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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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Biswas S, Niedzwiedzki DM, Pakrasi HB. Energy dissipation efficiency in the CP43 assembly intermediate complex of photosystem II. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2023; 1864:148982. [PMID: 37146928 DOI: 10.1016/j.bbabio.2023.148982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/10/2023] [Accepted: 04/20/2023] [Indexed: 05/07/2023]
Abstract
Photosystem II in oxygenic organisms is a large membrane bound rapidly turning over pigment protein complex. During its biogenesis, multiple assembly intermediates are formed, including the CP43-preassembly complex (pCP43). To understand the energy transfer dynamics in pCP43, we first engineered a His-tagged version of the CP43 in a CP47-less strain of the cyanobacterium Synechocystis 6803. Isolated pCP43 from this engineered strain was subjected to advanced spectroscopic analysis to evaluate its excitation energy dissipation characteristics. These included measurements of steady-state absorption and fluorescence emission spectra for which correlation was tested with Stepanov relation. Comparison of fluorescence excitation and absorptance spectra determined that efficiency of energy transfer from β-carotene to chlorophyll a is 39 %. Time-resolved fluorescence images of pCP43-bound Chl a were recorded on streak camera, and fluorescence decay dynamics were evaluated with global fitting. These demonstrated that the decay kinetics strongly depends on temperature and buffer used to disperse the protein sample and fluorescence decay lifetime was estimated in 3.2-5.7 ns time range, depending on conditions. The pCP43 complex was also investigated with femtosecond and nanosecond time-resolved absorption spectroscopy upon excitation of Chl a and β-carotene to reveal pathways of singlet excitation relaxation/decay, Chl a triplet dynamics and Chl a → β-carotene triplet state sensitization process. The latter demonstrated that Chl a triplet in the pCP43 complex is not efficiently quenched by carotenoids. Finally, detailed kinetic analysis of the rise of the population of β-carotene triplets determined that the time constant of the carotenoid triplet sensitization is 40 ns.
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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 & Chemical Engineering, Washington University, St. Louis, MO 63130, USA.
| | - Himadri B Pakrasi
- Department of Biology, Washington University, St. Louis, MO 63130, USA.
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Nie Y, Foster CSP, Zhu T, Yao R, Duchêne DA, Ho SYW, Zhong B. Accounting for Uncertainty in the Evolutionary Timescale of Green Plants Through Clock-Partitioning and Fossil Calibration Strategies. Syst Biol 2020; 69:1-16. [PMID: 31058981 DOI: 10.1093/sysbio/syz032] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Revised: 04/30/2019] [Accepted: 05/02/2019] [Indexed: 11/13/2022] Open
Abstract
Establishing an accurate evolutionary timescale for green plants (Viridiplantae) is essential to understanding their interaction and coevolution with the Earth's climate and the many organisms that rely on green plants. Despite being the focus of numerous studies, the timing of the origin of green plants and the divergence of major clades within this group remain highly controversial. Here, we infer the evolutionary timescale of green plants by analyzing 81 protein-coding genes from 99 chloroplast genomes, using a core set of 21 fossil calibrations. We test the sensitivity of our divergence-time estimates to various components of Bayesian molecular dating, including the tree topology, clock models, clock-partitioning schemes, rate priors, and fossil calibrations. We find that the choice of clock model affects date estimation and that the independent-rates model provides a better fit to the data than the autocorrelated-rates model. Varying the rate prior and tree topology had little impact on age estimates, with far greater differences observed among calibration choices and clock-partitioning schemes. Our analyses yield date estimates ranging from the Paleoproterozoic to Mesoproterozoic for crown-group green plants, and from the Ediacaran to Middle Ordovician for crown-group land plants. We present divergence-time estimates of the major groups of green plants that take into account various sources of uncertainty. Our proposed timeline lays the foundation for further investigations into how green plants shaped the global climate and ecosystems, and how embryophytes became dominant in terrestrial environments.
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Affiliation(s)
- Yuan Nie
- College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
| | - Charles S P Foster
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Tianqi Zhu
- National Center for Mathematics and Interdisciplinary Sciences, Key Laboratory of Random Complex Structures and Data Science, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100000, China
| | - Ru Yao
- College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
| | - David A Duchêne
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Bojian Zhong
- College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
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Middepogu A, Hou J, Gao X, Lin D. Effect and mechanism of TiO 2 nanoparticles on the photosynthesis of Chlorella pyrenoidosa. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 161:497-506. [PMID: 29913418 DOI: 10.1016/j.ecoenv.2018.06.027] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 06/07/2018] [Accepted: 06/09/2018] [Indexed: 05/15/2023]
Abstract
Titanium dioxide nanoparticles (n-TiO2) have been used in numerous applications, which results in their release into aquatic ecosystems and impact algal populations. A possible toxic mechanism of n-TiO2 on algae is via the disruption of the photosynthetic biochemical pathways, which yet remains to be demonstrated. In this study, Chlorella pyrenoidosa was exposed to different concentrations (0, 0.1, 1, 5, 10, and 20 mg/L) of a type of anatase n-TiO2, and the physiological, biochemical, and molecular responses involved in photosynthesis were investigated. The 96 h half growth inhibition concentration (IC50) of the n-TiO2 to algae was determined to be 9.1 mg/L. A variety of cellular and sub-cellular damages were observed, especially the blurry lamellar structure of thylakoids, indicating the n-TiO2 impaired the photosynthetic function of chloroplasts. Malondialdehyde (MDA) and glutathione disulfide (GSSG) significantly increased while the glutathione (GSH) content decreased. This implies the increased consumption of GSH by the increased intracellular oxidative stress upon n-TiO2 was insufficient to eliminate the lipid peroxidation. The contents of photosynthetic pigments, including chlorophyll a (Chl a) and phycobiliproteins (PBPs) in the exposed algal cells increased along with the up-regulation of genes encoding Chl a and photosystem II (PS II), which could be explained by a compensatory effect to overcome the toxicity induced by the n-TiO2. On the other hand, the photosynthetic activity was significantly inhibited, indicating the impairment on the photosynthesis via damaging the reaction center of PS II. In addition, lower productions of adenosine triphosphate (ATP) and glucose, together with the change of gene expressions suggested that the n-TiO2 disrupted the material and energy metabolisms in the photosynthesis. These findings support a paradigm shift of the toxic mechanism of n-TiO2 from physical and oxidative damages to metabolic disturbances, and emphasize the threat to the photosynthesis of algae in contaminated areas.
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Affiliation(s)
- Ayyaraju Middepogu
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Jie Hou
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Xuan Gao
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Daohui Lin
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Zhejiang University, Hangzhou 310058, China.
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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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Ioannidis NE, Kotzabasis K. Could structural similarity of specific domains between animal globins and plant antenna proteins provide hints important for the photoprotection mechanism? J Theor Biol 2015; 364:71-9. [PMID: 25218499 DOI: 10.1016/j.jtbi.2014.08.049] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Revised: 07/30/2014] [Accepted: 08/28/2014] [Indexed: 11/26/2022]
Abstract
Non photochemical quenching is a fundamental mechanism in photosynthesis, which protects plants against excess excitation energy and is of crucial importance for their survival and fitness. In the last decades hundreds of papers have appeared that describe the role of antenna regulation in protection or the so called qE response. However, the exact quenching site is still obscure. Previously overlooked features of the antenna may provide hints towards the elucidation of its functionality and of the quenching mechanism. Recently it was demonstrated that the catalytic domain of human myoglobin that binds the pigment (i.e. heme) is similar in structure to the domain of the light harvesting complex II of pea that binds Chl a 614 (former known as b3). In addition, it is well accepted that conformational changes of the chlorophyll macrocycle result in reversible changes of fluorescence (the lowest fluorescence corresponds to non planar macrocycle). Here we put forward a hypothesis regarding the molecular mechanism that leads to the formation of a quenching center inside the antenna proteins. Our main suggestion is that a conformational change of helix H5 (known also as helix D) forces conformational changes in the macrocycle of Chl a 614 is implicated in the ΔA535 absorbance change and quenching during photoprotective qE. The specific features (some of them similar to those of heme domain of globins) of the b3 domain account for these traits. The model predicts that antenna proteins having b3 pigments (i.e. LHCII, CP29, CP26) can act as potential quenchers.
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Affiliation(s)
- Nikolaos E Ioannidis
- Department of Biology, University of Crete, Voutes University Campus, GR-70013 Heraklion, Crete, Greece.
| | - Kiriakos Kotzabasis
- Department of Biology, University of Crete, Voutes University Campus, GR-70013 Heraklion, Crete, Greece
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The Extended Light-Harvesting Complex (LHC) Protein Superfamily: Classification and Evolutionary Dynamics. FUNCTIONAL GENOMICS AND EVOLUTION OF PHOTOSYNTHETIC SYSTEMS 2012. [DOI: 10.1007/978-94-007-1533-2_11] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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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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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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Jermiin LS, Ho JWK, Lau KW, Jayaswal V. SeqVis: a tool for detecting compositional heterogeneity among aligned nucleotide sequences. Methods Mol Biol 2009; 537:65-91. [PMID: 19378140 DOI: 10.1007/978-1-59745-251-9_4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
Compositional heterogeneity is a poorly appreciated attribute of aligned nucleotide and amino acid sequences. It is a common property of molecular phylogenetic data, and it has been found to occur across sequences and/or across sites. Most molecular phylogenetic methods assume that the sequences have evolved under globally stationary, reversible, and homogeneous conditions, implying that the sequences should be compositionally homogeneous. The presence of the above-mentioned compositional heterogeneity implies that the sequences must have evolved under more general conditions than is commonly assumed. Consequently, there is a need for reliable methods to detect under what conditions alignments of nucleotides or amino acids may have evolved. In this chapter, we describe one such program. SeqVis is designed to survey aligned nucleotide sequences. We discuss pros-et-cons of this program in the context of other methods to detect compositional heterogeneity and violated phylogenetic assumptions. The benefits provided by SeqVis are demonstrated in two studies of alignments of nucleotides, one of which contained 7542 nucleotides from 53 species.
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Affiliation(s)
- Lars Sommer Jermiin
- School of Biological Sciences, Centre for Mathematical Biology and Sydney Bioinformatics, University of Sydney, Sydney, Australia
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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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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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