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Phycobilisomes and Phycobiliproteins in the Pigment Apparatus of Oxygenic Photosynthetics: From Cyanobacteria to Tertiary Endosymbiosis. Int J Mol Sci 2023; 24:ijms24032290. [PMID: 36768613 PMCID: PMC9916406 DOI: 10.3390/ijms24032290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/15/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023] Open
Abstract
Eukaryotic photosynthesis originated in the course of evolution as a result of the uptake of some unstored cyanobacterium and its transformation to chloroplasts by an ancestral heterotrophic eukaryotic cell. The pigment apparatus of Archaeplastida and other algal phyla that emerged later turned out to be arranged in the same way. Pigment-protein complexes of photosystem I (PS I) and photosystem II (PS II) are characterized by uniform structures, while the light-harvesting antennae have undergone a series of changes. The phycobilisome (PBS) antenna present in cyanobacteria was replaced by Chl a/b- or Chl a/c-containing pigment-protein complexes in most groups of photosynthetics. In the form of PBS or phycobiliprotein aggregates, it was inherited by members of Cyanophyta, Cryptophyta, red algae, and photosynthetic amoebae. Supramolecular organization and architectural modifications of phycobiliprotein antennae in various algal phyla in line with the endosymbiotic theory of chloroplast origin are the subject of this review.
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Jacobson TB, Callaghan MM, Amador-Noguez D. Hostile Takeover: How Viruses Reprogram Prokaryotic Metabolism. Annu Rev Microbiol 2021; 75:515-539. [PMID: 34348026 DOI: 10.1146/annurev-micro-060621-043448] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
To reproduce, prokaryotic viruses must hijack the cellular machinery of their hosts and redirect it toward the production of viral particles. While takeover of the host replication and protein synthesis apparatus has long been considered an essential feature of infection, recent studies indicate that extensive reprogramming of host primary metabolism is a widespread phenomenon among prokaryotic viruses that is required to fulfill the biosynthetic needs of virion production. In this review we provide an overview of the most significant recent findings regarding virus-induced reprogramming of prokaryotic metabolism and suggest how quantitative systems biology approaches may be used to provide a holistic understanding of metabolic remodeling during lytic viral infection. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Tyler B Jacobson
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; , , .,Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53726, USA.,Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Melanie M Callaghan
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; , , .,Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Daniel Amador-Noguez
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; , , .,Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53726, USA.,Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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Adir N, Bar-Zvi S, Harris D. The amazing phycobilisome. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1861:148047. [PMID: 31306623 DOI: 10.1016/j.bbabio.2019.07.002] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Revised: 06/19/2019] [Accepted: 07/09/2019] [Indexed: 10/26/2022]
Abstract
Cyanobacteria and red-algae share a common light-harvesting complex which is different than all other complexes that serve as photosynthetic antennas - the Phycobilisome (PBS). The PBS is found attached to the stromal side of thylakoid membranes, filling up most of the gap between individual thylakoids. The PBS self assembles from similar homologous protein units that are soluble and contain conserved cysteine residues that covalently bind the light absorbing chromophores, linear tetra-pyrroles. Using similar construction principles, the PBS can be as large as 16.8 MDa (68×45×39nm), as small as 1.2 MDa (24 × 11.5 × 11.5 nm), and in some unique cases smaller still. The PBS can absorb light between 450 nm to 650 nm and in some cases beyond 700 nm, depending on the species, its composition and assembly. In this review, we will present new observations and structures that expand our understanding of the distinctive properties that make the PBS an amazing light harvesting system. At the end we will suggest why the PBS, for all of its excellent properties, was discarded by photosynthetic organisms that arose later in evolution such as green algae and higher plants.
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Affiliation(s)
- Noam Adir
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 32000, Israel.
| | - Shira Bar-Zvi
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Dvir Harris
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 32000, Israel
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4
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Parallel phylogeography of Prochlorococcus and Synechococcus. ISME JOURNAL 2018; 13:430-441. [PMID: 30283146 DOI: 10.1038/s41396-018-0287-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 09/11/2018] [Accepted: 09/14/2018] [Indexed: 11/08/2022]
Abstract
The globally abundant marine Cyanobacteria Prochlorococcus and Synechococcus share many physiological traits but presumably have different evolutionary histories and associated phylogeography. In Prochlorococcus, there is a clear phylogenetic hierarchy of ecotypes, whereas multiple Synechococcus clades have overlapping physiologies and environmental distributions. However, microbial traits are associated with different phylogenetic depths. Using this principle, we reclassified diversity at different phylogenetic levels and compared the phylogeography. We sequenced the genetic diversity of Prochlorococcus and Synechococcus from 339 samples across the tropical Pacific Ocean and North Atlantic Ocean using a highly variable phylogenetic marker gene (rpoC1). We observed clear parallel niche distributions of ecotypes leading to high Pianka's Index values driven by distinct shifts at two transition points. The first transition point at 6°N distinguished ecotypes adapted to warm waters but separated by macronutrient content. At 39°N, ecotypes adapted to warm, low macronutrient vs. colder, high macronutrient waters shifted. Finally, we detected parallel vertical and regional single-nucleotide polymorphism microdiversity within clades from both Prochlorococcus and Synechococcus, suggesting uniquely adapted populations at very specific depths, as well as between the Atlantic and Pacific Oceans. Overall, this study demonstrates that Prochlorococcus and Synechococcus have shared phylogenetic organization of traits and associated phylogeography.
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Agostoni M, Lucker BF, Smith MA, Kanazawa A, Blanchard GJ, Kramer DM, Montgomery BL. Competition-based phenotyping reveals a fitness cost for maintaining phycobilisomes under fluctuating light in the cyanobacterium Fremyella diplosiphon. ALGAL RES 2016. [DOI: 10.1016/j.algal.2016.02.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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6
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Lea-Smith DJ, Bombelli P, Dennis JS, Scott SA, Smith AG, Howe CJ. Phycobilisome-Deficient Strains of Synechocystis sp. PCC 6803 Have Reduced Size and Require Carbon-Limiting Conditions to Exhibit Enhanced Productivity. PLANT PHYSIOLOGY 2014; 165:705-714. [PMID: 24760817 PMCID: PMC4044857 DOI: 10.1104/pp.114.237206] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 04/17/2014] [Indexed: 05/21/2023]
Abstract
Reducing excessive light harvesting in photosynthetic organisms may increase biomass yields by limiting photoinhibition and increasing light penetration in dense cultures. The cyanobacterium Synechocystis sp. PCC 6803 harvests light via the phycobilisome, which consists of an allophycocyanin core and six radiating rods, each with three phycocyanin (PC) discs. Via targeted gene disruption and alterations to the promoter region, three mutants with two (pcpcT→C) and one (ΔCpcC1C2:pcpcT→C) PC discs per rod or lacking PC (olive) were generated. Photoinhibition and chlorophyll levels decreased upon phycobilisome reduction, although greater penetration of white light was observed only in the PC-deficient mutant. In all strains cultured at high cell densities, most light was absorbed by the first 2 cm of the culture. Photosynthesis and respiration rates were also reduced in the ΔCpcC1C2:pcpcT→C and olive mutants. Cell size was smaller in the pcpcT→C and olive strains. Growth and biomass accumulation were similar between the wild-type and pcpcT→C under a variety of conditions. Growth and biomass accumulation of the olive mutant were poorer in carbon-saturated cultures but improved in carbon-limited cultures at higher light intensities, as they did in the ΔCpcC1C2:pcpcT→C mutant. This study shows that one PC disc per rod is sufficient for maximal light harvesting and biomass accumulation, except under conditions of high light and carbon limitation, and two or more are sufficient for maximal oxygen evolution. To our knowledge, this study is the first to measure light penetration in bulk cultures of cyanobacteria and offers important insights into photobioreactor design.
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Affiliation(s)
- David J Lea-Smith
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (D.J.L.-S., P.B., C.J.H.);Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB2 3RA, United Kingdom (J.S.D.);Department of Engineering, University of Cambridge, Cambridge CB2 1PZ, United Kingdom (S.A.S.); andDepartment of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (A.G.S.)
| | - Paolo Bombelli
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (D.J.L.-S., P.B., C.J.H.);Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB2 3RA, United Kingdom (J.S.D.);Department of Engineering, University of Cambridge, Cambridge CB2 1PZ, United Kingdom (S.A.S.); andDepartment of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (A.G.S.)
| | - John S Dennis
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (D.J.L.-S., P.B., C.J.H.);Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB2 3RA, United Kingdom (J.S.D.);Department of Engineering, University of Cambridge, Cambridge CB2 1PZ, United Kingdom (S.A.S.); andDepartment of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (A.G.S.)
| | - Stuart A Scott
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (D.J.L.-S., P.B., C.J.H.);Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB2 3RA, United Kingdom (J.S.D.);Department of Engineering, University of Cambridge, Cambridge CB2 1PZ, United Kingdom (S.A.S.); andDepartment of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (A.G.S.)
| | - Alison G Smith
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (D.J.L.-S., P.B., C.J.H.);Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB2 3RA, United Kingdom (J.S.D.);Department of Engineering, University of Cambridge, Cambridge CB2 1PZ, United Kingdom (S.A.S.); andDepartment of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (A.G.S.)
| | - Christopher J Howe
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (D.J.L.-S., P.B., C.J.H.);Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB2 3RA, United Kingdom (J.S.D.);Department of Engineering, University of Cambridge, Cambridge CB2 1PZ, United Kingdom (S.A.S.); andDepartment of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (A.G.S.)
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Qin S, Lin H, Jiang P. Advances in genetic engineering of marine algae. Biotechnol Adv 2012; 30:1602-13. [PMID: 22634258 DOI: 10.1016/j.biotechadv.2012.05.004] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Revised: 05/12/2012] [Accepted: 05/18/2012] [Indexed: 12/28/2022]
Abstract
Algae are a component of bait sources for animal aquaculture, and they produce abundant valuable compounds for the chemical industry and human health. With today's fast growing demand for algae biofuels and the profitable market for cosmetics and pharmaceuticals made from algal natural products, the genetic engineering of marine algae has been attracting increasing attention as a crucial systemic technology to address the challenge of the biomass feedstock supply for sustainable industrial applications and to modify the metabolic pathway for the more efficient production of high-value products. Nevertheless, to date, only a few marine algae species can be genetically manipulated. In this article, an updated account of the research progress in marine algal genomics is presented along with methods for transformation. In addition, vector construction and gene selection strategies are reviewed. Meanwhile, a review on the progress of bioreactor technologies for marine algae culture is also revisited.
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Affiliation(s)
- Song Qin
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, Shandong, China.
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8
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Everroad RC, Wood AM. Phycoerythrin evolution and diversification of spectral phenotype in marine Synechococcus and related picocyanobacteria. Mol Phylogenet Evol 2012; 64:381-92. [PMID: 22588203 DOI: 10.1016/j.ympev.2012.04.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Revised: 04/12/2012] [Accepted: 04/20/2012] [Indexed: 10/28/2022]
Abstract
In marine Synechococcus there is evidence for the adaptive evolution of spectrally distinct forms of the major light harvesting pigment phycoerythrin (PE). Recent research has suggested that these spectral forms of PE have a different evolutionary history than the core genome. However, a lack of explicit statistical testing of alternative hypotheses or for selection on these genes has made it difficult to evaluate the evolutionary relationships between spectral forms of PE or the role horizontal gene transfer (HGT) may have had in the adaptive phenotypic evolution of the pigment system in marine Synechococcus. In this work, PE phylogenies of picocyanobacteria with known spectral phenotypes, including newly co-isolated strains of marine Synechococcus from the Gulf of Mexico, were constructed to explore the diversification of spectral phenotype and PE evolution in this group more completely. For the first time, statistical evaluation of competing evolutionary hypotheses and tests for positive selection on the PE locus in picocyanobacteria were performed. Genes for PEs associated with specific PE spectral phenotypes formed strongly supported monophyletic clades within the PE tree with positive directional selection driving evolution towards higher phycourobilin (PUB) content. The presence of the PUB-lacking phenotype in PE-containing marine picocyanobacteria from cyanobacterial lineages identified as Cyanobium is best explained by HGT into this group from marine Synechococcus. Taken together, these data provide strong examples of adaptive evolution of a single phenotypic trait in bacteria via mutation, positive directional selection and horizontal gene transfer.
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Affiliation(s)
- R Craig Everroad
- Institute for Ecology and Evolutionary Biology, formerly Center for Ecology and Evolutionary Biology, 5289 University of Oregon, Eugene, OR 97403, USA.
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9
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Bay RA, Bielawski JP. Recombination Detection Under Evolutionary Scenarios Relevant to Functional Divergence. J Mol Evol 2012; 73:273-86. [DOI: 10.1007/s00239-011-9473-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Accepted: 11/07/2011] [Indexed: 12/01/2022]
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10
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Wiethaus J, Busch AWU, Kock K, Leichert LI, Herrmann C, Frankenberg-Dinkel N. CpeS is a lyase specific for attachment of 3Z-PEB to Cys82 of {beta}-phycoerythrin from Prochlorococcus marinus MED4. J Biol Chem 2010; 285:37561-9. [PMID: 20876568 DOI: 10.1074/jbc.m110.172619] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In contrast to the majority of cyanobacteria, the unicellular marine cyanobacterium Prochlorococcus marinus MED4 uses an intrinsic divinyl-chlorophyll-dependent light-harvesting system for photosynthesis. Despite the absence of phycobilisomes, this high-light adapted strain possesses β-phycoerythrin (CpeB), an S-type lyase (CpeS), and enzymes for the biosynthesis of phycoerythrobilin (PEB) and phycocyanobilin. Of all linear tetrapyrroles synthesized by Prochlorococcus including their 3Z- and 3E-isomers, CpeS binds both isomers of PEB and its biosynthetic precursor 15,16-dihydrobiliverdin (DHBV). However, dimerization of CpeS is independent of bilins, which are tightly bound in a complex at a ratio of 1:1. Although bilin binding by CpeS is fast, transfer to CpeB is rather slow. CpeS is able to attach 3E-PEB and 3Z-PEB to dimeric CpeB but not DHBV. CpeS transfer of 3Z-PEB exclusively yields correctly bound βCys(82)-PEB, whereas βCys(82)-DHBV is a side product of 3E-PEB transfer. Spontaneous 3E- and 3Z-PEB addition to CpeB is faulty, and products are in both cases βCys(82)-DHBV and likely a PEB bound at βCys(82) in a non-native configuration. Our data indicate that CpeS is specific for 3Z-PEB transfer to βCys(82) of phycoerythrin and essential for the correct configuration of the attachment product.
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Affiliation(s)
- Jessica Wiethaus
- Department of Physiology of Microorganisms, Faculty of Biology and Biotechnology, Ruhr-University Bochum, Universitaetsstrasse 150, 44780 Bochum, Germany
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11
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Structure of the novel 14kDa fragment of α-subunit of phycoerythrin from the starving cyanobacterium Phormidium tenue. J Struct Biol 2010; 171:247-55. [DOI: 10.1016/j.jsb.2010.05.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2008] [Revised: 05/07/2010] [Accepted: 05/18/2010] [Indexed: 11/20/2022]
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12
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Partensky F, Garczarek L. Prochlorococcus: advantages and limits of minimalism. ANNUAL REVIEW OF MARINE SCIENCE 2010; 2:305-331. [PMID: 21141667 DOI: 10.1146/annurev-marine-120308-081034] [Citation(s) in RCA: 167] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Prochlorococcus is the key phytoplanktonic organism of tropical gyres, large ocean regions that are depleted of the essential macronutrients needed for photosynthesis and cell growth. This cyanobacterium has adapted itself to oligotrophy by minimizing the resources necessary for life through a drastic reduction of cell and genome sizes. This rarely observed strategy in free-living organisms has conferred on Prochlorococcus a considerable advantage over other phototrophs, including its closest relative Synechococcus, for life in this vast yet little variable ecosystem. However, this strategy seems to reach its limits in the upper layer of the S Pacific gyre, the most oligotrophic region of the world ocean. By losing some important genes and/or functions during evolution, Prochlorococcus has seemingly become dependent on co-occurring microorganisms. In this review, we present some of the recent advances in the ecology, biology, and evolution of Prochlorococcus, which because of its ecological importance and tiny genome is rapidly imposing itself as a model organism in environmental microbiology.
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Affiliation(s)
- Frédéric Partensky
- UPMC-Université Paris 06, Station Biologique, 29682 Roscoff cedex, France.
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Scanlan DJ, Ostrowski M, Mazard S, Dufresne A, Garczarek L, Hess WR, Post AF, Hagemann M, Paulsen I, Partensky F. Ecological genomics of marine picocyanobacteria. Microbiol Mol Biol Rev 2009; 73:249-99. [PMID: 19487728 PMCID: PMC2698417 DOI: 10.1128/mmbr.00035-08] [Citation(s) in RCA: 446] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Marine picocyanobacteria of the genera Prochlorococcus and Synechococcus numerically dominate the picophytoplankton of the world ocean, making a key contribution to global primary production. Prochlorococcus was isolated around 20 years ago and is probably the most abundant photosynthetic organism on Earth. The genus comprises specific ecotypes which are phylogenetically distinct and differ markedly in their photophysiology, allowing growth over a broad range of light and nutrient conditions within the 45 degrees N to 40 degrees S latitudinal belt that they occupy. Synechococcus and Prochlorococcus are closely related, together forming a discrete picophytoplankton clade, but are distinguishable by their possession of dissimilar light-harvesting apparatuses and differences in cell size and elemental composition. Synechococcus strains have a ubiquitous oceanic distribution compared to that of Prochlorococcus strains and are characterized by phylogenetically discrete lineages with a wide range of pigmentation. In this review, we put our current knowledge of marine picocyanobacterial genomics into an environmental context and present previously unpublished genomic information arising from extensive genomic comparisons in order to provide insights into the adaptations of these marine microbes to their environment and how they are reflected at the genomic level.
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Affiliation(s)
- D J Scanlan
- Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom.
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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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15
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Beale SI. Photosynthetic Pigments: Perplexing Persistent Prevalence of ‘Superfluous’ Pigment Production. Curr Biol 2008; 18:R342-3. [DOI: 10.1016/j.cub.2008.02.064] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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16
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Zhao F, Qin S. Comparative molecular population genetics of phycoerythrin locus in Prochlorococcus. Genetica 2006; 129:291-9. [PMID: 16897463 DOI: 10.1007/s10709-006-0010-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2005] [Accepted: 04/19/2006] [Indexed: 11/29/2022]
Abstract
As the only remainder type of phycobiliproteins in Prochlorococcus, the actual role of phycoerythrin still remains unknown. Previous studies revealed that two different forms of phycoerythrin gene were found in two ecotypes of Prochlorococcus that are specifically adapted to either high light (HL) or low light (LL) conditions. Here we analyze patterns of phycoerythrin nucleotide variation in the HL- and LL-Prochlorococcus populations. Our analyses reveal a significantly greater number of non-synonymous fixed substitutions in peB and peA than expected based on interspecific comparisons. This pattern of excess non-synonymous fixed substitutions is not seen in other five phycoerythrin-related genes (peZ/V/Y/T/S). Several neutrality statistical tests indicate an excess of rare frequency polymorphisms in the LL-Prochlorococcus data, but an excess of intermediate frequency polymorphisms in the HL-Prochlorococcus data. Distributions of the positively selected sites identified using the likelihood ratio test, when mapped onto the phycoerythrin tertiary structure, reveal that HL- and LL-phycoerythrin should be under different selective patterns. These findings may provide insights into the likely role of selection at the phycoerythrin locus and motivate further research to unveil the function of phycoerythrin in Prochlorococcus.
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Affiliation(s)
- Fangqing Zhao
- Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, China
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Chen M, Bibby TS, Nield J, Larkum A, Barber J. Iron deficiency induces a chlorophyll d-binding Pcb antenna system around Photosystem I in Acaryochloris marina. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2005; 1708:367-74. [PMID: 15975547 DOI: 10.1016/j.bbabio.2005.05.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2005] [Revised: 05/10/2005] [Accepted: 05/16/2005] [Indexed: 11/26/2022]
Abstract
The prochlorophyte-like cyanobacterium Acaryochloris marina contains two pcb genes, pcbA and pcbC, which encode chlorophyll (Chl) d-binding antenna proteins PcbA and PcbC, respectively. Using real-time reverse transcriptase polymerase chain reaction (RT-PCR), it is shown that when Acaryochloris cells are grown in an iron-deficient medium, the transcription of the pcbC gene is up-regulated compared to that of pcbA. Biochemical and immunological analyses indicated that under the same iron-deficient conditions, the level of Photosystem I (PSI) decreased compared with that of Photosystem II (PSII). Electron microscopy revealed that concomitant with these changes was the formation of Pcb-PSI supercomplexes which, in their largest form, were composed of 18 Pcb subunits forming a ring around the trimeric PSI reaction centre core. Mass spectrometry indicated that the PcbC protein is the main constituent of this outer PSI antenna system. It is therefore concluded that in Acaryochloris, the PcbC protein forms an antenna for PSI when iron levels become limiting and in this way compensates for the drop in the level of PSI relative to PSII which occurs under these conditions.
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Affiliation(s)
- Min Chen
- School of Biological Sciences, University of Sydney, NSW 2006, Australia
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Sullivan MB, Coleman ML, Weigele P, Rohwer F, Chisholm SW. Three Prochlorococcus cyanophage genomes: signature features and ecological interpretations. PLoS Biol 2005; 3:e144. [PMID: 15828858 PMCID: PMC1079782 DOI: 10.1371/journal.pbio.0030144] [Citation(s) in RCA: 436] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2004] [Accepted: 02/23/2005] [Indexed: 11/19/2022] Open
Abstract
The oceanic cyanobacteria Prochlorococcus are globally important, ecologically diverse primary producers. It is thought that their viruses (phages) mediate population sizes and affect the evolutionary trajectories of their hosts. Here we present an analysis of genomes from three Prochlorococcus phages: a podovirus and two myoviruses. The morphology, overall genome features, and gene content of these phages suggest that they are quite similar to T7-like (P-SSP7) and T4-like (P-SSM2 and P-SSM4) phages. Using the existing phage taxonomic framework as a guideline, we examined genome sequences to establish “core” genes for each phage group. We found the podovirus contained 15 of 26 core T7-like genes and the two myoviruses contained 43 and 42 of 75 core T4-like genes. In addition to these core genes, each genome contains a significant number of “cyanobacterial” genes, i.e., genes with significant best BLAST hits to genes found in cyanobacteria. Some of these, we speculate, represent “signature” cyanophage genes. For example, all three phage genomes contain photosynthetic genes (psbA, hliP) that are thought to help maintain host photosynthetic activity during infection, as well as an aldolase family gene (talC) that could facilitate alternative routes of carbon metabolism during infection. The podovirus genome also contains an integrase gene (int) and other features that suggest it is capable of integrating into its host. If indeed it is, this would be unprecedented among cultured T7-like phages or marine cyanophages and would have significant evolutionary and ecological implications for phage and host. Further, both myoviruses contain phosphate-inducible genes (phoH and pstS) that are likely to be important for phage and host responses to phosphate stress, a commonly limiting nutrient in marine systems. Thus, these marine cyanophages appear to be variations of two well-known phages—T7 and T4—but contain genes that, if functional, reflect adaptations for infection of photosynthetic hosts in low-nutrient oceanic environments. An analysis of the genome sequences of three phages capable of infecting marine unicellular cyanobacteria Prochlorococcus reveals they are genetically complex with intriguing adaptations related to their oceanic environment
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Affiliation(s)
- Matthew B Sullivan
- 1Joint Program in Biological Oceanography, Woods Hole Oceanographic Institution and Massachusetts Institute of TechnologyCambridge, MassachusettsUnited States of America
| | - Maureen L Coleman
- 2Department of Civil and Environmental Engineering, Massachusetts Institute of TechnologyCambridge, MassachusettsUnited States of America
| | - Peter Weigele
- 3Department of Biology, Massachusetts Institute of TechnologyCambridge, MassachusettsUnited States of America
| | - Forest Rohwer
- 4Department of Biology, San Diego State UniversitySan Diego, CaliforniaUnited States of America
| | - Sallie W Chisholm
- 2Department of Civil and Environmental Engineering, Massachusetts Institute of TechnologyCambridge, MassachusettsUnited States of America
- 3Department of Biology, Massachusetts Institute of TechnologyCambridge, MassachusettsUnited States of America
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Rocap G, Larimer FW, Lamerdin J, Malfatti S, Chain P, Ahlgren NA, Arellano A, Coleman M, Hauser L, Hess WR, Johnson ZI, Land M, Lindell D, Post AF, Regala W, Shah M, Shaw SL, Steglich C, Sullivan MB, Ting CS, Tolonen A, Webb EA, Zinser ER, Chisholm SW. Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature 2003; 424:1042-7. [PMID: 12917642 DOI: 10.1038/nature01947] [Citation(s) in RCA: 681] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2003] [Accepted: 07/25/2003] [Indexed: 11/09/2022]
Abstract
The marine unicellular cyanobacterium Prochlorococcus is the smallest-known oxygen-evolving autotroph. It numerically dominates the phytoplankton in the tropical and subtropical oceans, and is responsible for a significant fraction of global photosynthesis. Here we compare the genomes of two Prochlorococcus strains that span the largest evolutionary distance within the Prochlorococcus lineage and that have different minimum, maximum and optimal light intensities for growth. The high-light-adapted ecotype has the smallest genome (1,657,990 base pairs, 1,716 genes) of any known oxygenic phototroph, whereas the genome of its low-light-adapted counterpart is significantly larger, at 2,410,873 base pairs (2,275 genes). The comparative architectures of these two strains reveal dynamic genomes that are constantly changing in response to myriad selection pressures. Although the two strains have 1,350 genes in common, a significant number are not shared, and these have been differentially retained from the common ancestor, or acquired through duplication or lateral transfer. Some of these genes have obvious roles in determining the relative fitness of the ecotypes in response to key environmental variables, and hence in regulating their distribution and abundance in the oceans.
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Affiliation(s)
- Gabrielle Rocap
- School of Oceanography, University Of Washington, Seattle, Washington 98195, USA
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Steglich C, Post AF, Hess WR. Analysis of natural populations of Prochlorococcus spp. in the northern Red Sea using phycoerythrin gene sequences. Environ Microbiol 2003; 5:681-90. [PMID: 12871235 DOI: 10.1046/j.1462-2920.2003.00456.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Marine cyanobacteria of the genus Prochlorococcus belong to one of two ecotypes that are specifically adapted to either low light (LL) or high light (HL) conditions. Previous analyses of the differences in pigmentation and gene complement revealed that LL-adapted ecotypes carry a gene cluster to produce a functional phycoerythrin, whereas in the fully sequenced genome of the HL-adapted strain MED4, only a single and free-standing cpeB gene occurs. This gene encodes a derived form of beta-phycoerythrin, the function of which has remained enigmatic so far. Here, an analysis of HL-adapted Prochlorococcus strains from different ocean provinces revealed the presence of a cpeB gene highly similar to that of MED4. To investigate whether the presence of particular phycoerythrin genes is a common characteristic of the LL- and HL-adapted ecotypes, primer sets targeting specific motifs in LL-cpeB and HL-cpeB were designed for polymerase chain reaction (PCR) analysis of Red Sea phytoplankton. A major PCR product for Prochlorococcus HL-cpeB was obtained from samples taken at 5-70 m depth and for LL-cpeB from 70-125 m. The high sensitivity of this approach allowed the detection of HL-cpeB down to 100 m and LL-cpeB as deep as 175 m. DNA sequence and phylogenetic analysis of 70 individual clones for HL-cpeB and of 68 clones for LL-cpeB revealed a monophyletic origin for the HL and LL sequences respectively. This study shows that cpeB sequences are suitable as very sensitive molecular markers for the study of natural populations of Prochlorococcus. The low sequence divergence of HL-cpeB among Prochlorococcus strains, which have been isolated from the Mediterranean Sea, the Arabian Sea and the Southern Pacific Ocean as well as in populations from the Red Sea, suggests the HL-cpeB gene to be conserved and its product to be functional in Prochlorococcus.
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Affiliation(s)
- Claudia Steglich
- Humboldt-University, Department of Biology, Chausseestr. 117, D-10115 Berlin, Germany
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21
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Green BR. The Evolution of Light-harvesting Antennas. LIGHT-HARVESTING ANTENNAS IN PHOTOSYNTHESIS 2003. [DOI: 10.1007/978-94-017-2087-8_4] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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22
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The Photosynthetic Apparatus of Chlorophyll b- and d-Containing Oxyphotobacteria. PHOTOSYNTHESIS IN ALGAE 2003. [DOI: 10.1007/978-94-007-1038-2_3] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Gómez-García MR, Serrano A. Expression studies of two paralogous ppa genes encoding distinct Family I pyrophosphatases in marine unicellular cyanobacteria reveal inactivation of the typical cyanobacterial gene. Biochem Biophys Res Commun 2002; 295:890-7. [PMID: 12127978 DOI: 10.1016/s0006-291x(02)00776-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Genome sequence analyses revealed the occurrence of two paralogous ppa genes potentially encoding distinct Family I inorganic pyrophosphatases (sPPases, EC3.6.1.1) in the marine unicellular cyanobacteria Prochlorococcus marinus strains MED4 and MIT9313 and Synechococcus sp. WH8102. Protein sequence alignment and phylogenetic analysis indicated that the ppa gene proper of cyanobacteria (ppa1) encodes a presumably inactive mutant enzyme whereas the second gene (ppa2) might encode an active sPPase closely related to those of some proteobacteria. Heterologous expression of the two cloned P. marinus MED4 ppa genes in Escherichia coli confirmed this proposal, only the inactive ppa1 product being immunodetected by anti-cyanobacterial sPPase antibodies. A possible scenario of ppa gene inactivation and replacement in the context of the postulated rapid diversification of marine unicellular cyanobacteria, the most abundant photosynthetic prokaryotes in the oceans, is discussed.
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Affiliation(s)
- María R Gómez-García
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, Avda. Américo Vespucio s/n, Seville, Spain
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Ting CS, Rocap G, King J, Chisholm SW. Cyanobacterial photosynthesis in the oceans: the origins and significance of divergent light-harvesting strategies. Trends Microbiol 2002; 10:134-42. [PMID: 11864823 DOI: 10.1016/s0966-842x(02)02319-3] [Citation(s) in RCA: 264] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Prochlorococcus and Synechococcus are abundant unicellular cyanobacteria and major participants in global carbon cycles. Although they are closely related and often coexist in the same ocean habitat, they possess very different photosynthetic light-harvesting antennas. Whereas Synechococcus and the majority of cyanobacteria use phycobilisomes, Prochlorococcus has evolved to use a chlorophyll a(2)/b(2) light-harvesting complex. Here, we present a scenario to explain how the Prochlorococcus antenna might have evolved in an ancestral cyanobacterium in iron-limited oceans, resulting in the diversification of the Prochlorococcus and marine Synechococcus lineages from a common phycobilisome-containing ancestor. Differences in the absorption properties and cellular costs between chlorophyll a(2)/b(2) and phycobilisome antennas in extant Prochlorococcus and Synechococcus appear to play a role in differentiating their ecological niches in the ocean environment.
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Affiliation(s)
- Claire S Ting
- Dept of Biology, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA 02139, USA
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