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Biswas S, Niedzwiedzki DM, Liberton M, Pakrasi HB. Phylogenetic and spectroscopic insights on the evolution of core antenna proteins in cyanobacteria. PHOTOSYNTHESIS RESEARCH 2023:10.1007/s11120-023-01046-6. [PMID: 37737529 DOI: 10.1007/s11120-023-01046-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 08/31/2023] [Indexed: 09/23/2023]
Abstract
Light harvesting by antenna systems is the initial step in a series of electron-transfer reactions in all photosynthetic organisms, leading to energy trapping by reaction center proteins. Cyanobacteria are an ecologically diverse group and are the simplest organisms capable of oxygenic photosynthesis. The primary light-harvesting antenna in cyanobacteria is the large membrane extrinsic pigment-protein complex called the phycobilisome. In addition, cyanobacteria have also evolved specialized membrane-intrinsic chlorophyll-binding antenna proteins that transfer excitation energy to the reaction centers of photosystems I and II (PSI and PSII) and dissipate excess energy through nonphotochemical quenching. Primary among these are the CP43 and CP47 proteins of PSII, but in addition, some cyanobacteria also use IsiA and the prochlorophyte chlorophyll a/b binding (Pcb) family of proteins. Together, these proteins comprise the CP43 family of proteins owing to their sequence similarity with CP43. In this article, we have revisited the evolution of these chlorophyll-binding antenna proteins by examining their protein sequences in parallel with their spectral properties. Our phylogenetic and spectroscopic analyses support the idea of a common ancestor for CP43, IsiA, and Pcb proteins, and suggest that PcbC might be a distant ancestor of IsiA. The similar spectral properties of CP47 and IsiA suggest a closer evolutionary relationship between these proteins compared to CP43.
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Affiliation(s)
- Sandeep Biswas
- Department of Biology, Washington University, St. Louis, MO, 63130, USA
| | - Dariusz M Niedzwiedzki
- Center for Solar Energy and Energy Storage, Washington University, St. Louis, MO, 63130, USA
- Department of Energy, Environmental and Chemical Engineering, Washington University, St. Louis, MO, 63130, USA
| | - Michelle Liberton
- Department of Biology, Washington University, St. Louis, MO, 63130, USA
| | - Himadri B Pakrasi
- Department of Biology, Washington University, St. Louis, MO, 63130, USA.
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2
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Pinevich AV, Averina SG. On the Edge of the Rainbow: Red-Shifted Chlorophylls and Far-Red Light Photoadaptation in Cyanobacteria. Microbiology (Reading) 2022. [DOI: 10.1134/s0026261722602019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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3
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Oliver T, Sánchez-Baracaldo P, Larkum AW, Rutherford AW, Cardona T. Time-resolved comparative molecular evolution of oxygenic photosynthesis. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2021; 1862:148400. [PMID: 33617856 PMCID: PMC8047818 DOI: 10.1016/j.bbabio.2021.148400] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 02/01/2021] [Accepted: 02/12/2021] [Indexed: 12/15/2022]
Abstract
Oxygenic photosynthesis starts with the oxidation of water to O2, a light-driven reaction catalysed by photosystem II. Cyanobacteria are the only prokaryotes capable of water oxidation and therefore, it is assumed that the origin of oxygenic photosynthesis is a late innovation relative to the origin of life and bioenergetics. However, when exactly water oxidation originated remains an unanswered question. Here we use phylogenetic analysis to study a gene duplication event that is unique to photosystem II: the duplication that led to the evolution of the core antenna subunits CP43 and CP47. We compare the changes in the rates of evolution of this duplication with those of some of the oldest well-described events in the history of life: namely, the duplication leading to the Alpha and Beta subunits of the catalytic head of ATP synthase, and the divergence of archaeal and bacterial RNA polymerases and ribosomes. We also compare it with more recent events such as the duplication of Cyanobacteria-specific FtsH metalloprotease subunits and the radiation leading to Margulisbacteria, Sericytochromatia, Vampirovibrionia, and other clades containing anoxygenic phototrophs. We demonstrate that the ancestral core duplication of photosystem II exhibits patterns in the rates of protein evolution through geological time that are nearly identical to those of the ATP synthase, RNA polymerase, or the ribosome. Furthermore, we use ancestral sequence reconstruction in combination with comparative structural biology of photosystem subunits, to provide additional evidence supporting the premise that water oxidation had originated before the ancestral core duplications. Our work suggests that photosynthetic water oxidation originated closer to the origin of life and bioenergetics than can be documented based on phylogenetic or phylogenomic species trees alone.
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Affiliation(s)
- Thomas Oliver
- Department of Life Sciences, Imperial College London, London, UK
| | | | | | | | - Tanai Cardona
- Department of Life Sciences, Imperial College London, London, UK.
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4
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Pinevich AV. Chloroplast history clarified by the criterion of light-harvesting complex. Biosystems 2020; 196:104173. [PMID: 32534171 DOI: 10.1016/j.biosystems.2020.104173] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/19/2020] [Accepted: 05/21/2020] [Indexed: 01/13/2023]
Abstract
Bacterial essence of mitochondria and chloroplasts was initially proclaimed in general outline. Later, the remarkable insight gave way to an elaborate hypothesis. Finally, it took shape of a theory confirmed by molecular biology data. In particular, the rrn operon, which is the key phylogeny marker, locates chloroplasts on the tree of Cyanobacteria. Chloroplast ancestry and diversity can be also traced with the rpoС and psbA genes, rbc operon, and other molecular criteria of prime importance. Another criterion, also highly reliable, is light-harvesting complex (LHC). LHC pigment and protein moieties specify light acclimation strategies in evolutionary retrospect and modern biosphere. The onset of symbiosis between eukaryotic host and pre-chloroplast, as well as further mutual adjustment of partners depended on physiological competence of LHC. In this review, the criterion of LHC is applied to the origin and diversity of chloroplasts. In particular, ancient cyanobacterium possessing tandem antenna (encoded by the cbp genes and the pbp genes, correspondingly), and defined as a prochlorophyte, is argued to be chloroplast ancestor.
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Affiliation(s)
- Alexander V Pinevich
- St. Petersburg State University, Department of Microbiology, St. Petersburg, Russia.
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Li ZK, Yin YC, Zhang LD, Zhang ZC, Dai GZ, Chen M, Qiu BS. The identification of IsiA proteins binding chlorophyll d in the cyanobacterium Acaryochloris marina. PHOTOSYNTHESIS RESEARCH 2018; 135:165-175. [PMID: 28378245 DOI: 10.1007/s11120-017-0379-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Accepted: 03/30/2017] [Indexed: 06/07/2023]
Abstract
The bioavailable iron in many aquatic ecosystems is extremely low, and limits the growth and photosynthetic activity of phytoplankton. In response to iron limitation, a group of chlorophyll-binding proteins known as iron stress-induced proteins are induced and serve as accessory light-harvesting components for photosystems under iron limitation. In the present study, we investigated physiological features of Acaryochloris marina in response to iron-deficient conditions. The growth doubling time under iron-deficient conditions was prolonged to ~3.4 days compared with 1.9 days under normal culture conditions, accompanied with dramatically decreased chlorophyll content. The isolation of chlorophyll-binding protein complexes using sucrose density gradient centrifugation shows six main green bands and three main fluorescence components of 712, 728, and 748 nm from the iron-deficient culture. The fluorescence components of 712 and 728 nm co-exist in the samples collected from iron-deficient and iron-replete cultures and are attributed to Chl d-binding accessory chlorophyll-binding antenna proteins and also from photosystem II. A new chlorophyll-binding protein complex with its main fluorescence peak at 748 nm was observed and enriched in the heaviest fraction from the samples collected from the iron-deficient culture only. Combining western blotting analysis using antibodies of CP47 (PSII), PsaC (PSI) and IsiA and proteomic analysis on an excised protein band at ~37 kDa, the heaviest fraction (-F6) isolated from iron-deficient culture contained Chl d-bound PSI-IsiA supercomplexes. The PSII-antenna supercomplexes isolated from iron-replete conditions showed two fluorescence peaks of 712 and 728 nm, which can be assigned as 6-transmembrane helix chlorophyll-binding antenna and photosystem II fluorescence, respectively, which is supported by protein analysis of the fractions (F5 and F6).
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Affiliation(s)
- Zheng-Ke Li
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, 430079, Hubei, People's Republic of China
| | - Yan-Chao Yin
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, 430079, Hubei, People's Republic of China
| | - Lu-Dan Zhang
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, 430079, Hubei, People's Republic of China
| | - Zhong-Chun Zhang
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, 430079, Hubei, People's Republic of China
| | - Guo-Zheng Dai
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, 430079, Hubei, People's Republic of China
| | - Min Chen
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia.
| | - Bao-Sheng Qiu
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, 430079, Hubei, People's Republic of China.
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Zanello P. The competition between chemistry and biology in assembling iron–sulfur derivatives. Molecular structures and electrochemistry. Part V. {[Fe4S4](SCysγ)4} proteins. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2016.10.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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7
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Rockwell NC, Martin SS, Lim S, Lagarias JC, Ames JB. Characterization of Red/Green Cyanobacteriochrome NpR6012g4 by Solution Nuclear Magnetic Resonance Spectroscopy: A Protonated Bilin Ring System in Both Photostates. Biochemistry 2015; 54:2581-600. [DOI: 10.1021/bi501548t] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Nathan C. Rockwell
- Department of Molecular
and Cellular Biology and ‡Department of Chemistry, University of California, Davis, California 95616, United States
| | - Shelley S. Martin
- Department of Molecular
and Cellular Biology and ‡Department of Chemistry, University of California, Davis, California 95616, United States
| | - Sunghyuk Lim
- Department of Molecular
and Cellular Biology and ‡Department of Chemistry, University of California, Davis, California 95616, United States
| | - J. Clark Lagarias
- Department of Molecular
and Cellular Biology and ‡Department of Chemistry, University of California, Davis, California 95616, United States
| | - James B. Ames
- Department of Molecular
and Cellular Biology and ‡Department of Chemistry, University of California, Davis, California 95616, United States
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8
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Wahadoszamen M, D'Haene S, Ara AM, Romero E, Dekker JP, Grondelle RV, Berera R. Identification of common motifs in the regulation of light harvesting: The case of cyanobacteria IsiA. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:486-492. [PMID: 25615585 DOI: 10.1016/j.bbabio.2015.01.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 11/27/2014] [Accepted: 01/12/2015] [Indexed: 10/24/2022]
Abstract
When cyanobacteria are grown under iron-limited or other oxidative stress conditions the iron stress inducible pigment-protein IsiA is synthesized in variable amounts. IsiA accumulates in aggregates inside the photosynthetic membrane that strongly dissipate chlorophyll excited state energy. In this paper we applied Stark fluorescence (SF) spectroscopy at 77K to IsiA aggregates to gain insight into the nature of the emitting and energy dissipating state(s). Our study shows that two emitting states are present in the system, one emitting at 684 nm and the other emitting at about 730 nm. The new 730 nm state exhibits strongly reduced fluorescence (F) together with a large charge transfer character. We discuss these findings in the light of the energy dissipation mechanisms involved in the regulation of photosynthesis in plants, cyanobacteria and diatoms. Our results suggest that photosynthetic organisms have adopted common mechanisms to cope with the deleterious effects of excess light under unfavorable growth conditions.
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Affiliation(s)
- Md Wahadoszamen
- Biophysics of Photosynthesis/Physics of Energy, Department of Physics Astronomy, Faculty of Sciences, VU University Amsterdam, The Netherlands; Department of Physics, University of Dhaka, Dhaka 1000, Bangladesh.
| | - Sandrine D'Haene
- Biophysics of Photosynthesis/Physics of Energy, Department of Physics Astronomy, Faculty of Sciences, VU University Amsterdam, The Netherlands
| | - Anjue Mane Ara
- Biophysics of Photosynthesis/Physics of Energy, Department of Physics Astronomy, Faculty of Sciences, VU University Amsterdam, The Netherlands; Department of Physics, Jagannath University, Dhaka 1100, Bangladesh
| | - Elisabet Romero
- Biophysics of Photosynthesis/Physics of Energy, Department of Physics Astronomy, Faculty of Sciences, VU University Amsterdam, The Netherlands
| | - Jan P Dekker
- Biophysics of Photosynthesis/Physics of Energy, Department of Physics Astronomy, Faculty of Sciences, VU University Amsterdam, The Netherlands
| | - Rienk van Grondelle
- Biophysics of Photosynthesis/Physics of Energy, Department of Physics Astronomy, Faculty of Sciences, VU University Amsterdam, The Netherlands
| | - Rudi Berera
- Biophysics of Photosynthesis/Physics of Energy, Department of Physics Astronomy, Faculty of Sciences, VU University Amsterdam, The Netherlands.
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9
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Abstract
Chlorophylls are magnesium-tetrapyrrole molecules that play essential roles in photosynthesis. All chlorophylls have similar five-membered ring structures, with variations in the side chains and/or reduction states. Formyl group substitutions on the side chains of chlorophyll a result in the different absorption properties of chlorophyll b, chlorophyll d, and chlorophyll f. These formyl substitution derivatives exhibit different spectral shifts according to the formyl substitution position. Not only does the presence of various types of chlorophylls allow the photosynthetic organism to harvest sunlight at different wavelengths to enhance light energy input, but the pigment composition of oxygenic photosynthetic organisms also reflects the spectral properties on the surface of the Earth. Two major environmental influencing factors are light and oxygen levels, which may play central roles in the regulatory pathways leading to the different chlorophylls. I review the biochemical processes of chlorophyll biosynthesis and their regulatory mechanisms.
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Affiliation(s)
- Min Chen
- School of Biological Sciences, University of Sydney, Sydney, New South Wales 2006, Australia;
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10
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Loughlin P, Lin Y, Chen M. Chlorophyll d and Acaryochloris marina: current status. PHOTOSYNTHESIS RESEARCH 2013; 116:277-93. [PMID: 23615924 DOI: 10.1007/s11120-013-9829-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 04/14/2013] [Indexed: 05/03/2023]
Abstract
The discovery of the chlorophyll d-containing cyanobacterium Acaryochloris marina in 1996 precipitated a shift in our understanding of oxygenic photosynthesis. The presence of the red-shifted chlorophyll d in the reaction centre of the photosystems of Acaryochloris has opened up new avenues of research on photosystem energetics and challenged the unique status of chlorophyll a in oxygenic photosynthesis. In this review, we detail the chemistry and role of chlorophyll d in photosynthesis and summarise the unique adaptations that have allowed the proliferation of Acaryochloris in diverse ecological niches around the world.
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Affiliation(s)
- Patrick Loughlin
- School of Biological Sciences (A08), University of Sydney, Sydney, NSW, 2006, Australia
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11
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Chen M, Scheer H. Extending the limits of natural photosynthesis and implications for technical light harvesting. J PORPHYR PHTHALOCYA 2013. [DOI: 10.1142/s1088424612300108] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Photosynthetic organisms provide, directly or indirectly, the energy that sustains life on earth by harvesting light from the sun. The amount of light impinging on the surface of the earth vastly surpasses the energy needs of life including man. Harvesting the sun is, therefore, an option for a sustainable energy source: directly by improving biomass production, indirectly by coupling it to the production of hydrogen for fuel or, conceptually, by using photosynthetic strategies for technological solutions based on non-biological or hybrid materials. In this review, we summarize the various light climates on earth, the primary reactions responsible for light harvesting and transduction to chemical energy in photosynthesis, and the mechanisms of competitively adapting the photosynthetic apparatus to the ever-changing light conditions. The focus is on oxygenic photosynthesis, its adaptation to the various light-climates by specialized pigments and on the extension of its limits by the evolution of red-shifted chlorophylls. The implications for potential technical solutions are briefly discussed.
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Affiliation(s)
- Min Chen
- School of Biological Sciences, University of Sydney, Sydney NSW 2006, Australia
| | - Hugo Scheer
- Dept-Biologie 1, Botanik, Universität München, 80638 München, Germany
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12
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Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing. Proc Natl Acad Sci U S A 2012; 110:1053-8. [PMID: 23277585 DOI: 10.1073/pnas.1217107110] [Citation(s) in RCA: 519] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The cyanobacterial phylum encompasses oxygenic photosynthetic prokaryotes of a great breadth of morphologies and ecologies; they play key roles in global carbon and nitrogen cycles. The chloroplasts of all photosynthetic eukaryotes can trace their ancestry to cyanobacteria. Cyanobacteria also attract considerable interest as platforms for "green" biotechnology and biofuels. To explore the molecular basis of their different phenotypes and biochemical capabilities, we sequenced the genomes of 54 phylogenetically and phenotypically diverse cyanobacterial strains. Comparison of cyanobacterial genomes reveals the molecular basis for many aspects of cyanobacterial ecophysiological diversity, as well as the convergence of complex morphologies without the acquisition of novel proteins. This phylum-wide study highlights the benefits of diversity-driven genome sequencing, identifying more than 21,000 cyanobacterial proteins with no detectable similarity to known proteins, and foregrounds the diversity of light-harvesting proteins and gene clusters for secondary metabolite biosynthesis. Additionally, our results provide insight into the distribution of genes of cyanobacterial origin in eukaryotic nuclear genomes. Moreover, this study doubles both the amount and the phylogenetic diversity of cyanobacterial genome sequence data. Given the exponentially growing number of sequenced genomes, this diversity-driven study demonstrates the perspective gained by comparing disparate yet related genomes in a phylum-wide context and the insights that are gained from it.
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14
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Mohr R, Voss B, Schliep M, Kurz T, Maldener I, Adams DG, Larkum ADW, Chen M, Hess WR. A new chlorophyll d-containing cyanobacterium: evidence for niche adaptation in the genus Acaryochloris. ISME JOURNAL 2010; 4:1456-69. [PMID: 20505751 DOI: 10.1038/ismej.2010.67] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Chlorophyll d is a photosynthetic pigment that, based on chemical analyses, has only recently been recognized to be widespread in oceanic and lacustrine environments. However, the diversity of organisms harbouring this pigment is not known. Until now, the unicellular cyanobacterium Acaryochloris marina is the only characterized organism that uses chlorophyll d as a major photopigment. In this study we describe a new cyanobacterium possessing a high amount of chlorophyll d, which was isolated from waters around Heron Island, Great Barrier Reef (23° 26' 31.2″ S, 151° 54' 50.4″ E). The 16S ribosomal RNA is 2% divergent from the two previously described isolates of A. marina, which were isolated from waters around the Palau islands (Pacific Ocean) and the Salton Sea lake (California), suggesting that it belongs to a different clade within the genus Acaryochloris. An overview sequence analysis of its genome based on Illumina technology yielded 871 contigs with an accumulated length of 8 371 965 nt. Their analysis revealed typical features associated with Acaryochloris, such as an extended gene family for chlorophyll-binding proteins. However, compared with A. marina MBIC11017, distinct genetic, morphological and physiological differences were observed. Light saturation is reached at lower light intensities, Chl d/a ratios are less variable with light intensity and the phycobiliprotein phycocyanin is lacking, suggesting that cyanobacteria of the genus Acaryochloris occur in distinct ecotypes. These data characterize Acaryochloris as a niche-adapted cyanobacterium and show that more rigorous attempts are worthwhile to isolate, cultivate and analyse chlorophyll d-containing cyanobacteria for understanding the ecophysiology of these organisms.
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Affiliation(s)
- Remus Mohr
- Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, Freiburg, Germany
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15
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Zhang Y, Chen M, Church WB, Lau KW, Larkum AWD, Jermiin LS. The molecular structure of the IsiA–Photosystem I supercomplex, modelled from high-resolution, crystal structures of Photosystem I and the CP43 protein. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1797:457-65. [PMID: 20064486 DOI: 10.1016/j.bbabio.2010.01.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2009] [Revised: 12/31/2009] [Accepted: 01/05/2010] [Indexed: 11/30/2022]
Affiliation(s)
- Yinan Zhang
- School of Biological Sciences, University of Sydney, Sydney, NSW, Australia
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16
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Yang D, Qing Y, Min C. Incorporation of the chlorophyll d-binding light-harvesting protein from Acaryochloris marina and its localization within the photosynthetic apparatus of Synechocystis sp. PCC6803. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1797:204-11. [DOI: 10.1016/j.bbabio.2009.10.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2009] [Revised: 10/11/2009] [Accepted: 10/14/2009] [Indexed: 11/30/2022]
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17
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Chen M, Floetenmeyer M, Bibby TS. Supramolecular organization of phycobiliproteins in the chlorophyll d
-containing cyanobacterium Acaryochloris marina. FEBS Lett 2009; 583:2535-9. [DOI: 10.1016/j.febslet.2009.07.012] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2009] [Revised: 07/02/2009] [Accepted: 07/02/2009] [Indexed: 12/21/2022]
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Ting CS, Ramsey ME, Wang YL, Frost AM, Jun E, Durham T. Minimal genomes, maximal productivity: comparative genomics of the photosystem and light-harvesting complexes in the marine cyanobacterium, Prochlorococcus. PHOTOSYNTHESIS RESEARCH 2009; 101:1-19. [PMID: 19557544 DOI: 10.1007/s11120-009-9455-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2008] [Accepted: 06/04/2009] [Indexed: 05/28/2023]
Abstract
Although Prochlorococcus isolates possess the smallest genomes of any extant photosynthetic organism, this genus numerically dominates vast regions of the world's subtropical and tropical open oceans and has evolved to become an important contributor to global biogeochemical cycles. The sequencing of 12 Prochlorococcus genomes provides a glimpse of the extensive genetic heterogeneity and, thus, physiological potential of the lineage. In this study, we present an up-to-date comparative analysis of major proteins of the photosynthetic apparatus in 12 Prochlorococcus genomes. Our analyses reveal a striking diversity within the Prochlorococcus lineage in the major protein complexes of the photosynthetic apparatus. The heterogeneity that has evolved in the photosynthetic apparatus suggests versatility in strategies for optimizing photosynthesis under conditions of environmental variability and stress. This diversity could be particularly important in ensuring the survival of a lineage whose individuals have evolved minimal genomes and, thus, relatively limited repertoires for responding to environmental challenges.
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Affiliation(s)
- Claire S Ting
- Thompson Biology Lab, Department of Biology, Williams College, Williamstown, MA 01267, USA.
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19
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Bibby TS, Zhang Y, Chen M. Biogeography of photosynthetic light-harvesting genes in marine phytoplankton. PLoS One 2009; 4:e4601. [PMID: 19240807 PMCID: PMC2644788 DOI: 10.1371/journal.pone.0004601] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2008] [Accepted: 01/03/2009] [Indexed: 01/05/2023] Open
Abstract
Background Photosynthetic light-harvesting proteins are the mechanism by which energy enters the marine ecosystem. The dominant prokaryotic photoautotrophs are the cyanobacterial genera Prochlorococcus and Synechococcus that are defined by two distinct light-harvesting systems, chlorophyll-bound protein complexes or phycobilin-bound protein complexes, respectively. Here, we use the Global Ocean Sampling (GOS) Project as a unique and powerful tool to analyze the environmental diversity of photosynthetic light-harvesting genes in relation to available metadata including geographical location and physical and chemical environmental parameters. Methods All light-harvesting gene fragments and their metadata were obtained from the GOS database, aligned using ClustalX and classified phylogenetically. Each sequence has a name indicative of its geographic location; subsequent biogeographical analysis was performed by correlating light-harvesting gene budgets for each GOS station with surface chlorophyll concentration. Conclusion/Significance Using the GOS data, we have mapped the biogeography of light-harvesting genes in marine cyanobacteria on ocean-basin scales and show that an environmental gradient exists in which chlorophyll concentration is correlated to diversity of light-harvesting systems. Three functionally distinct types of light-harvesting genes are defined: (1) the phycobilisome (PBS) genes of Synechococcus; (2) the pcb genes of Prochlorococcus; and (3) the iron-stress-induced (isiA) genes present in some marine Synechococcus. At low chlorophyll concentrations, where nutrients are limited, the Pcb-type light-harvesting system shows greater genetic diversity; whereas at high chlorophyll concentrations, where nutrients are abundant, the PBS-type light-harvesting system shows higher genetic diversity. We interpret this as an environmental selection of specific photosynthetic strategy. Importantly, the unique light-harvesting system isiA is found in the iron-limited, high-nutrient low-chlorophyll region of the equatorial Pacific. This observation demonstrates the ecological importance of isiA genes in enabling marine Synechococcus to acclimate to iron limitation and suggests that the presence of this gene can be a natural biomarker for iron limitation in oceanic environments.
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Affiliation(s)
- Thomas S. Bibby
- School of Ocean and Earth Sciences, National Oceanography Centre, Southampton, United Kingdom
- School of Biological Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Yinan Zhang
- School of Biological Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Min Chen
- School of Biological Sciences, University of Sydney, Sydney, New South Wales, Australia
- * E-mail:
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20
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Chen M, Zhang Y. Tracking the molecular evolution of photosynthesis through characterization of atomic contents of the photosynthetic units. PHOTOSYNTHESIS RESEARCH 2008; 97:255-261. [PMID: 18766462 DOI: 10.1007/s11120-008-9356-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2007] [Accepted: 08/13/2008] [Indexed: 05/26/2023]
Abstract
Oxygen molecules have a great impact on protein evolution. We have performed a comparative study of key photosynthetic proteins in order to seek the answer to the question; did the evolutionary substitution of oxygen- and nitrogen-containing residues in the photosynthetic proteins correspond to nutrient constraints and metabolic optimization? The D1 peptide in RC II complexes has higher oxygen-containing amino acid residues and PufL/PufM have lower oxygen content in their peptides. In this article, we also discuss the possible influences of micro-environment and the available nutrients on the protein structure and their atomic distribution.
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Affiliation(s)
- Min Chen
- School of Biological Sciences, University of Sydney, Sydney, NSW, 2006, Australia.
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Niche adaptation and genome expansion in the chlorophyll d-producing cyanobacterium Acaryochloris marina. Proc Natl Acad Sci U S A 2008; 105:2005-10. [PMID: 18252824 DOI: 10.1073/pnas.0709772105] [Citation(s) in RCA: 175] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Acaryochloris marina is a unique cyanobacterium that is able to produce chlorophyll d as its primary photosynthetic pigment and thus efficiently use far-red light for photosynthesis. Acaryochloris species have been isolated from marine environments in association with other oxygenic phototrophs, which may have driven the niche-filling introduction of chlorophyll d. To investigate these unique adaptations, we have sequenced the complete genome of A. marina. The DNA content of A. marina is composed of 8.3 million base pairs, which is among the largest bacterial genomes sequenced thus far. This large array of genomic data is distributed into nine single-copy plasmids that code for >25% of the putative ORFs. Heavy duplication of genes related to DNA repair and recombination (primarily recA) and transposable elements could account for genetic mobility and genome expansion. We discuss points of interest for the biosynthesis of the unusual pigments chlorophyll d and alpha-carotene and genes responsible for previously studied phycobilin aggregates. Our analysis also reveals that A. marina carries a unique complement of genes for these phycobiliproteins in relation to those coding for antenna proteins related to those in Prochlorococcus species. The global replacement of major photosynthetic pigments appears to have incurred only minimal specializations in reaction center proteins to accommodate these alternate pigments. These features clearly show that the genus Acaryochloris is a fitting candidate for understanding genome expansion, gene acquisition, ecological adaptation, and photosystem modification in the cyanobacteria.
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