cyanobacteria. Free Radic Biol Med 2019; 140:200-205. [PMID: 30930297 DOI: 10.1016/j.freeradbiomed.2019.03.029] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 03/05/2019] [Accepted: 03/26/2019] [Indexed: 01/23/2023]
Abstract
For well over a hundred years, members of the bacterial phylum Cyanobacteria have been considered strictly photosynthetic microorganisms, reflected in their classification as "blue-green algae" in the botanical code. Recently, genomes recovered from environmental sequencing surveys representing two major uncultured basal lineages (classes) of Cyanobacteria have been found to completely lack photosynthetic and CO2 fixation genes. The most likely explanation for this finding is that oxygenic photosynthesis was not an ancestral feature of the Cyanobacteria, and rather originated following divergence of the primary lines of descent. Here we describe recent findings on the evolution of aerobic respiration in the non-photosynthetic cyanobacterial classes, and how this has been interpreted by researchers interested in the evolution of oxygenic photosynthesis.
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Affiliation(s)
- Rochelle M Soo
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia.
| | - James Hemp
- Department of Internal Medicine, University of Utah, Salt Lake City, UT, USA
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia
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5
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Magnabosco C, Moore KR, Wolfe JM, Fournier GP. Dating phototrophic microbial lineages with reticulate gene histories. GEOBIOLOGY 2018; 16:179-189. [PMID: 29384268 PMCID: PMC5873394 DOI: 10.1111/gbi.12273] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 12/23/2017] [Indexed: 05/19/2023]
Abstract
Phototrophic bacteria are among the most biogeochemically significant organisms on Earth and are physiologically related through the use of reaction centers to collect photons for energy metabolism. However, the major phototrophic lineages are not closely related to one another in bacterial phylogeny, and the origins of their respective photosynthetic machinery remain obscured by time and low sequence similarity. To better understand the co-evolution of Cyanobacteria and other ancient anoxygenic phototrophic lineages with respect to geologic time, we designed and implemented a variety of molecular clocks that use horizontal gene transfer (HGT) as additional, relative constraints. These HGT constraints improve the precision of phototroph divergence date estimates and indicate that stem green non-sulfur bacteria are likely the oldest phototrophic lineage. Concurrently, crown Cyanobacteria age estimates ranged from 2.2 Ga to 2.7 Ga, with stem Cyanobacteria diverging ~2.8 Ga. These estimates provide a several hundred Ma window for oxygenic photosynthesis to evolve prior to the Great Oxidation Event (GOE) ~2.3 Ga. In all models, crown green sulfur bacteria diversify after the loss of the banded iron formations from the sedimentary record (~1.8 Ga) and may indicate the expansion of the lineage into a new ecological niche following the GOE. Our date estimates also provide a timeline to investigate the temporal feasibility of different photosystem HGT events between phototrophic lineages. Using this approach, we infer that stem Cyanobacteria are unlikely to be the recipient of an HGT of photosystem I proteins from green sulfur bacteria but could still have been either the HGT donor or the recipient of photosystem II proteins with green non-sulfur bacteria, prior to the GOE. Together, these results indicate that HGT-constrained molecular clocks are useful tools for the evaluation of various geological and evolutionary hypotheses, using the evolutionary histories of both genes and organismal lineages.
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Affiliation(s)
- C. Magnabosco
- Flatiron Institute Center for Computational BiologySimons FoundationNew York, NYUSA
| | - K. R. Moore
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
| | - J. M. Wolfe
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
| | - G. P. Fournier
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
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6
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Martin WF, Bryant DA, Beatty JT. A physiological perspective on the origin and evolution of photosynthesis. FEMS Microbiol Rev 2018; 42:205-231. [PMID: 29177446 PMCID: PMC5972617 DOI: 10.1093/femsre/fux056] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 11/20/2017] [Indexed: 12/22/2022] Open
Abstract
The origin and early evolution of photosynthesis are reviewed from an ecophysiological perspective. Earth's first ecosystems were chemotrophic, fueled by geological H2 at hydrothermal vents and, required flavin-based electron bifurcation to reduce ferredoxin for CO2 fixation. Chlorophyll-based phototrophy (chlorophototrophy) allowed autotrophs to generate reduced ferredoxin without electron bifurcation, providing them access to reductants other than H2. Because high-intensity, short-wavelength electromagnetic radiation at Earth's surface would have been damaging for the first chlorophyll (Chl)-containing cells, photosynthesis probably arose at hydrothermal vents under low-intensity, long-wavelength geothermal light. The first photochemically active pigments were possibly Zn-tetrapyrroles. We suggest that (i) after the evolution of red-absorbing Chl-like pigments, the first light-driven electron transport chains reduced ferredoxin via a type-1 reaction center (RC) progenitor with electrons from H2S; (ii) photothioautotrophy, first with one RC and then with two, was the bridge between H2-dependent chemolithoautotrophy and water-splitting photosynthesis; (iii) photothiotrophy sustained primary production in the photic zone of Archean oceans; (iv) photosynthesis arose in an anoxygenic cyanobacterial progenitor; (v) Chl a is the ancestral Chl; and (vi), anoxygenic chlorophototrophic lineages characterized so far acquired, by horizontal gene transfer, RCs and Chl biosynthesis with or without autotrophy, from the architects of chlorophototrophy-the cyanobacterial lineage.
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Affiliation(s)
- William F Martin
- Institute for Molecular Evolution, University of Düsseldorf, D-40225 Düsseldorf, Germany
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - J Thomas Beatty
- Department of Microbiology and Immunology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
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7
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Khadka B, Adeolu M, Blankenship RE, Gupta RS. Novel insights into the origin and diversification of photosynthesis based on analyses of conserved indels in the core reaction center proteins. PHOTOSYNTHESIS RESEARCH 2017; 131:159-171. [PMID: 27638319 DOI: 10.1007/s11120-016-0307-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 09/07/2016] [Indexed: 06/06/2023]
Abstract
The evolution and diversification of different types of photosynthetic reaction centers (RCs) remains an important unresolved problem. We report here novel sequence features of the core proteins from Type I RCs (RC-I) and Type II RCs (RC-II) whose analyses provide important insights into the evolution of the RCs. The sequence alignments of the RC-I core proteins contain two conserved inserts or deletions (indels), a 3 amino acid (aa) indel that is uniquely found in all RC-I homologs from Cyanobacteria (both PsaA and PsaB) and a 1 aa indel that is specifically shared by the Chlorobi and Acidobacteria homologs. Ancestral sequence reconstruction provides evidence that the RC-I core protein from Heliobacteriaceae (PshA), lacking these indels, is most closely related to the ancestral RC-I protein. Thus, the identified 3 aa and 1 aa indels in the RC-I protein sequences must have been deletions, which occurred, respectively, in an ancestor of the modern Cyanobacteria containing a homodimeric form of RC-I and in a common ancestor of the RC-I core protein from Chlorobi and Acidobacteria. We also report a conserved 1 aa indel in the RC-II protein sequences that is commonly shared by all homologs from Cyanobacteria but not found in the homologs from Chloroflexi, Proteobacteria and Gemmatimonadetes. Ancestral sequence reconstruction provides evidence that the RC-II subunits lacking this indel are more similar to the ancestral RC-II protein. The results of flexible structural alignments of the indel-containing region of the RC-II protein with the homologous region in the RC-I core protein, which shares structural similarity with the RC-II homologs, support the view that the 1 aa indel present in the RC-II homologs from Cyanobacteria is a deletion, which was not present in the ancestral form of the RC-II protein. Our analyses of the conserved indels found in the RC-I and RC-II proteins, thus, support the view that the earliest photosynthetic lineages with living descendants likely contained only a single RC (RC-I or RC-II), and the presence of both RC-I and RC-II in a linked state, as found in the modern Cyanobacteria, is a derivation from these earlier phototrophs.
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Affiliation(s)
- Bijendra Khadka
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8N 3Z5, Canada
| | - Mobolaji Adeolu
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8N 3Z5, Canada
| | - Robert E Blankenship
- Department of Biology and Department of Chemistry, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8N 3Z5, Canada.
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8
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Cardona T. A fresh look at the evolution and diversification of photochemical reaction centers. PHOTOSYNTHESIS RESEARCH 2015; 126:111-34. [PMID: 25512103 PMCID: PMC4582080 DOI: 10.1007/s11120-014-0065-x] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 12/05/2014] [Indexed: 05/18/2023]
Abstract
In this review, I reexamine the origin and diversification of photochemical reaction centers based on the known phylogenetic relations of the core subunits, and with the aid of sequence and structural alignments. I show, for example, that the protein folds at the C-terminus of the D1 and D2 subunits of Photosystem II, which are essential for the coordination of the water-oxidizing complex, were already in place in the most ancestral Type II reaction center subunit. I then evaluate the evolution of reaction centers in the context of the rise and expansion of the different groups of bacteria based on recent large-scale phylogenetic analyses. I find that the Heliobacteriaceae family of Firmicutes appears to be the earliest branching of the known groups of phototrophic bacteria; however, the origin of photochemical reaction centers and chlorophyll synthesis cannot be placed in this group. Moreover, it becomes evident that the Acidobacteria and the Proteobacteria shared a more recent common phototrophic ancestor, and this is also likely for the Chloroflexi and the Cyanobacteria. Finally, I argue that the discrepancies among the phylogenies of the reaction center proteins, chlorophyll synthesis enzymes, and the species tree of bacteria are best explained if both types of photochemical reaction centers evolved before the diversification of the known phyla of phototrophic bacteria. The primordial phototrophic ancestor must have had both Type I and Type II reaction centers.
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Affiliation(s)
- Tanai Cardona
- Department of Life Sciences, Imperial College London, Exhibition Road, London, SW7 2AZ, UK.
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9
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Sousa FL, Shavit-Grievink L, Allen JF, Martin WF. Chlorophyll biosynthesis gene evolution indicates photosystem gene duplication, not photosystem merger, at the origin of oxygenic photosynthesis. Genome Biol Evol 2013; 5:200-16. [PMID: 23258841 PMCID: PMC3595025 DOI: 10.1093/gbe/evs127] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
An open question regarding the evolution of photosynthesis is how cyanobacteria came to possess the two reaction center (RC) types, Type I reaction center (RCI) and Type II reaction center (RCII). The two main competing theories in the foreground of current thinking on this issue are that either 1) RCI and RCII are related via lineage divergence among anoxygenic photosynthetic bacteria and became merged in cyanobacteria via an event of large-scale lateral gene transfer (also called "fusion" theories) or 2) the two RC types are related via gene duplication in an ancestral, anoxygenic but protocyanobacterial phototroph that possessed both RC types before making the transition to using water as an electron donor. To distinguish between these possibilities, we studied the evolution of the core (bacterio)chlorophyll biosynthetic pathway from protoporphyrin IX (Proto IX) up to (bacterio)chlorophyllide a. The results show no dichotomy of chlorophyll biosynthesis genes into RCI- and RCII-specific chlorophyll biosynthetic clades, thereby excluding models of fusion at the origin of cyanobacteria and supporting the selective-loss hypothesis. By considering the cofactor demands of the pathway and the source genes from which several steps in chlorophyll biosynthesis are derived, we infer that the cell that first synthesized chlorophyll was a cobalamin-dependent, heme-synthesizing, diazotrophic anaerobe.
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Affiliation(s)
- Filipa L Sousa
- Institute of Molecular Evolution, University of Düsseldorf, Düsseldorf, Germany.
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10
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Hochkoeppler A, Landau EM, Venturoli G, Zannoni D, Feick R, Luisi PL. Photochemistry of a photosynthetic reaction center immobilized in lipidic cubic phases. Biotechnol Bioeng 2012; 46:93-8. [PMID: 18623268 DOI: 10.1002/bit.260460202] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Photosynthetic reaction centers, isolated and purified from the facultative phototrophic bacterium Chloroflexus aurantiacus, were immobilized in optically transparent lipidic cubic phases composed of 42% (w/w) 1-palmitoyl-2-hydroxy-sn-glycero-3-phosphocholine and 58% (w/w) water. The immobilized photosynthetic protein retains its native properties, as indicated by visible and circular dichroic spectra. The ground state visible spectrum of the immobilized reaction centers is very similar to the corresponding spectrum in aqueous solution, indicating that the protein pigments are not extracted into the lipidic regions of the cubic phase. The secondary structure of the protein is maintained in the immobilized state, as determined by far-UV circular dichroism spectroscopy in the 200- to 250-nm range. Moreover, immobilized reaction centers retain their photochemical activity: a reversible photo-oxidation of the primary electron donor (P) is seen upon continuous illumination. Furthermore, the entrappment of reaction centers does not affect the kinetics of charge recombination between the photo-oxidized primary donor (P(+)) and the photoreduced primary quinone acceptor, generated by a short flash of light. Reaction centers devoided of the secondary quinone acceptor can be easily reconstituted in cubic phases by means of their coimmobilization with 1,4-naphtoquinone. Indeed, the kinetics for charge recombination in reconstituted reaction centers is dramatically slower than the corresponding kinetics in the unreconstituted protein. Interestingly, immobilized reaction centers are significantly stabilized as compared with reaction centers in aqueous solution: the integrity of the protein in the cubic phase is maintained for at least 5 months, whereas in water solution 50% of the activity is lost within 2 months. (c) 1995 John Wiley & Sons, Inc.
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Affiliation(s)
- A Hochkoeppler
- Department of Biology, University of Bologna, Via Irnerio 42, 40126 Bologna, Italy
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11
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Abstract
Energy conversion of sunlight by photosynthetic organisms has changed Earth and life on it. Photosynthesis arose early in Earth's history, and the earliest forms of photosynthetic life were almost certainly anoxygenic (non-oxygen evolving). The invention of oxygenic photosynthesis and the subsequent rise of atmospheric oxygen approximately 2.4 billion years ago revolutionized the energetic and enzymatic fundamentals of life. The repercussions of this revolution are manifested in novel biosynthetic pathways of photosynthetic cofactors and the modification of electron carriers, pigments, and existing and alternative modes of photosynthetic carbon fixation. The evolutionary history of photosynthetic organisms is further complicated by lateral gene transfer that involved photosynthetic components as well as by endosymbiotic events. An expanding wealth of genetic information, together with biochemical, biophysical, and physiological data, reveals a mosaic of photosynthetic features. In combination, these data provide an increasingly robust framework to formulate and evaluate hypotheses concerning the origin and evolution of photosynthesis.
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12
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Mimuro M, Tomo T, Tsuchiya T. Two unique cyanobacteria lead to a traceable approach of the first appearance of oxygenic photosynthesis. PHOTOSYNTHESIS RESEARCH 2008; 97:167-176. [PMID: 18568415 DOI: 10.1007/s11120-008-9311-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2007] [Accepted: 05/08/2008] [Indexed: 05/26/2023]
Abstract
The evolutionary route from anoxygenic photosynthetic bacteria to oxygenic cyanobacteria is discontinuous in terms of photochemical/photophysical reaction systems. It is difficult to describe this transition process simply because there are no recognized intermediary organisms between the two bacterial groups. Gloeobacter violaceus PCC 7421 might be a model organism that is suitable for analysis because it still possesses primordial characteristics such as the absence of thylakoid membranes. Whole genome analysis and biochemical and biophysical surveys of G. violaceus have favored the hypothesis that it is an intermediary organism. On the other hand, species differentiation is an evolutionary process that could be driven by changes in a small number of genes, and this process might give fair information more in details by monitoring of those genes. Comparative studies of genes, including those in Acaryochloris marina MBIC 11017, have provided information relevant to species differentiation; in particular, the acquisition of a new pigment, chlorophyll d, and changes in amino acid sequences have been informative. Here, based on experimental evidence from these two species, we discuss some of the evolutionary pathways for the appearance and differentiation of cyanobacteria.
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Affiliation(s)
- Mamoru Mimuro
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto 606-8501, Japan.
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13
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Mix LJ, Haig D, Cavanaugh CM. Phylogenetic analyses of the core antenna domain: investigating the origin of photosystem I. J Mol Evol 2005; 60:153-63. [PMID: 15785845 DOI: 10.1007/s00239-003-0181-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2003] [Accepted: 07/29/2004] [Indexed: 10/25/2022]
Abstract
Phototrophy, the conversion of light to biochemical energy, occurs throughout the Bacteria and plants, however, debate continues over how different phototrophic mechanisms and the bacteria that contain them are related. There are two types of phototrophic mechanisms in the Bacteria: reaction center type 1 (RC1) has core and core antenna domains that are parts of a single polypeptide, whereas reaction center type 2 (RC2) is composed of short core proteins without antenna domains. In cyanobacteria, RC2 is associated with separate core antenna proteins that are homologous to the core antenna domains of RC1. We reconstructed evolutionary relationships among phototrophic mechanisms based on a phylogeny of core antenna domains/proteins. Core antenna domains of 46 polypeptides were aligned, including the RC1 core proteins of heliobacteria, green sulfur bacteria, and photosystem I (PSI) of cyanobacteria and plastids, plus core antenna proteins of photosystem II (PSII) from cyanobacteria and plastids. Maximum likelihood, parsimony, and neighbor joining methods all supported a single phylogeny in which PSII core antenna proteins (PsbC, PsbB) arose within the cyanobacteria from duplications of the RC1-associated core antenna domains and accessory antenna proteins (IsiA, PcbA, PcbC) arose from duplications of PsbB. The data indicate an evolutionary history of RC1 in which an initially homodimeric reaction center was vertically transmitted to green sulfur bacteria, heliobacteria, and an ancestor of cyanobacteria. A heterodimeric RC1 (=PSI) then arose within the cyanobacterial lineage. In this scenario, the current diversity of core antenna domains/proteins is explained without a need to invoke horizontal transfer.
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Affiliation(s)
- Lucas J Mix
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
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14
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Boucher Y, Douady CJ, Papke RT, Walsh DA, Boudreau MER, Nesbø CL, Case RJ, Doolittle WF. Lateral gene transfer and the origins of prokaryotic groups. Annu Rev Genet 2004; 37:283-328. [PMID: 14616063 DOI: 10.1146/annurev.genet.37.050503.084247] [Citation(s) in RCA: 279] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Lateral gene transfer (LGT) is now known to be a major force in the evolution of prokaryotic genomes. To date, most analyses have focused on either (a) verifying phylogenies of individual genes thought to have been transferred, or (b) estimating the fraction of individual genomes likely to have been introduced by transfer. Neither approach does justice to the ability of LGT to effect massive and complex transformations in basic biology. In some cases, such transformation will be manifested as the patchy distribution of a seemingly fundamental property (such as aerobiosis or nitrogen fixation) among the members of a group classically defined by the sharing of other properties (metabolic, morphological, or molecular, such as small subunit ribosomal RNA sequence). In other cases, the lineage of recipients so transformed may be seen to comprise a new group of high taxonomic rank ("class" or even "phylum"). Here we review evidence for an important role of LGT in the evolution of photosynthesis, aerobic respiration, nitrogen fixation, sulfate reduction, methylotrophy, isoprenoid biosynthesis, quorum sensing, flotation (gas vesicles), thermophily, and halophily. Sometimes transfer of complex gene clusters may have been involved, whereas other times separate exchanges of many genes must be invoked.
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Affiliation(s)
- Yan Boucher
- Program in Evolutionary Biology, Canadian Institute for Advanced Research, Department of Biochemistry, Sir Charles Tupper Medical Building, 5859 University Avenue, Halifax, Nova Scotia, Canada, B3H 4H7
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15
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Nakamura C, Hasegawa M, Nakamura N, Miyake J. Rapid and specific detection of herbicides using a self-assembled photosynthetic reaction center from purple bacterium on an SPR chip. Biosens Bioelectron 2003; 18:599-603. [PMID: 12706568 DOI: 10.1016/s0956-5663(03)00030-7] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
In this study, a direct detection system for herbicides inhibiting photosynthetic electron transfer was developed using the photosynthetic reaction center (RC) from the purple bacterium, Rhodobacter sphaeroides, and surface plasmon resonance (SPR) apparatus. The heavy-subunit-histidine-tagged RCs (HHisRCs) were immobilized on an SPR sensor chip via nickel chelation chemistry as a binder for one of the triazine herbicides, atrazine. Immediately after injection of atrazine solution on the HHisRCs-immobilized chip, the SPR responses increased and reached plateaus within 1 min. The SPR signals were proportional to the sample concentrations of atrazine in the range 1-100 microg/ml. To evaluate the binding specificity to atrazine, chlorinated aromatic herbicides, DCMU and MCPP, were investigated using the HHisRCs-immobilized chip. An RC inhibitor, DCMU, could also be detected with a higher detection limit of 20 microg/ml than atrazine (1 microg/ml). MCPP showed no signals because its inhibition mechanism against plants is different from that of atrazine and DCMU. These results indicated that the sensor chip immobilized RCs could be used for the specific detection of photosynthetic inhibitors.
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Affiliation(s)
- Chikashi Nakamura
- Tissue Biosensor Team, Tissue Engineering Research Center, National Institute of Advanced Industrial Science and Technology, 1-1-1 Higashi, 305-8562, Tsukuba, Japan.
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16
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Abstract
The origin of photosynthesis is a fundamental biological question that has eluded researchers for decades. The complexity of the origin and evolution of photosynthesis is a result of multiple photosynthetic components having independent evolutionary pathways. Indeed, evolutionary scenarios have been established for only a few photosynthetic components. Phylogenetic analysis of Mg-tetrapyrrole biosynthesis genes indicates that most anoxygenic photosynthetic organisms are ancestral to oxygen-evolving cyanobacteria and that the purple bacterial lineage may contain the most ancestral form of this pigment biosynthesis pathway. The evolutionary path of type I and type II reaction center apoproteins is still unresolved owing to the fact that a unified evolutionary tree cannot be generated for these divergent reaction center subunits. However, evidence for a cytochrome b origin for the type II reaction center apoproteins is emerging. Based on the combined information for both photopigments and reaction centers, a unified theory for the evolution of reaction center holoproteins is provided. Further insight into the evolution of photosynthesis will have to rely on additional broader sampling of photosynthesis genes from divergent photosynthetic bacteria.
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Affiliation(s)
- Jin Xiong
- Department of Biology, Texas A&M University, College Station, Texas 77843, USA.
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17
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Baymann F, Brugna M, Mühlenhoff U, Nitschke W. Daddy, where did (PS)I come from? BIOCHIMICA ET BIOPHYSICA ACTA 2001; 1507:291-310. [PMID: 11687221 DOI: 10.1016/s0005-2728(01)00209-2] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The reacton centre I (RCI)-type photosystems from plants, cyano-, helio- and green sulphur bacteria are compared and the essential properties of an archetypal RCI are deduced. Species containing RCI-type photosystems most probably cluster together on a common branch of the phylogenetic tree. The predicted branching order is green sulphur, helio- and cyanobacteria. Striking similarities between RCI- and RCII-type photosystems recently became apparent in the three-dimensional structures of photosystem I (PSI), PSII and RCII. The phylogenetic relationship between all presently known photosystems is analysed suggesting (a) RCI as the ancestral photosystem and (b) the descendence of PSII from RCI via gene duplication and gene splitting. An evolutionary model trying to rationalise available data is presented.
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Affiliation(s)
- F Baymann
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Biologie Structurale et Microbiologie, Marseille, France
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18
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Sétif P, Seo D, Sakurai H. Photoreduction and reoxidation of the three iron-sulfur clusters of reaction centers of green sulfur bacteria. Biophys J 2001; 81:1208-19. [PMID: 11509338 PMCID: PMC1301603 DOI: 10.1016/s0006-3495(01)75779-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Iron-sulfur clusters are the terminal electron acceptors of the photosynthetic reaction centers of green sulfur bacteria and photosystem I. We have studied electron-transfer reactions involving these clusters in the green sulfur bacterium Chlorobium tepidum, using flash-absorption spectroscopic measurements. We show for the first time that three different clusters, named F(X), F(1), and F(2), can be photoreduced at room temperature during a series of consecutive flashes. The rates of electron escape to exogenous acceptors depend strongly upon the number of reduced clusters. When two or three clusters are reduced, the escape is biphasic, with the fastest phase being 12-14-fold faster than the slowest phase, which is similar to that observed after single reduction. This is explained by assuming that escape involves mostly the second reducible cluster. Evidence is thus provided for a functional asymmetry between the two terminal acceptors F(1) and F(2). From multiple-flash experiments, it was possible to derive the intrinsic recombination rates between P840(+) and reduced iron-sulfur clusters: values of 7, 14, and 59 s(-1) were found after one, two and three electron reduction of the clusters, respectively. The implications of our results for the relative redox potentials of the three clusters are discussed.
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Affiliation(s)
- P Sétif
- Commissariat à l'Energie Atomique, Département de Biologie Cellulaire et Moléculaire, Section de Bioénergétique and CNRS URA 2096, 91191 Gif sur Yvette, France.
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19
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Direct triazine herbicide detection using a self-assembled photosynthetic reaction center from purple bacterium. BIOTECHNOL BIOPROC E 2000. [DOI: 10.1007/bf02931940] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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20
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Spyridaki A, Fritzsch G, Kouimtzoglou E, Baciou L, Ghanotakis D. The natural product capsaicin inhibits photosynthetic electron transport at the reducing side of photosystem II and purple bacterial reaction center: structural details of capsaicin binding. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1459:69-76. [PMID: 10924900 DOI: 10.1016/s0005-2728(00)00114-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Capsaicin, a natural quinone analog, was found to block electron transport, in both plant photosystem II (PSII) and bacterial reaction center (RC) from Rhodobacter sphaeroides, at the QB site. The mode of action of capsaicin was investigated by O2 evolution measurements and fluoresence induction studies in the case of PSII, and flash-induced absorbance spectroscopy in the case of the bacterial RC. Structural details of capsaicin binding to the bacterial RC complex were determined by X-ray crystallographic analysis.
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Affiliation(s)
- A Spyridaki
- Department of Chemistry, University of Crete, Heraklion, Greece
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21
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Xiong J, Inoue K, Bauer CE. Tracking molecular evolution of photosynthesis by characterization of a major photosynthesis gene cluster from Heliobacillus mobilis. Proc Natl Acad Sci U S A 1998; 95:14851-6. [PMID: 9843979 PMCID: PMC24539 DOI: 10.1073/pnas.95.25.14851] [Citation(s) in RCA: 140] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A DNA sequence has been obtained for a 35.6-kb genomic segment from Heliobacillus mobilis that contains a major cluster of photosynthesis genes. A total of 30 ORFs were identified, 20 of which encode enzymes for bacteriochlorophyll and carotenoid biosynthesis, reaction-center (RC) apoprotein, and cytochromes for cyclic electron transport. Donor side electron-transfer components to the RC include a putative RC-associated cytochrome c553 and a unique four-large-subunit cytochrome bc complex consisting of Rieske Fe-S protein (encoded by petC), cytochrome b6 (petB), subunit IV (petD), and a diheme cytochrome c (petX). Phylogenetic analysis of various photosynthesis gene products indicates a consistent grouping of oxygenic lineages that are distinct and descendent from anoxygenic lineages. In addition, H. mobilis was placed as the closest relative to cyanobacteria, which form a monophyletic origin to chloroplast-based photosynthetic lineages. The consensus of the photosynthesis gene trees also indicates that purple bacteria are the earliest emerging photosynthetic lineage. Our analysis also indicates that an ancient gene-duplication event giving rise to the paralogous bchI and bchD genes predates the divergence of all photosynthetic groups. In addition, our analysis of gene duplication of the photosystem I and photosystem II core polypeptides supports a "heterologous fusion model" for the origin and evolution of oxygenic photosynthesis.
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Affiliation(s)
- J Xiong
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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22
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Rhee KH, Morris EP, Barber J, Kühlbrandt W. Three-dimensional structure of the plant photosystem II reaction centre at 8 A resolution. Nature 1998; 396:283-6. [PMID: 9834037 DOI: 10.1038/24421] [Citation(s) in RCA: 256] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Photosystem II is a multisubunit enzyme complex involved in plant photosynthesis. It uses solar energy to catalyse the breakdown of water to reducing equivalents and molecular oxygen. Native photosystem II comprises more than 25 different subunits, and has a relative molecular mass of more than 600K. Here we report the three-dimensional structure of a photosystem II subcomplex, containing the proteins D1, D2, CP47 and cytochrome b-559, determined by electron crystallography. This CP47 reaction centre, which has a relative molecular mass of 160K, can perform light-mediated energy and electron-transfer reactions but is unable to oxidize water. The complex contains 23 transmembrane alpha-helices, of which 16 have been assigned to the D1, D2 and CP47 proteins. The arrangement of these helices is remarkably similar to that of the helices in the reaction centres of purple bacteria and of plant photosystem I, indicating a common evolutionary origin for these assemblies. The map suggests that redox cofactors in the D1-D2 complex are located in positions analogous to those in the bacterial reaction centre, but the distance between the chlorophylls corresponding to the bacterial 'special pair' is significantly larger.
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Affiliation(s)
- K H Rhee
- Max-Planck-Institut für Biophysik, Abteilung Strukturbiologie, Frankfurt am Main, Germany
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23
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Schubert WD, Klukas O, Saenger W, Witt HT, Fromme P, Krauss N. A common ancestor for oxygenic and anoxygenic photosynthetic systems: a comparison based on the structural model of photosystem I. J Mol Biol 1998; 280:297-314. [PMID: 9654453 DOI: 10.1006/jmbi.1998.1824] [Citation(s) in RCA: 195] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The 4 A structural model of photosystem I (PSI) has elucidated essential features of this protein complex. Inter alia, it demonstrates that the core proteins of PSI, PsaA and PsaB each consist of an N-terminal antenna-binding domain, and a C-terminal reaction center (RC)-domain. A comparison of the RC-domain of PSI and the photosynthetic RC of purple bacteria (PbRC), reveals significantly analogous structures. This provides the structural support for the hypothesis that the two RC-types (I and II) share a common evolutionary origin. Apart from a similar set of constituent cofactors of the electron transfer system, the analogous features include a comparable cofactor arrangement and a corresponding secondary structure motif of the RC-cores. Despite these analogies, significant differences are evident, particularly as regards the distances between and the orientation of individual cofactors, and the length and orientation of alpha-helices. Inferred roles of conserved amino acids are discussed for PSI, photosystem II (PSII), photosystem C (PSC, green sulfur bacteria) and photosystem H (PSH, heliobacteria). Significant sequence homology between the N-terminal, antenna-binding domains of the core proteins of type-I RCs, PsaA, PsaB, PscA and PshA (of PSI, PSC and PSH respectively) with the antenna-binding subunits CP43 and CP47 of PSII indicate that PSII has a modular structure comparable to that of PSI.
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Affiliation(s)
- W D Schubert
- Institut für Kristallographie, Freie Universität Berlin, Takustr. 6, Berlin, D-14195, Germany
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24
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25
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Kusumoto N, Inoue K, Sakurai H. Spectroscopic studies of bound cytochrome c and an iron-sulfur center in a purified reaction center complex from the green sulfur bacterium Chlorobium tepidum. PHOTOSYNTHESIS RESEARCH 1995; 43:107-112. [PMID: 24306743 DOI: 10.1007/bf00042967] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/1994] [Accepted: 12/07/1994] [Indexed: 06/02/2023]
Abstract
Flash-induced optical kinetics at room temperature of cytochrome (Cyt) c 551 and an Fe-S center (CFA/CFB) bound to a purified reaction center (RC) complex from the green sulfur photosynthetic bacterium Chlorobium tepidum were studied. At 551 nm, the flash-induced absorbance change decayed with a t 1/2 of several hundred ms, and the decay was accelerated by 1-methoxy-5-methylphenazinium methyl sulfate (mPMS). In the blue region, the absorbance change was composed of mPMS-dependent (Cyt) and mPMS-independent component (CFA/CFB) which decayed with a t 1/2 of ∼400-650 ms. Decay of the latter was effectively accelerated by benzyl viologen (Em -360 mV) and methyl viologen (-440 mV), and less effectively by triquat (-540 mV). The difference spectrum of Cyt c had negative peaks at 551, ∼520 and ∼420 nm, with a positive rise at ∼440 to ∼500 nm. The difference spectrum of CFA/CFB resembled P430 of PSI, and had a broad negative peak at 430∼435 nm.
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Affiliation(s)
- N Kusumoto
- Department of Biology, School of Education, Waseda University, 169-50, Tokyo, Japan
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26
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Kleinherenbrink FA, Chiou HC, LoBrutto R, Blankenship RE. Spectroscopic evidence for the presence of an iron-sulfur center similar to Fx of Photosystem I in Heliobacillus mobilis. PHOTOSYNTHESIS RESEARCH 1994; 41:115-123. [PMID: 11539856 DOI: 10.1007/bf02184151] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Treatment of membranes of Heliobacillus mobilis with high concentrations of the chaotropic agent urea resulted in the removal of the iron-sulfur centers FA and FB from the reaction center, as indicated by EPR spectra under strongly reducing conditions. In urea-treated membranes, transient absorption measurements upon a laser flash indicated a recombination between the photo-oxidized primary donor P798+ and a reduced acceptor with a time constant of 20 ms at room temperature. Benzylviologen, vitamin K-3 and methylene blue were found to accept electrons from the reduced acceptor efficiently. A differential extinction coefficient of 225-240 mM-1 cm-1 at 798 nm was determined from experiments in the presence of methylene blue. Transient absorption difference spectra between 400 and 500 nm in the presence and absence of artificial acceptors indicated that the electron acceptor involved in the 20 ms recombination has an absorption spectrum similar to that of an iron-sulfur center. This iron-sulfur center was assigned to be analogous to Fx of Photosystem I. Our results provide evidence in support of the presence of Fx in heliobacteria, which was proposed on the basis of the reaction center polypeptide sequence (Liebl et al. (1993) Proc. Natl. Acad. Sci. USA 90: 7124-7128). Implications for the electron transfer pathway in the reaction center of heliobacteria are discussed.
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Affiliation(s)
- F A Kleinherenbrink
- Department of Chemistry and Biochemistry, Arizona State University, Tempe 85287-1604, USA
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27
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Skulachev VP. Bioenergetics: the evolution of molecular mechanisms and the development of bioenergetic concepts. Antonie Van Leeuwenhoek 1994; 65:271-84. [PMID: 7832586 DOI: 10.1007/bf00872213] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Possible routes for the evolution of cell energetics are considered. It is assumed that u.v. light was the primary energy source for the precursors of the primordial living cell and that primitive energetics might have been based on the use of the adenine moiety of ADP as the u.v. chromophore. It is proposed that the excitation of the adenine residue facilitated phosphorylation of its amino group with subsequent transfer of a phosphoryl group to the terminal phosphate of ADP to form ATP. ATP-driven carbohydrate synthesis is considered as a mechanism for storing u.v.-derived energy, which was then used in the dark. Glycolysis presumably produced compounds like ethanol and CO2, which easily penetrate the membrane and therefore were lost by the cell. Later lactate-producing glycolysis appeared, the end product being non-penetrant and, hence, retained inside the cell to be utilized to regenerate carbohydrates when light energy became available. Production of lactate was accompanied by accumulation of equimolar H+. To avoid acidification of the cell interior, an F0-type H+ channel was employed. Later it was supplemented with F1. This allowed the ATP energy to be used for 'uphill' H+ pumping to the medium, which was acidified due to glycolytic activity of the cells. In the subsequent course of evolution, u.v. light was replaced by visible light, which has lower energy but is less dangerous for the cell. It is assumed that bacteriorhodopsin, a simple and very stable light-driven H+ pump which still exists in halophilic and thermophilic Archaea, was the primary system utilizing visible light. The delta mu-H+ formed was used to reverse the H(+)-ATPase, which began to function as H(+)-ATP-synthase. Later, bacteriorhodopsin photosynthesis was substituted by a more efficient chlorophyll photosynthesis, producing not only ATP, but also carbohydrates. O2, a side product of this process, was consumed by the H(+)-motive respiratory chain to form delta mu-H+ in the dark. At the next stage of evolution, a parallel energy-transducing mechanism appeared which employed Na+ instead of H+ as the coupling ion (the Na+ cycle).(ABSTRACT TRUNCATED AT 400 WORDS)
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Affiliation(s)
- V P Skulachev
- Department of Bioenergetics, A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Russia
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28
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Abstract
It is proposed that there is a single evolutionary origin for photosynthetic reaction centers and also for most light-harvesting chlorophyll proteins. It is generally accepted that the purple bacterial reaction center (quinone-reducing photosystem) and the plant and cyanobacterial PSII (oxygen-evolving photosystem) are homologous. It is also apparent that the green sulfur bacterial reaction center is homologous to cyanobacterial PSI (the pyridine nucleotide reducing photosystem). However, it is less obvious that PSI is related to the purple bacterial reaction center. It is herein proposed that PSI represents a gene fusion of the precursors of small light harvesting bacteriochlorophyll proteins from purple bacteria and purple bacterial reaction centers. Furthermore, it is proposed that reaction centers evolved from the membrane-spanning cytochrome b of the cytochrome bc1 complex and that most membrane-spanning cytochromes may have a common origin.
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Affiliation(s)
- T E Meyer
- Department of Biochemistry, University of Arizona, Tucson 85721
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29
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Blankenship RE. Protein structure, electron transfer and evolution of prokaryotic photosynthetic reaction centers. Antonie Van Leeuwenhoek 1994; 65:311-29. [PMID: 7832589 DOI: 10.1007/bf00872216] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Photosynthetic reaction centers from a variety of organisms have been isolated and characterized. The groups of prokaryotic photosynthetic organisms include the purple bacteria, the filamentous green bacteria, the green sulfur bacteria and the heliobacteria as anoxygenic representatives as well as the cyanobacteria and prochlorophytes as oxygenic representatives. This review focuses on structural and functional comparisons of the various groups of photosynthetic reaction centers and considers possible evolutionary scenarios to explain the diversity of existing photosynthetic organisms.
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Affiliation(s)
- R E Blankenship
- Department of Chemistry and Biochemistry, Arizona State University, Tempe 85287-1604
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30
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Kleinherenbrink F, Ikegami I, Hiraishi A, Otte S, Amesz J. Electron transfer in menaquinone-depleted membranes of Heliobacterium chlorum. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 1993. [DOI: 10.1016/0005-2728(93)90085-t] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Allen JF. Protein phosphorylation in regulation of photosynthesis. BIOCHIMICA ET BIOPHYSICA ACTA 1992; 1098:275-335. [PMID: 1310622 DOI: 10.1016/s0005-2728(09)91014-3] [Citation(s) in RCA: 498] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- J F Allen
- Department of Biology, University of Oslo, Blindern, Norway
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33
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Blankenship RE. Origin and early evolution of photosynthesis. PHOTOSYNTHESIS RESEARCH 1992; 33:91-111. [PMID: 11538390 DOI: 10.1007/bf00039173] [Citation(s) in RCA: 216] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/1991] [Accepted: 03/12/1992] [Indexed: 05/24/2023]
Abstract
Photosynthesis was well-established on the earth at least 3.5 thousand million years ago, and it is widely believed that these ancient organisms had similar metabolic capabilities to modern cyanobacteria. This requires that development of two photosystems and the oxygen evolution capability occurred very early in the earth's history, and that a presumed phase of evolution involving non-oxygen evolving photosynthetic organisms took place even earlier. The evolutionary relationships of the reaction center complexes found in all the classes of currently existing organisms have been analyzed using sequence analysis and biophysical measurements. The results indicate that all reaction centers fall into two basic groups, those with pheophytin and a pair of quinones as early acceptors, and those with iron sulfur clusters as early acceptors. No simple linear branching evolutionary scheme can account for the distribution patterns of reaction centers in existing photosynthetic organisms, and lateral transfer of genetic information is considered as a likely possibility. Possible scenarios for the development of primitive reaction centers into the heterodimeric protein structures found in existing reaction centers and for the development of organisms with two linked photosystems are presented.
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Affiliation(s)
- R E Blankenship
- Department of Chemistry and Biochemistry, Arizona State University, Tempe 85287-1604, USA
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34
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Margulies MM. Sequence similarity between Photosystems I and II. Identification of a Photosystem I reaction center transmembrane helix that is similar to transmembrane helix IV of the D2 subunit of Photosystem II and the M subunit of the non-sulfur purple and flexible green bacteria. PHOTOSYNTHESIS RESEARCH 1991; 29:133-147. [PMID: 24415151 DOI: 10.1007/bf00036217] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/1991] [Accepted: 07/02/1991] [Indexed: 06/03/2023]
Abstract
There are basic structural similarities between plant PS II and bacterial RCs of the Chloroflexaceae and Rhodospirillaceae. These RCs are referred to as PS II-type RCs. A similar relationship of PS I RC to PS II-type RCs has not been established. Although plant PS I and PS II RCs show structural and functional differences, they also share similarities. Therefore, the A and B polypeptides of PS I were searched for PS II D1 and D2 polypeptide-like sequences. An alignment without gaps was found between PS II-type D2/M helix IV and PS I B helix X, as well as a weaker alignment of PS II-type D1/L with PS I B helix X. No comparable alignment with PS I A was found. In the M/D2 alignment there were eight identities and some conservative substitutions in twenty nine residues. PS I B helix X appeared to contain a modified chlorophyll dimer and monomer binding site and a modified non-heme iron-quinone binding site. The conserved residue sequence was found only in RC polypeptides. The proposed chlorophyll dimer-monomer binding site was located transmembrane from the iron-sulfur cluster X binding site. The conserved residues generally are those that interact with prosthetic groups. Half of the conserved residues are located on the same side of the helix. Thus, although there are impediments to concluding firmly that PS I B helix X has a functional and evolutionary relatedness to the D2 PS II and bacterial M RC polypeptides, our analysis gives reasonable support to the idea.
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Affiliation(s)
- M M Margulies
- Climate Stress Laboratory, Agriculture Research Service, USDA, 046 A BARC West, 20705, Beltsville, MD, USA
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35
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Liebetanz R, Hornberger U, Drews G. Organization of the genes coding for the reaction-centre L and M subunits and B870 antenna polypeptides alpha and beta from the aerobic photosynthetic bacterium Erythrobacter species OCH114. Mol Microbiol 1991; 5:1459-68. [PMID: 1787796 DOI: 10.1111/j.1365-2958.1991.tb00792.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In the aerobic photosynthetic bacterium Erythrobacter species OCH114 the structural genes coding for the light-harvesting (LH) complex B870 and the reaction-centre (RC) polypeptides (the gene products of the pufB, pufA, pufL and pufM genes) are mapped on a 2.728 kbp EcoRI fragment. Sequencing of this fragment revealed that the deduced amino acid sequences contain 50 (B870 beta), 52 (B850 alpha), 283 (RCL) and 331 (RCM) residues with the corresponding molecular weights of 5592, 5814, 31364, and 37671, respectively. In the corresponding mRNA a 'hairpin' structure (delta G degrees = -26.6 kcal) is predicted to be located immediately downstream of pufA. The RC and LH polypeptides are highly homologous to those of the purple photosynthetic bacteria Rhodobacter capsulatus, Rhodobacter sphaeroides and Rhodopseudomonas viridis. Directly downstream of pufM there is an open reading frame (ORF) of unknown size. Partial sequencing indicates that this ORF is highly homologous to the cytochrome subunit of the photosynthetic reaction centre from R. viridis. In the puf operon no pufQ or pufX genes could be found, but the bchA gene is located upstream of that operon. Plasmid pESS8.9 containing the 2.728 kbp EcoRI fragment reconstituted a photoinactive mutant of Erythrobacter species OCH114. Comparative analysis of the DNA region upstream of the puf operon and of bacteriochlorophyll (Bchl) synthesis indicated that Bchl synthesis and puf gene expression are regulated differently in Erythrobacter and purple bacteria, respectively.
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Affiliation(s)
- R Liebetanz
- Institute of Biology II, Albert-Ludwigs-University Freiburg, Germany
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36
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Abstract
The following is an outline of the direction of research into the evolutionary origins of photosynthesis as revealed by the study of cytochromes c. Determination of the numbers of kinds of cytochromes, their structures, their functional roles, and their distribution are the principal kinds of data being collected and analyzed. A hypothesis on the origin of photosynthesis is presented.
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Affiliation(s)
- T E Meyer
- Department of Biochemistry, University of Arizona, Tucson
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