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Bryant DA, Gisriel CJ. The structural basis for light harvesting in organisms producing phycobiliproteins. THE PLANT CELL 2024; 36:4036-4064. [PMID: 38652697 PMCID: PMC11449063 DOI: 10.1093/plcell/koae126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/13/2024] [Accepted: 03/20/2024] [Indexed: 04/25/2024]
Abstract
Cyanobacteria, red algae, and cryptophytes produce 2 classes of proteins for light harvesting: water-soluble phycobiliproteins (PBP) and membrane-intrinsic proteins that bind chlorophylls (Chls) and carotenoids. In cyanobacteria, red algae, and glaucophytes, phycobilisomes (PBS) are complexes of brightly colored PBP and linker (assembly) proteins. To date, 6 structural classes of PBS have been described: hemiellipsoidal, block-shaped, hemidiscoidal, bundle-shaped, paddle-shaped, and far-red-light bicylindrical. Two additional antenna complexes containing single types of PBP have also been described. Since 2017, structures have been reported for examples of all of these complexes except bundle-shaped PBS by cryogenic electron microscopy. PBS range in size from about 4.6 to 18 mDa and can include ∼900 polypeptides and bind >2000 chromophores. Cyanobacteria additionally produce membrane-associated proteins of the PsbC/CP43 superfamily of Chl a/b/d-binding proteins, including the iron-stress protein IsiA and other paralogous Chl-binding proteins (CBP) that can form antenna complexes with Photosystem I (PSI) and/or Photosystem II (PSII). Red and cryptophyte algae also produce CBP associated with PSI but which belong to the Chl a/b-binding protein superfamily and which are unrelated to the CBP of cyanobacteria. This review describes recent progress in structure determination for PBS and the Chl proteins of cyanobacteria, red algae, and cryptophytan algae.
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Affiliation(s)
- Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
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2
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Ślesak I, Ślesak H. From cyanobacteria and cyanophages to chloroplasts: the fate of the genomes of oxyphototrophs and the genes encoding photosystem II proteins. THE NEW PHYTOLOGIST 2024; 242:1055-1067. [PMID: 38439684 DOI: 10.1111/nph.19633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 02/02/2024] [Indexed: 03/06/2024]
Abstract
Chloroplasts are the result of endosymbiosis of cyanobacterial organisms with proto-eukaryotes. The psbA, psbD and psbO genes are present in all oxyphototrophs and encode the D1/D2 proteins of photosystem II (PSII) and PsbO, respectively. PsbO is a peripheral protein that stabilizes the O2-evolving complex in PSII. Of these genes, psbA and psbD remained in the chloroplastic genome, while psbO was transferred to the nucleus. The genomes of selected cyanobacteria, chloroplasts and cyanophages carrying psbA and psbD, respectively, were analysed. The highest density of genes and coding sequences (CDSs) was estimated for the genomes of cyanophages, cyanobacteria and chloroplasts. The synonymous mutation rate (rS) of psbA and psbD in chloroplasts remained almost unchanged and is lower than that of psbO. The results indicate that the decreasing genome size in chloroplasts is more similar to the genome reduction observed in contemporary endosymbiotic organisms than in streamlined genomes of free-living cyanobacteria. The rS of atpA, which encodes the α-subunit of ATP synthase in chloroplasts, suggests that psbA and psbD, and to a lesser extent psbO, are ancient and conservative and arose early in the evolution of oxygenic photosynthesis. The role of cyanophages in the evolution of oxyphototrophs and chloroplastic genomes is discussed.
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Affiliation(s)
- Ireneusz Ślesak
- The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek 21, 30-239, Kraków, Poland
| | - Halina Ślesak
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387, Kraków, Poland
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Jung P, Briegel-Williams L, Werner L, Jost E, Schultz M, Nürnberg DJ, Grube M, Lakatos M. A direct PCR approach with low-biomass insert opens new horizons for molecular sciences on cryptogam communities. Appl Environ Microbiol 2024; 90:e0002424. [PMID: 38349146 PMCID: PMC10952543 DOI: 10.1128/aem.00024-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 01/19/2024] [Indexed: 03/21/2024] Open
Abstract
Molecular sequence data have transformed research on cryptogams (e.g., lichens, microalgae, fungi, and symbionts thereof) but methods are still strongly hampered by the small size and intermingled growth of the target organisms, poor cultivability and detrimental effects of their secondary metabolites. Here, we aim to showcase examples on which a modified direct PCR approach for diverse aspects of molecular work on environmental samples concerning biocrusts, biofilms, and cryptogams gives new options for the research community. Unlike traditional approaches, this methodology only requires biomass equivalent to colonies and fragments of 0.2 mm in diameter, which can be picked directly from the environmental sample, and includes a quick DNA lysis followed by a standardized PCR cycle that allows co-cycling of various organisms/target regions in the same run. We demonstrate that this modified method can (i) amplify the most widely used taxonomic gene regions and those used for applied and environmental sciences from single colonies and filaments of free-living cyanobacteria, bryophytes, fungi, and lichens, including their mycobionts, chlorobionts, and cyanobionts from both isolates and in situ material during co-cycling; (ii) act as a tool to confirm that the dominant lichen photobiont was isolated from the original sample; and (iii) optionally remove inhibitory secondary lichen substances. Our results represent examples which highlight the method's potential for future applications covering mycology, phycology, biocrusts, and lichenology, in particular.IMPORTANCECyanobacteria, green algae, lichens, and other cryptogams play crucial roles in complex microbial systems such as biological soil crusts of arid biomes or biofilms in caves. Molecular investigations on environmental samples or isolates of these microorganisms are often hampered by their dense aggregation, small size, or metabolism products which complicate DNA extraction and subsequent PCRs. Our work presents various examples of how a direct DNA extraction and PCR method relying on low biomass inserts can overcome these common problems and discusses additional applications of the workflow including adaptations.
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Affiliation(s)
- Patrick Jung
- Department of Integrative Biotechnology, University of Applied Sciences Kaiserslautern, Pirmasens, Germany
| | - Laura Briegel-Williams
- Department of Integrative Biotechnology, University of Applied Sciences Kaiserslautern, Pirmasens, Germany
| | - Lina Werner
- Department of Integrative Biotechnology, University of Applied Sciences Kaiserslautern, Pirmasens, Germany
| | - Emily Jost
- Department of Integrative Biotechnology, University of Applied Sciences Kaiserslautern, Pirmasens, Germany
| | - Matthias Schultz
- Institute for Plant Science and Microbiology, Herbarium Hamburgense, University of Hamburg, Hamburg, Germany
| | - Dennis J. Nürnberg
- Institute of Experimental Physics, Freie Universität Berlin, Berlin, Germany
- Dahlem Centre for Plant Sciences, Freie Universität Berlin, Berlin, Germany
| | - Martin Grube
- Institute of Biology, University of Graz, Graz, Austria
| | - Michael Lakatos
- Department of Integrative Biotechnology, University of Applied Sciences Kaiserslautern, Pirmasens, Germany
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4
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Rockwell NC, Lagarias JC. Cyanobacteriochromes from Gloeobacterales Provide New Insight into the Diversification of Cyanobacterial Photoreceptors. J Mol Biol 2024; 436:168313. [PMID: 37839679 PMCID: PMC11218821 DOI: 10.1016/j.jmb.2023.168313] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/15/2023] [Accepted: 10/10/2023] [Indexed: 10/17/2023]
Abstract
The phytochrome superfamily comprises three groups of photoreceptors sharing a conserved GAF (cGMP-specific phosphodiesterases, cyanobacterial adenylate cyclases, and formate hydrogen lyase transcription activator FhlA) domain that uses a covalently attached linear tetrapyrrole (bilin) chromophore to sense light. Knotted red/far-red phytochromes are widespread in both bacteria and eukaryotes, but cyanobacteria also contain knotless red/far-red phytochromes and cyanobacteriochromes (CBCRs). Unlike typical phytochromes, CBCRs require only the GAF domain for bilin binding, chromophore ligation, and full, reversible photoconversion. CBCRs can sense a wide range of wavelengths (ca. 330-750 nm) and can regulate phototaxis, second messenger metabolism, and optimization of the cyanobacterial light-harvesting apparatus. However, the origins of CBCRs are not well understood: we do not know when or why CBCRs evolved, or what selective advantages led to retention of early CBCRs in cyanobacterial genomes. In the current work, we use the increasing availability of genomes and metagenome-assembled-genomes from early-branching cyanobacteria to explore the origins of CBCRs. We reaffirm the earliest branches in CBCR evolution. We also show that early-branching cyanobacteria contain late-branching CBCRs, implicating early appearance of CBCRs during cyanobacterial evolution. Moreover, we show that early-branching CBCRs behave as integrators of light and pH, providing a potential unique function for early CBCRs that led to their retention and subsequent diversification. Our results thus provide new insight into the origins of these diverse cyanobacterial photoreceptors.
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Affiliation(s)
- Nathan C Rockwell
- 31 Briggs Hall, Department of Molecular and Cell Biology, One Shields Avenue, University of California at Davis, Davis, CA 95616, USA.
| | - J Clark Lagarias
- 31 Briggs Hall, Department of Molecular and Cell Biology, One Shields Avenue, University of California at Davis, Davis, CA 95616, USA.
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5
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Demoulin CF, Lara YJ, Lambion A, Javaux EJ. Oldest thylakoids in fossil cells directly evidence oxygenic photosynthesis. Nature 2024; 625:529-534. [PMID: 38172638 DOI: 10.1038/s41586-023-06896-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 11/23/2023] [Indexed: 01/05/2024]
Abstract
Today oxygenic photosynthesis is unique to cyanobacteria and their plastid relatives within eukaryotes. Although its origin before the Great Oxidation Event is still debated1-4, the accumulation of O2 profoundly modified the redox chemistry of the Earth and the evolution of the biosphere, including complex life. Understanding the diversification of cyanobacteria is thus crucial to grasping the coevolution of our planet and life, but their early fossil record remains ambiguous5. Extant cyanobacteria include the thylakoid-less Gloeobacter-like group and the remainder of cyanobacteria that acquired thylakoid membranes6,7. The timing of this divergence is indirectly estimated at between 2.7 and 2.0 billion years ago (Ga) based on molecular clocks and phylogenies8-11 and inferred from the earliest undisputed fossil record of Eoentophysalis belcherensis, a 2.018-1.854 Ga pleurocapsalean cyanobacterium preserved in silicified stromatolites12,13. Here we report the oldest direct evidence of thylakoid membranes in a parallel-to-contorted arrangement within the enigmatic cylindrical microfossils Navifusa majensis from the McDermott Formation, Tawallah Group, Australia (1.78-1.73 Ga), and in a parietal arrangement in specimens from the Grassy Bay Formation, Shaler Supergroup, Canada (1.01-0.9 Ga). This discovery extends their fossil record by at least 1.2 Ga and provides a minimum age for the divergence of thylakoid-bearing cyanobacteria at roughly 1.75 Ga. It allows the unambiguous identification of early oxygenic photosynthesizers and a new redox proxy for probing early Earth ecosystems, highlighting the importance of examining the ultrastructure of fossil cells to decipher their palaeobiology and early evolution.
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Affiliation(s)
- Catherine F Demoulin
- Early Life Traces & Evolution-Astrobiology, UR Astrobiology, University of Liège, Liège, Belgium.
| | - Yannick J Lara
- Early Life Traces & Evolution-Astrobiology, UR Astrobiology, University of Liège, Liège, Belgium
| | - Alexandre Lambion
- Early Life Traces & Evolution-Astrobiology, UR Astrobiology, University of Liège, Liège, Belgium
| | - Emmanuelle J Javaux
- Early Life Traces & Evolution-Astrobiology, UR Astrobiology, University of Liège, Liège, Belgium.
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Strullu-Derrien C, Fercoq F, Gèze M, Kenrick P, Martos F, Selosse MA, Benzerara K, Knoll AH. Hapalosiphonacean cyanobacteria (Nostocales) thrived amid emerging embryophytes in an early Devonian (407-million-year-old) landscape. iScience 2023; 26:107338. [PMID: 37520734 PMCID: PMC10382934 DOI: 10.1016/j.isci.2023.107338] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 06/11/2023] [Accepted: 07/06/2023] [Indexed: 08/01/2023] Open
Abstract
Cyanobacteria have a long evolutionary history, well documented in marine rocks. They are also abundant and diverse in terrestrial environments; however, although phylogenies suggest that the group colonized land early in its history, paleontological documentation of this remains limited. The Rhynie chert (407 Ma), our best preserved record of early terrestrial ecosystems, provides an opportunity to illuminate aspects of cyanobacterial diversity and ecology as plants began to radiate across the land surface. We used light microscopy and super-resolution confocal laser scanning microscopy to study a new population of Rhynie cyanobacteria; we also reinvestigated previously described specimens that resemble the new fossils. Our study demonstrates that all are part of a single fossil species belonging to the Hapalosiphonaceae (Nostocales). Along with other Rhynie microfossils, these remains show that the accommodation of morphologically complex cyanobacteria to terrestrial ecosystems transformed by embryophytes was well underway more than 400 million years ago.
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Affiliation(s)
- Christine Strullu-Derrien
- Institut Systématique Évolution Biodiversité (UMR 7205), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, UA, 75005 Paris, France
- Science Group, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Frédéric Fercoq
- Unité Molécules de Communication et Adaptation des Micro-organismes (MCAM, UMR7245), Muséum national d’Histoire naturelle, CNRS, 75005 Paris, France
| | - Marc Gèze
- Unité Molécules de Communication et Adaptation des Micro-organismes (MCAM, UMR7245), Muséum national d’Histoire naturelle, CNRS, 75005 Paris, France
| | - Paul Kenrick
- Science Group, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Florent Martos
- Institut Systématique Évolution Biodiversité (UMR 7205), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, UA, 75005 Paris, France
| | - Marc-André Selosse
- Institut Systématique Évolution Biodiversité (UMR 7205), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, UA, 75005 Paris, France
- Institut Universitaire de France, 75005 Paris, France
- Department of Plant Taxonomy and Nature Conservation, University of Gdańsk, 80-308 Gdańsk, Poland
| | - Karim Benzerara
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (UMR 7590), CNRS, Muséum national d'Histoire naturelle, Sorbonne Université, 75005 Paris, France
| | - Andrew H. Knoll
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
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Němečková K, Mareš J, Procházková L, Culka A, Košek F, Wierzchos J, Nedbalová L, Dudák J, Tymlová V, Žemlička J, Kust A, Zima J, Nováková E, Jehlička J. Gypsum endolithic phototrophs under moderate climate (Southern Sicily): their diversity and pigment composition. Front Microbiol 2023; 14:1175066. [PMID: 37485515 PMCID: PMC10359912 DOI: 10.3389/fmicb.2023.1175066] [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: 02/27/2023] [Accepted: 05/15/2023] [Indexed: 07/25/2023] Open
Abstract
In this study, we used microscopic, spectroscopic, and molecular analysis to characterize endolithic colonization in gypsum (selenites and white crystalline gypsum) from several sites in Sicily. Our results showed that the dominant microorganisms in these environments are cyanobacteria, including: Chroococcidiopsis sp., Gloeocapsopsis pleurocapsoides, Gloeocapsa compacta, and Nostoc sp., as well as orange pigmented green microalgae from the Stephanospherinia clade. Single cell and filament sequencing coupled with 16S rRNA amplicon metagenomic profiling provided new insights into the phylogenetic and taxonomic diversity of the endolithic cyanobacteria. These organisms form differently pigmented zones within the gypsum. Our metagenomic profiling also showed differences in the taxonomic composition of endoliths in different gypsum varieties. Raman spectroscopy revealed that carotenoids were the most common pigments present in the samples. Other pigments such as gloeocapsin and scytonemin were also detected in the near-surface areas, suggesting that they play a significant role in the biology of endoliths in this environment. These pigments can be used as biomarkers for basic taxonomic identification, especially in case of cyanobacteria. The findings of this study provide new insights into the diversity and distribution of phototrophic microorganisms and their pigments in gypsum in Southern Sicily. Furthemore, this study highlights the complex nature of endolithic ecosystems and the effects of gypsum varieties on these communities, providing additional information on the general bioreceptivity of these environments.
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Affiliation(s)
- Kateřina Němečková
- Institute of Geochemistry, Mineralogy and Mineral Resources, Faculty of Science, Charles University, Prague, Czechia
| | - Jan Mareš
- Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czechia
- Center Algatech, Institute of Microbiology, The Czech Academy of Sciences, Třeboň, Czechia
| | - Lenka Procházková
- Department of Ecology, Faculty of Science, Charles University, Prague, Czechia
| | - Adam Culka
- Institute of Geochemistry, Mineralogy and Mineral Resources, Faculty of Science, Charles University, Prague, Czechia
| | - Filip Košek
- Institute of Geochemistry, Mineralogy and Mineral Resources, Faculty of Science, Charles University, Prague, Czechia
| | - Jacek Wierzchos
- Department of Biochemistry and Microbial Ecology, Museo Nacional de Ciencias Naturales - Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Linda Nedbalová
- Department of Ecology, Faculty of Science, Charles University, Prague, Czechia
| | - Jan Dudák
- Institute of Experimental and Applied Physics, Czech Technical University in Prague, Prague, Czechia
| | - Veronika Tymlová
- Institute of Experimental and Applied Physics, Czech Technical University in Prague, Prague, Czechia
| | - Jan Žemlička
- Institute of Experimental and Applied Physics, Czech Technical University in Prague, Prague, Czechia
| | - Andreja Kust
- Department of Earth and Planetary Science, University of Berkeley, Berkeley, CA, United States
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States
| | - Jan Zima
- Department of Parasitology, Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Eva Nováková
- Department of Parasitology, Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Jan Jehlička
- Institute of Geochemistry, Mineralogy and Mineral Resources, Faculty of Science, Charles University, Prague, Czechia
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Pessi IS, Popin RV, Durieu B, Lara Y, Tytgat B, Savaglia V, Roncero-Ramos B, Hultman J, Verleyen E, Vyverman W, Wilmotte A. Novel diversity of polar Cyanobacteria revealed by genome-resolved metagenomics. Microb Genom 2023; 9:mgen001056. [PMID: 37417735 PMCID: PMC10438808 DOI: 10.1099/mgen.0.001056] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 05/30/2023] [Indexed: 07/08/2023] Open
Abstract
Benthic microbial mats dominated by Cyanobacteria are important features of polar lakes. Although culture-independent studies have provided important insights into the diversity of polar Cyanobacteria, only a handful of genomes have been sequenced to date. Here, we applied a genome-resolved metagenomics approach to data obtained from Arctic, sub-Antarctic and Antarctic microbial mats. We recovered 37 metagenome-assembled genomes (MAGs) of Cyanobacteria representing 17 distinct species, most of which are only distantly related to genomes that have been sequenced so far. These include (i) lineages that are common in polar microbial mats such as the filamentous taxa Pseudanabaena, Leptolyngbya, Microcoleus/Tychonema and Phormidium; (ii) the less common taxa Crinalium and Chamaesiphon; (iii) an enigmatic Chroococcales lineage only distantly related to Microcystis; and (iv) an early branching lineage in the order Gloeobacterales that is distributed across the cold biosphere, for which we propose the name Candidatus Sivonenia alaskensis. Our results show that genome-resolved metagenomics is a powerful tool for expanding our understanding of the diversity of Cyanobacteria, especially in understudied remote and extreme environments.
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Affiliation(s)
- Igor S. Pessi
- Department of Microbiology, University of Helsinki, Helsinki, Finland
- Helsinki Institute of Sustainability Science (HELSUS), Helsinki, Finland
| | - Rafael V. Popin
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Benoit Durieu
- InBioS – Centre for Protein Engineering, University of Liège, Liège, Belgium
| | - Yannick Lara
- Early Life Traces & Evolution-Astrobiology, UR-Astrobiology, University of Liège, Liège, Belgium
| | - Bjorn Tytgat
- Laboratory of Protistology & Aquatic Ecology, Ghent University, Ghent, Belgium
| | - Valentina Savaglia
- InBioS – Centre for Protein Engineering, University of Liège, Liège, Belgium
- Laboratory of Protistology & Aquatic Ecology, Ghent University, Ghent, Belgium
| | - Beatriz Roncero-Ramos
- InBioS – Centre for Protein Engineering, University of Liège, Liège, Belgium
- Department of Plant Biology and Ecology, University of Sevilla, Sevilla, Spain
| | - Jenni Hultman
- Department of Microbiology, University of Helsinki, Helsinki, Finland
- Helsinki Institute of Sustainability Science (HELSUS), Helsinki, Finland
- Natural Resources Institute Finland (LUKE), Helsinki, Finland
| | - Elie Verleyen
- Laboratory of Protistology & Aquatic Ecology, Ghent University, Ghent, Belgium
| | - Wim Vyverman
- Laboratory of Protistology & Aquatic Ecology, Ghent University, Ghent, Belgium
| | - Annick Wilmotte
- InBioS – Centre for Protein Engineering, University of Liège, Liège, Belgium
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Rockwell NC, Lagarias JC. GUN4 appeared early in cyanobacterial evolution. PNAS NEXUS 2023; 2:pgad131. [PMID: 37152672 PMCID: PMC10156173 DOI: 10.1093/pnasnexus/pgad131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 03/15/2023] [Accepted: 04/06/2023] [Indexed: 05/09/2023]
Abstract
Photosynthesis relies on chlorophylls, which are synthesized via a common tetrapyrrole trunk pathway also leading to heme, vitamin B12, and other pigmented cofactors. The first committed step for chlorophyll biosynthesis is insertion of magnesium into protoporphyrin IX by magnesium chelatase. Magnesium chelatase is composed of H-, I-, and D-subunits, with the tetrapyrrole substrate binding to the H-subunit. This subunit is rapidly inactivated in the presence of substrate, light, and oxygen, so oxygenic photosynthetic organisms require mechanisms to protect magnesium chelatase from similar loss of function. An additional protein, GUN4, binds to the H-subunit and to tetrapyrroles. GUN4 has been proposed to serve this protective role via its ability to bind linear tetrapyrroles (bilins). In the current work, we probe the origins of bilin binding by GUN4 via comparative phylogenetic analysis and biochemical validation of a conserved bilin-binding motif. Based on our results, we propose that bilin-binding GUN4 proteins arose early in cyanobacterial evolution and that this early acquisition represents an ancient adaptation for maintaining chlorophyll biosynthesis in the presence of light and oxygen.
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Affiliation(s)
- Nathan C Rockwell
- Department of Molecular and Cell Biology, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - J Clark Lagarias
- Department of Molecular and Cell Biology, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
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10
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Strunecký O, Ivanova AP, Mareš J. An updated classification of cyanobacterial orders and families based on phylogenomic and polyphasic analysis. JOURNAL OF PHYCOLOGY 2023; 59:12-51. [PMID: 36443823 DOI: 10.1111/jpy.13304] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 11/16/2022] [Indexed: 06/15/2023]
Abstract
Cyanobacterial taxonomy is facing a period of rapid changes thanks to the ease of 16S rRNA gene sequencing and established workflows for description of new taxa. Since the last comprehensive review of the cyanobacterial system in 2014 until 2021, at least 273 species in 140 genera were newly described. These taxa were mainly placed into previously defined orders and families although several new families were proposed. However, the classification of most taxa still relied on hierarchical relationships inherited from the classical morphological taxonomy. Similarly, the obviously polyphyletic orders such as Synechococcales and Oscillatoriales were left unchanged. In this study, the rising number of genomic sequences of cyanobacteria and well-described reference strains allowed us to reconstruct a robust phylogenomic tree for taxonomic purposes. A less robust but better sampled 16S rRNA gene phylogeny was mapped to the phylogenomic backbone. Based on both these phylogenies, a polyphasic classification throughout the whole phylum of Cyanobacteria was created, with ten new orders and fifteen new families. The proposed system of cyanobacterial orders and families relied on a phylogenomic tree but still employed phenotypic apomorphies where possible to make it useful for professionals in the field. It was, however, confirmed that morphological convergence of phylogenetically distant taxa was a frequent phenomenon in cyanobacteria. Moreover, the limited phylogenetic informativeness of the 16S rRNA gene, resulting in ambiguous phylogenies above the genus level, emphasized the integration of genomic data as a prerequisite for the conclusive taxonomic placement of a vast number of cyanobacterial genera in the future.
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Affiliation(s)
- Otakar Strunecký
- Faculty of Fisheries and Protection of Waters, CENAKVA, Institute of Aquaculture and Protection of Waters, University of South Bohemia in České Budějovice, Na Sádkách 1780, 370 05, České Budějovice, Czech Republic
| | - Anna Pavlovna Ivanova
- Faculty of Fisheries and Protection of Waters, CENAKVA, Institute of Aquaculture and Protection of Waters, University of South Bohemia in České Budějovice, Na Sádkách 1780, 370 05, České Budějovice, Czech Republic
| | - Jan Mareš
- Biology Centre of the CAS, Institute of Hydrobiology, Na Sádkách 702/7, 370 05, České Budějovice, Czech Republic
- Faculty of Science, Department of Botany, University of South Bohemia, Branišovská 1760, 370 05, České Budějovice, Czech Republic
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Kohata R, Lim H, Kanamoto Y, Murakami A, Fujita Y, Tanaka A, Swingley W, Ito H, Tanaka R. Heterologous complementation systems verify the mosaic distribution of three distinct protoporphyrinogen IX oxidase in the cyanobacterial phylum. JOURNAL OF PLANT RESEARCH 2023; 136:107-115. [PMID: 36357749 DOI: 10.1007/s10265-022-01423-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/31/2022] [Indexed: 06/16/2023]
Abstract
The pathways for synthesizing tetrapyrroles, including heme and chlorophyll, are well-conserved among organisms, despite the divergence of several enzymes in these pathways. Protoporphyrinogen IX oxidase (PPOX), which catalyzes the last common step of the heme and chlorophyll biosynthesis pathways, is encoded by three phylogenetically-unrelated genes, hemY, hemG and hemJ. All three types of homologues are present in the cyanobacterial phylum, showing a mosaic phylogenetic distribution. Moreover, a few cyanobacteria appear to contain two types of PPOX homologues. Among the three types of cyanobacterial PPOX homologues, only a hemJ homologue has been experimentally verified for its functionality. An objective of this study is to provide experimental evidence for the functionality of the cyanobacterial PPOX homologues by using two heterologous complementation systems. First, we introduced hemY and hemJ homologues from Gloeobacter violaceus PCC7421, hemY homologue from Trichodesmium erythraeum, and hemG homologue from Prochlorococcus marinus MIT9515 into a ΔhemG strain of E. coli. hemY homologues from G. violaceus and T. erythraeum, and the hemG homologue of P. marinus complimented the E. coli strain. Subsequently, we attempted to replace the endogenous hemJ gene of the cyanobacterium Synechocystis sp. PCC6803 with the four PPOX homologues mentioned above. Except for hemG from P. marinus, the other PPOX homologues substituted the function of hemJ in Synechocystis. These results show that all four homologues encode functional PPOX. The transformation of Synechocystis with G. violaceus hemY homologue rendered the cells sensitive to an inhibitor of the HemY-type PPOX, acifluorfen, indicating that the hemY homologue is sensitive to this inhibitor, while the wild-type G. violaceus was tolerant to it, most likely due to the presence of HemJ protein. These results provide an additional level of evidence that G. violaceus contains two types of functional PPOX.
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Affiliation(s)
- Ryoya Kohata
- Institute of Low Temperature Science, Hokkaido University, N19W8, Kita-Ku, Sapporo, 060-0819, Japan
| | - HyunSeok Lim
- Institute of Low Temperature Science, Hokkaido University, N19W8, Kita-Ku, Sapporo, 060-0819, Japan
| | - Yuki Kanamoto
- Research Center of Inland Seas, Kobe University, Awaji, 656-2401, Japan
| | - Akio Murakami
- Research Center of Inland Seas, Kobe University, Awaji, 656-2401, Japan
- Department of Biology, Graduate School of Science, Kobe University, Kobe, 657-8501, Japan
| | - Yuichi Fujita
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601, Japan
| | - Ayumi Tanaka
- Institute of Low Temperature Science, Hokkaido University, N19W8, Kita-Ku, Sapporo, 060-0819, Japan
| | - Wesley Swingley
- Department of Biological Sciences, Northern Illinois University, DeKalb, IL, 60115, USA
| | - Hisashi Ito
- Institute of Low Temperature Science, Hokkaido University, N19W8, Kita-Ku, Sapporo, 060-0819, Japan
| | - Ryouichi Tanaka
- Institute of Low Temperature Science, Hokkaido University, N19W8, Kita-Ku, Sapporo, 060-0819, Japan.
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12
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Davison PA, Tu W, Xu J, Della Valle S, Thompson IP, Hunter CN, Huang WE. Engineering a Rhodopsin-Based Photo-Electrosynthetic System in Bacteria for CO 2 Fixation. ACS Synth Biol 2022; 11:3805-3816. [PMID: 36264158 PMCID: PMC9680020 DOI: 10.1021/acssynbio.2c00397] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A key goal of synthetic biology is to engineer organisms that can use solar energy to convert CO2 to biomass, chemicals, and fuels. We engineered a light-dependent electron transfer chain by integrating rhodopsin and an electron donor to form a closed redox loop, which drives rhodopsin-dependent CO2 fixation. A light-driven proton pump comprising Gloeobacter rhodopsin (GR) and its cofactor retinal have been assembled in Ralstonia eutropha (Cupriavidus necator) H16. In the presence of light, this strain fixed inorganic carbon (or bicarbonate) leading to 20% growth enhancement, when formate was used as an electron donor. We found that an electrode from a solar panel can replace organic compounds to serve as the electron donor, mediated by the electron shuttle molecule riboflavin. In this new autotrophic and photo-electrosynthetic system, GR is augmented by an external photocell for reductive CO2 fixation. We demonstrated that this hybrid photo-electrosynthetic pathway can drive the engineered R. eutropha strain to grow using CO2 as the sole carbon source. In this system, a bioreactor with only two inputs, light and CO2, enables the R. eutropha strain to perform a rhodopsin-dependent autotrophic growth. Light energy alone, supplied by a solar panel, can drive the conversion of CO2 into biomass with a maximum electron transfer efficiency of 20%.
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Affiliation(s)
- Paul A. Davison
- Plants,
Photosynthesis and Soil, School of Biosciences, University of Sheffield, SheffieldS10 2TN, United Kingdom
| | - Weiming Tu
- Department
of Engineering Science, University of Oxford, OxfordOX1 3PJ, United Kingdom
| | - Jiabao Xu
- Department
of Engineering Science, University of Oxford, OxfordOX1 3PJ, United Kingdom
| | - Simona Della Valle
- Department
of Engineering Science, University of Oxford, OxfordOX1 3PJ, United Kingdom
| | - Ian P. Thompson
- Department
of Engineering Science, University of Oxford, OxfordOX1 3PJ, United Kingdom
| | - C. Neil Hunter
- Plants,
Photosynthesis and Soil, School of Biosciences, University of Sheffield, SheffieldS10 2TN, United Kingdom
| | - Wei E. Huang
- Department
of Engineering Science, University of Oxford, OxfordOX1 3PJ, United Kingdom,. Tel: +44 1865 283786
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13
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Application of Spectroscopic Methods for the Identification of Superoxide Dismutases in Cyanobacteria. Int J Mol Sci 2022; 23:ijms232213819. [PMID: 36430299 PMCID: PMC9692673 DOI: 10.3390/ijms232213819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/04/2022] [Accepted: 11/07/2022] [Indexed: 11/11/2022] Open
Abstract
Superoxide dismutases (SODs) belong to the group of metalloenzymes that remove superoxide anion radicals and they have been identified in three domains of life: Bacteria, Archaea and Eucarya. SODs in Synechocystis sp. PCC 6803, Gloeobacter violaceus CCALA 979, and Geitlerinema sp. ZHR1A were investigated. We hypothesized that iron (FeSOD) and/or manganese (MnSOD) dominate as active forms in these cyanobacteria. Activity staining and three different spectroscopic methods of SOD activity bands excised from the gels were used to identify a suitable metal in the separated samples. FeSODs or enzymes belonging to the Fe-MnSOD superfamily were detected. The spectroscopic analyses showed that only Fe is present in the SOD activity bands. We found FeSOD in Synechocystis sp. PCC 6803 while two forms in G. violaceus and Geitlerinema sp. ZHR1A: FeSOD1 and FeSOD2 were present. However, no active Cu/ZnSODs were identified in G. violaceus and Geitlerinema sp. ZHR1A. We have shown that selected spectroscopic techniques can be complementary to the commonly used method of staining for SOD activity in a gel. Furthermore, the occurrence of active SODs in the cyanobacteria studied is also discussed in the context of SOD evolution in oxyphotrophs.
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14
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Slonimskiy YB, Zupnik AO, Varfolomeeva LA, Boyko KM, Maksimov EG, Sluchanko NN. A primordial Orange Carotenoid Protein: Structure, photoswitching activity and evolutionary aspects. Int J Biol Macromol 2022; 222:167-180. [PMID: 36165868 DOI: 10.1016/j.ijbiomac.2022.09.131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 09/13/2022] [Accepted: 09/14/2022] [Indexed: 11/28/2022]
Abstract
Cyanobacteria are photosynthesizing prokaryotes responsible for the Great Oxygenation Event on Earth ~2.5 Ga years ago. They use a specific photoprotective mechanism based on the 35-kDa photoactive Orange Carotenoid Protein (OCP), a promising target for developing novel optogenetic tools and for biomass engineering. The two-domain OCP presumably stems from domain fusion, yet the primitive thylakoid-less cyanobacteria Gloeobacter encodes a complete OCP. Its photosynthesis regulation lacks the so-called Fluorescence Recovery Protein (FRP), which in Synechocystis inhibits OCP-mediated phycobilisome fluorescence quenching, and Gloeobacter OCP belongs to the recently defined, heterogeneous clade OCPX (GlOCPX), the least characterized compared to OCP2 and especially OCP1 clades. Here, we describe the first crystal structure of OCPX, which explains unique functional adaptations of Gloeobacter OCPX compared to OCP1 from Synechocystis. We show that monomeric GlOCPX exploits a remarkable intramolecular locking mechanism stabilizing its dark-adapted state and exhibits drastically accelerated, less temperature-dependent recovery after photoactivation. While GlOCPX quenches Synechocystis phycobilisomes similar to Synechocystis OCP1, it evades interaction with and regulation by FRP from other species and likely uses alternative mechanisms for fluorescence recovery. This analysis of a primordial OCPX sheds light on its evolution, rationalizing renaming and subdivision of the OCPX clade into subclades - OCP3a, OCP3b, OCP3c.
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Affiliation(s)
- Yury B Slonimskiy
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russian Federation
| | - Andrei O Zupnik
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russian Federation
| | - Larisa A Varfolomeeva
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russian Federation
| | - Konstantin M Boyko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russian Federation
| | - Eugene G Maksimov
- M.V. Lomonosov Moscow State University, Faculty of Biology, 119991 Moscow, Russian Federation
| | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russian Federation.
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15
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Luz R, Cordeiro R, Fonseca A, Raposeiro PM, Gonçalves V. Distribution and diversity of cyanobacteria in the Azores Archipelago: An annotated checklist. Biodivers Data J 2022; 10:e87638. [PMID: 36761623 PMCID: PMC9848483 DOI: 10.3897/bdj.10.e87638] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 07/19/2022] [Indexed: 11/12/2022] Open
Abstract
Background Knowledge about cyanobacteria diversity in the Azores is spread over several publications, dating from 1874, with some of them not generally available to the scientific community due to their restricted access. The dispersion and sometimes inaccessibility of this information hinder a deeper analysis and a better understanding of the biodiversity of the Azores Islands and more general ecological processes in oceanic islands. Here we present the first checklist of cyanobacteria for the Azores Archipelago with updated taxonomy of all recorded taxa. New information This work provides a compiled and annotated checklist of all known cyanobacteria from the Azores Archipelago with morphological identification from preserved samples and cultures, based on published literature. All records of taxa known to occur in the Azores were taxonomically updated. The present checklist comprises 225 taxa distributed by six orders (Chroococcales, Nostocales, Oscillatoriales, Pleurocapsales, Spirulinales and Synechococcales). Our literature review reveals that the Azores Archipelago hosts a high diversity of cyanobacteria, despite several overlooked habitats that may present great potential regarding cyanobacteria diversity. Increasing efforts to study these neglected habitats could contribute to the knowledge of cyanobacteria taxonomy. This checklist provides the basis for future works on the taxonomy and taxa richness of cyanobacteria in the Azores and the Atlantic Islands, as also for understanding and monitoring non-indigenous and invasive species.
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Affiliation(s)
- Rúben Luz
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Pólo dos Açores, Ponta Delgada, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Pólo dos AçoresPonta DelgadaPortugal,Faculdade de Ciências e Tecnologia, Universidade dos Açores, Ponta Delgada, PortugalFaculdade de Ciências e Tecnologia, Universidade dos AçoresPonta DelgadaPortugal
| | - Rita Cordeiro
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Pólo dos Açores, Ponta Delgada, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Pólo dos AçoresPonta DelgadaPortugal,Faculdade de Ciências e Tecnologia, Universidade dos Açores, Ponta Delgada, PortugalFaculdade de Ciências e Tecnologia, Universidade dos AçoresPonta DelgadaPortugal
| | - Amélia Fonseca
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Pólo dos Açores, Ponta Delgada, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Pólo dos AçoresPonta DelgadaPortugal,Faculdade de Ciências e Tecnologia, Universidade dos Açores, Ponta Delgada, PortugalFaculdade de Ciências e Tecnologia, Universidade dos AçoresPonta DelgadaPortugal
| | - Pedro Miguel Raposeiro
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Pólo dos Açores, Ponta Delgada, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Pólo dos AçoresPonta DelgadaPortugal,Faculdade de Ciências e Tecnologia, Universidade dos Açores, Ponta Delgada, PortugalFaculdade de Ciências e Tecnologia, Universidade dos AçoresPonta DelgadaPortugal
| | - Vítor Gonçalves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Pólo dos Açores, Ponta Delgada, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Pólo dos AçoresPonta DelgadaPortugal,Faculdade de Ciências e Tecnologia, Universidade dos Açores, Ponta Delgada, PortugalFaculdade de Ciências e Tecnologia, Universidade dos AçoresPonta DelgadaPortugal
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16
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Draft Genome Sequence of the Thermophilic Unicellular Cyanobacterium
Synechococcus
sp. Strain C9. Microbiol Resour Announc 2022; 11:e0029422. [PMID: 35876539 PMCID: PMC9387270 DOI: 10.1128/mra.00294-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This study presents the genome sequence of Synechococcus sp. strain C9 (= CCMEE 5213 = ATCC 700244), a thermophilic unicellular cyanobacterium that was originally isolated from a thermal pool at Octopus Spring, Yellowstone National Park, USA. The genome consists of a 2,958,309-bp chromosome with a GC content of 52.9% and 2,854 protein-coding sequences.
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17
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Carotenoid binding in Gloeobacteria rhodopsin provides insights into divergent evolution of xanthorhodopsin types. Commun Biol 2022; 5:512. [PMID: 35637261 PMCID: PMC9151804 DOI: 10.1038/s42003-022-03429-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 04/29/2022] [Indexed: 11/08/2022] Open
Abstract
The position of carotenoid in xanthorhodopsin has been elucidated. However, a challenging expression of this opsin and a complex biosynthesis carotenoid in the laboratory hold back the insightful study of this rhodopsin. Here, we demonstrated co-expression of the xanthorhodopsin type isolated from Gloeobacter violaceus PCC 7421-Gloeobacter rhodopsin (GR) with a biosynthesized keto-carotenoid (canthaxanthin) targeting the carotenoid binding site. Direct mutation-induced changes in carotenoid-rhodopsin interaction revealed three crucial features: (1) carotenoid locked motif (CLM), (2) carotenoid aligned motif (CAM), and color tuning serines (CTS). Our single mutation results at 178 position (G178W) confirmed inhibition of carotenoid binding; however, the mutants showed better stability and proton pumping, which was also observed in the case of carotenoid binding characteristics. These effects demonstrated an adaptation of microbial rhodopsin that diverges from carotenoid harboring, along with expression in the dinoflagellate Pyrocystis lunula rhodopsin and the evolutionary substitution model. The study highlights a critical position of the carotenoid binding site, which significantly allows another protein engineering approach in the microbial rhodopsin family.
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18
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Community Vertical Composition of the Laguna Negra Hypersaline Microbial Mat, Puna Region (Argentinean Andes). BIOLOGY 2022; 11:biology11060831. [PMID: 35741352 PMCID: PMC9220024 DOI: 10.3390/biology11060831] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 05/20/2022] [Accepted: 05/27/2022] [Indexed: 11/17/2022]
Abstract
The Altiplano-Puna region is a high-altitude plateau in South America characterized by extreme conditions, including the highest UV incidence on Earth. The Laguna Negra is a hypersaline lake located in the Catamarca Province, northwestern Argentina, where stromatolites and other microbialites are found, and where life is mostly restricted to microbial mats. In this study, a particular microbial mat that covers the shore of the lake was explored, to unravel its layer-by-layer vertical structure in response to the environmental stressors therein. Microbial community composition was assessed by high-throughput 16S rRNA gene sequencing and pigment content analyses, complemented with microscopy tools to characterize its spatial arrangement within the mat. The top layer of the mat has a remarkable UV-tolerance feature, characterized by the presence of Deinococcus-Thermus and deinoxanthin, which might reflect a shielding strategy to cope with high UV radiation. Chloroflexi and Deltaproteobacteria were abundant in the second and third underlying layers, respectively. The bottom layer harbors copious Halanaerobiaeota. Subspherical aggregates composed of calcite, extracellular polymeric substances, abundant diatoms, and other microorganisms were observed all along the mat as the main structural component. This detailed study provides insights into the strategies of microbial communities to thrive under high UV radiation and hypersalinity in high-altitude lakes in the Altiplano-Puna region.
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19
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20
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Song K, Baumgartner D, Hagemann M, Muro-Pastor AM, Maaß S, Becher D, Hess WR. AtpΘ is an inhibitor of F 0F 1 ATP synthase to arrest ATP hydrolysis during low-energy conditions in cyanobacteria. Curr Biol 2021; 32:136-148.e5. [PMID: 34762820 DOI: 10.1016/j.cub.2021.10.051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 10/14/2021] [Accepted: 10/22/2021] [Indexed: 10/19/2022]
Abstract
Biological processes in all living cells are powered by ATP, a nearly universal molecule of energy transfer. ATP synthases produce ATP utilizing proton gradients that are usually generated by either respiration or photosynthesis. However, cyanobacteria are unique in combining photosynthetic and respiratory electron transport chains in the same membrane system, the thylakoids. How cyanobacteria prevent the futile reverse operation of ATP synthase under unfavorable conditions pumping protons while hydrolyzing ATP is mostly unclear. Here, we provide evidence that the small protein AtpΘ, which is widely conserved in cyanobacteria, is mainly fulfilling this task. The expression of AtpΘ becomes induced under conditions such as darkness or heat shock, which can lead to a weakening of the proton gradient. Translational fusions of AtpΘ to the green fluorescent protein revealed targeting to the thylakoid membrane. Immunoprecipitation assays followed by mass spectrometry and far western blots identified subunits of ATP synthase as interacting partners of AtpΘ. ATP hydrolysis assays with isolated membrane fractions, as well as purified ATP synthase complexes, demonstrated that AtpΘ inhibits ATPase activity in a dose-dependent manner similar to the F0F1-ATP synthase inhibitor N,N-dicyclohexylcarbodimide. The results show that, even in a well-investigated process, crucial new players can be discovered if small proteins are taken into consideration and indicate that ATP synthase activity can be controlled in surprisingly different ways.
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Affiliation(s)
- Kuo Song
- University of Freiburg, Faculty of Biology, Genetics and Experimental Bioinformatics, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Desirée Baumgartner
- University of Freiburg, Faculty of Biology, Genetics and Experimental Bioinformatics, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Martin Hagemann
- University of Rostock, Institute of Biosciences, Plant Physiology Department, Albert-Einstein-Str. 3, 18059 Rostock, Germany
| | - Alicia M Muro-Pastor
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, 41092 Sevilla, Spain
| | - Sandra Maaß
- University of Greifswald, Department of Microbial Proteomics, Institute of Microbiology, 17489 Greifswald, Germany
| | - Dörte Becher
- University of Greifswald, Department of Microbial Proteomics, Institute of Microbiology, 17489 Greifswald, Germany
| | - Wolfgang R Hess
- University of Freiburg, Faculty of Biology, Genetics and Experimental Bioinformatics, Schänzlestr. 1, 79104 Freiburg, Germany.
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21
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Characterizing the Uncultivated Microbial Minority: towards Understanding the Roles of the Rare Biosphere in Microbial Communities. mSystems 2021; 6:e0077321. [PMID: 34427533 PMCID: PMC8407377 DOI: 10.1128/msystems.00773-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Microbial communities are frequently numerically dominated by just a few species. Often, the long “tail” of the rank-abundance plots of microbial communities constitutes the so-called “rare biosphere,” microorganisms that are highly diverse but are typically found in low abundance in these communities. Their presence in microbial communities has only recently become apparent with advances in high-throughput sequencing technologies. Despite their low numbers, they are thought to play important roles in their communities and may function as potential members to keep the communities intact and resilient. Their phylogenetic diversity also means that they are important subjects for better understanding the interplay between microbial diversity and evolution. I propose that more efforts should be put into characterizing these poorly understood and mostly unknown microbial lineages that hold vast potentials for our understanding of microbial diversity, ecology, and evolution of life on this planet.
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22
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Hauerová R, Hauer T, Kaštovský J, Komárek J, Lepšová-Skácelová O, Mareš J. Tenebriella gen. nov. - the dark twin of Oscillatoria. Mol Phylogenet Evol 2021; 165:107293. [PMID: 34391914 DOI: 10.1016/j.ympev.2021.107293] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 08/05/2021] [Accepted: 08/09/2021] [Indexed: 10/20/2022]
Abstract
Oscillatoria has long been known to be polyphyletic. After recent resequencing of the reference strain for this genus, many Oscillatoria-like groups phylogenetically distant from the type species O. princeps remained unresolved. Here we describe one of these groups as a new genus Tenebriella. Most of the studied strains originate from Central Europe, where they are able to form prominent microbial mats. Despite the overall Oscillatoria-like morphology, Tenebriella can be distinguished by darker trichomes and forms a separate monophyletic clade in phylogenies inferred from the 16S rRNA gene and two additional loci (rpoC1, rbcLX). Within Tenebriella we recognize two new species differing from each other by morphological and ecological characteristics. First species does not fit any known taxon description, and thus is described as a new species T. amphibia. The latter one corresponds with the information available for Oscillatoria curviceps Agardh ex Gomont, and thus new combination T. curviceps is proposed. The phylogenetic analyses of the 16S-23S ITS region together with the comparison of the hypothetical secondary structures confirmed recognition of these two species and additionally revealed presence of a morphologically cryptic species Tenebriella sp. The results corroborate frequent recurrence of convergent morphotypes in the evolution of cyanobacteria and justify further exploration even of the intensively studied European freshwaters using molecular phylogenetics to discover new and ecologically relevant taxa.
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Affiliation(s)
- Radka Hauerová
- University of South Bohemia, Faculty of Science, Branišovská 1760, 370 05, České Budějovice, Czech Republic; Biology Centre of the Czech Academy of Sciences, Institute of Soil Biology, Na Sádkách 702/7, 37005 České Budějovice, Czech Republic.
| | - Tomáš Hauer
- University of South Bohemia, Faculty of Science, Branišovská 1760, 370 05, České Budějovice, Czech Republic
| | - Jan Kaštovský
- University of South Bohemia, Faculty of Science, Branišovská 1760, 370 05, České Budějovice, Czech Republic
| | - Jiří Komárek
- University of South Bohemia, Faculty of Science, Branišovská 1760, 370 05, České Budějovice, Czech Republic; The Czech Academy of Sciences, Institute of Botany, Centre for Phycology, Dukelská 135, 379 82 Třeboň, Czech Republic
| | - Olga Lepšová-Skácelová
- University of South Bohemia, Faculty of Science, Branišovská 1760, 370 05, České Budějovice, Czech Republic
| | - Jan Mareš
- University of South Bohemia, Faculty of Science, Branišovská 1760, 370 05, České Budějovice, Czech Republic; Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, Na Sádkách 702/7, 37005 České Budějovice, Czech Republic
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23
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Slater B, Kosmützky D, Nisbet RER, Howe CJ. The Evolution of the Cytochrome c6 Family of Photosynthetic Electron Transfer Proteins. Genome Biol Evol 2021; 13:evab146. [PMID: 34165554 PMCID: PMC8358224 DOI: 10.1093/gbe/evab146] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2021] [Indexed: 12/15/2022] Open
Abstract
During photosynthesis, electrons are transferred between the cytochrome b6f complex and photosystem I. This is carried out by the protein plastocyanin in plant chloroplasts, or by either plastocyanin or cytochrome c6 in many cyanobacteria and eukaryotic algal species. There are three further cytochrome c6 homologs: cytochrome c6A in plants and green algae, and cytochromes c6B and c6C in cyanobacteria. The function of these proteins is unknown. Here, we present a comprehensive analysis of the evolutionary relationship between the members of the cytochrome c6 family in photosynthetic organisms. Our phylogenetic analyses show that cytochromes c6B and c6C are likely to be orthologs that arose from a duplication of cytochrome c6, but that there is no evidence for separate origins for cytochromes c6B and c6C. We therefore propose renaming cytochrome c6C as cytochrome c6B. We show that cytochrome c6A is likely to have arisen from cytochrome c6B rather than by an independent duplication of cytochrome c6, and present evidence for an independent origin of a protein with some of the features of cytochrome c6A in peridinin dinoflagellates. We conclude with a new comprehensive model of the evolution of the cytochrome c6 family which is an integral part of understanding the function of the enigmatic cytochrome c6 homologs.
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Affiliation(s)
- Barnaby Slater
- Department of Biochemistry, University of Cambridge, United Kingdom
| | - Darius Kosmützky
- Department of Biochemistry, University of Cambridge, United Kingdom
| | - R Ellen R Nisbet
- Department of Biochemistry, University of Cambridge, United Kingdom
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24
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Abstract
Photosynthetic Cyanobacteria and their descendants are the only known organisms capable of oxygenic photosynthesis. Their metabolism permanently changed the Earth’s surface and the evolutionary trajectory of life, but little is known about their evolutionary history. Genomes of the Gloeobacterales, an order of deeply divergent photosynthetic Cyanobacteria, may hold clues about the evolutionary process. However, there are only three published genomes within this order, and it is difficult to make broad inferences based on such little data. Here, I describe five species within the Gloeobacterales retrieved from publicly available databases and examine their photosynthetic gene content and the environments in which Gloeobacterales genomes and 16S rRNA gene sequences are found. The Gloeobacterales contain reduced photosystems and inhabit cold, wet-rock, and low-light environments. They are likely present in low abundances due to their low growth rate. Future searches for Gloeobacterales should target these environments, and samples should be deeply sequenced to capture the low-abundance taxa. Publicly available databases contain undescribed taxa within the Gloeobacterales. However, searching through all available data with current methods is computationally expensive. Therefore, new methods must be developed to search for these and other evolutionarily important taxa. Once identified, these novel photosynthetic Cyanobacteria will help illuminate the origin and evolution of oxygenic photosynthesis. IMPORTANCE Early branching photosynthetic Cyanobacteria such as the Gloeobacterales may provide clues into the evolutionary history of oxygenic photosynthesis, but there are few genomes or cultured taxa from this order. Five new metagenome-assembled genomes suggest that members of the Gloeobacterales all contain reduced photosystems and lack genes associated with thylakoids and circadian rhythms. Their distribution suggests that they may thrive in environments that are marginal for other species, including wet-rock and cold environments. These traits may aid in the discovery and cultivation of novel species in this clade.
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Rahmatpour N, Hauser DA, Nelson JM, Chen PY, Villarreal A JC, Ho MY, Li FW. A novel thylakoid-less isolate fills a billion-year gap in the evolution of Cyanobacteria. Curr Biol 2021; 31:2857-2867.e4. [PMID: 33989529 DOI: 10.1016/j.cub.2021.04.042] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/02/2021] [Accepted: 04/16/2021] [Indexed: 12/31/2022]
Abstract
Cyanobacteria have played pivotal roles in Earth's geological history, especially during the rise of atmospheric oxygen. However, our ability to infer the early transitions in Cyanobacteria evolution has been limited by their extremely lopsided tree of life-the vast majority of extant diversity belongs to Phycobacteria (or "crown Cyanobacteria"), while its sister lineage, Gloeobacteria, is depauperate and contains only two closely related species of Gloeobacter and a metagenome-assembled genome. Here, we describe a new cultured member of Gloeobacteria, Anthocerotibacter panamensis, isolated from a tropical hornwort. Anthocerotibacter diverged from Gloeobacter over 1.4 Ga ago and has low 16S rDNA identities with environmental samples. Our ultrastructural, physiological, and genomic analyses revealed that this species possesses a unique combination of traits that are exclusively shared with either Gloeobacteria or Phycobacteria. For example, similar to Gloeobacter, it lacks thylakoids and circadian clock genes, but the carotenoid biosynthesis pathway is typical of Phycobacteria. Furthermore, Anthocerotibacter has one of the most reduced gene sets for photosystems and phycobilisomes among Cyanobacteria. Despite this, Anthocerotibacter is capable of oxygenic photosynthesis under a wide range of light intensities, albeit with much less efficiency. Given its key phylogenetic position, distinct trait combination, and availability as a culture, Anthocerotibacter opens a new window to further illuminate the dawn of oxygenic photosynthesis.
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Affiliation(s)
| | | | | | - Pa Yu Chen
- Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Juan Carlos Villarreal A
- Department of Biology, Laval University, Quebec City, QC, Canada; Smithsonian Tropical Research Institute, Panama City, Panama
| | - Ming-Yang Ho
- Department of Life Science, National Taiwan University, Taipei, Taiwan; Institute of Plant Biology, National Taiwan University, Taipei, Taiwan.
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, USA; Plant Biology Section, Cornell University, Ithaca, NY, USA.
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26
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Ballesteros I, Terán P, Guamán-Burneo C, González N, Cruz A, Castillejo P. DNA barcoding approach to characterize microalgae isolated from freshwater systems in Ecuador. NEOTROPICAL BIODIVERSITY 2021. [DOI: 10.1080/23766808.2021.1920296] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Affiliation(s)
- Isabel Ballesteros
- AgroScience & Food Research Group, Universidad de las Américas, Quito, Ecuador
| | - Paulina Terán
- AgroScience & Food Research Group, Universidad de las Américas, Quito, Ecuador
| | | | - Nory González
- AgroScience & Food Research Group, Universidad de las Américas, Quito, Ecuador
| | - Alejandra Cruz
- Ingeniería en Biotecnología. Facultad de Ingenierías y Ciencias Aplicadas, Universidad de las Américas, Quito, Ecuador
| | - Pablo Castillejo
- Grupo de Investigación en Biodiversidad, Medio Ambiente y Salud (BIOMAS), Universidad de las Américas, Quito, Ecuador
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27
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The Role of Selected Wavelengths of Light in the Activity of Photosystem II in Gloeobacter violaceus. Int J Mol Sci 2021; 22:ijms22084021. [PMID: 33924720 PMCID: PMC8069770 DOI: 10.3390/ijms22084021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/09/2021] [Accepted: 04/12/2021] [Indexed: 01/03/2023] Open
Abstract
Gloeobacter violaceus is a cyanobacteria species with a lack of thylakoids, while photosynthetic antennas, i.e., phycobilisomes (PBSs), photosystem II (PSII), and I (PSI), are located in the cytoplasmic membrane. We verified the hypothesis that blue–red (BR) light supplemented with a far-red (FR), ultraviolet A (UVA), and green (G) light can affect the photosynthetic electron transport chain in PSII and explain the differences in the growth of the G. violaceus culture. The cyanobacteria were cultured under different light conditions. The largest increase in G. violaceus biomass was observed only under BR + FR and BR + G light. Moreover, the shape of the G. violaceus cells was modified by the spectrum with the addition of G light. Furthermore, it was found that both the spectral composition of light and age of the cyanobacterial culture affect the different content of phycobiliproteins in the photosynthetic antennas (PBS). Most likely, in cells grown under light conditions with the addition of FR and G light, the average antenna size increased due to the inactivation of some reaction centers in PSII. Moreover, the role of PSI and gloeorhodopsin as supplementary sources of metabolic energy in the G. violaceus growth is discussed.
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28
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Pascual-Aznar G, Konert G, Bečkov M, Kotabov E, Gardian Z, Knoppov J, Bučinsk L, Kaňa R, Sobotka R, Komenda J. Psb35 Protein Stabilizes the CP47 Assembly Module and Associated High-Light Inducible Proteins during the Biogenesis of Photosystem II in the Cyanobacterium Synechocystis sp. PCC6803. PLANT & CELL PHYSIOLOGY 2021; 62:178-190. [PMID: 33258963 DOI: 10.1093/pcp/pcaa148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 11/16/2020] [Indexed: 05/07/2023]
Abstract
Photosystem II (PSII) is a large membrane protein complex performing primary charge separation in oxygenic photosynthesis. The biogenesis of PSII is a complicated process that involves a coordinated linking of assembly modules in a precise order. Each such module consists of one large chlorophyll (Chl)-binding protein, number of small membrane polypeptides, pigments and other cofactors. We isolated the CP47 antenna module from the cyanobacterium Synechocystis sp. PCC 6803 and found that it contains a 11-kDa protein encoded by the ssl2148 gene. This protein was named Psb35 and its presence in the CP47 module was confirmed by the isolation of FLAG-tagged version of Psb35. Using this pulldown assay, we showed that the Psb35 remains attached to CP47 after the integration of CP47 into PSII complexes. However, the isolated Psb35-PSIIs were enriched with auxiliary PSII assembly factors like Psb27, Psb28-1, Psb28-2 and RubA while they lacked the lumenal proteins stabilizing the PSII oxygen-evolving complex. In addition, the Psb35 co-purified with a large unique complex of CP47 and photosystem I trimer. The absence of Psb35 led to a lower accumulation and decreased stability of the CP47 antenna module and associated high-light-inducible proteins but did not change the growth rate of the cyanobacterium under the variety of light regimes. Nevertheless, in comparison with WT, the Psb35-less mutant showed an accelerated pigment bleaching during prolonged dark incubation. The results suggest an involvement of Psb35 in the life cycle of cyanobacterial Chl-binding proteins, especially CP47.
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Affiliation(s)
- Guillem Pascual-Aznar
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Opatovick� ml�n, Novohradsk� 237, Třeboň 37981, Czech Republic
- Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovsk� 1760, Česk� Budějovice 37005, Czech Republic
| | - Grzegorz Konert
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Opatovick� ml�n, Novohradsk� 237, Třeboň 37981, Czech Republic
| | - Martina Bečkov
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Opatovick� ml�n, Novohradsk� 237, Třeboň 37981, Czech Republic
| | - Eva Kotabov
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Opatovick� ml�n, Novohradsk� 237, Třeboň 37981, Czech Republic
| | - Zdenko Gardian
- Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovsk� 1760, Česk� Budějovice 37005, Czech Republic
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovsk� 31, Česk� Budějovice 37005, Czech Republic
| | - Jana Knoppov
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Opatovick� ml�n, Novohradsk� 237, Třeboň 37981, Czech Republic
| | - Lenka Bučinsk
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Opatovick� ml�n, Novohradsk� 237, Třeboň 37981, Czech Republic
| | - Radek Kaňa
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Opatovick� ml�n, Novohradsk� 237, Třeboň 37981, Czech Republic
| | - Roman Sobotka
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Opatovick� ml�n, Novohradsk� 237, Třeboň 37981, Czech Republic
| | - Josef Komenda
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Opatovick� ml�n, Novohradsk� 237, Třeboň 37981, Czech Republic
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29
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Dahlgren KK, Gates C, Lee T, Cameron JC. Proximity-based proteomics reveals the thylakoid lumen proteome in the cyanobacterium Synechococcus sp. PCC 7002. PHOTOSYNTHESIS RESEARCH 2021; 147:177-195. [PMID: 33280076 PMCID: PMC7880944 DOI: 10.1007/s11120-020-00806-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 11/23/2020] [Indexed: 06/12/2023]
Abstract
Cyanobacteria possess unique intracellular organization. Many proteomic studies have examined different features of cyanobacteria to learn about the intracellular structures and their respective functions. While these studies have made great progress in understanding cyanobacterial physiology, the conventional fractionation methods used to purify cellular structures have limitations; specifically, certain regions of cells cannot be purified with existing fractionation methods. Proximity-based proteomics techniques were developed to overcome the limitations of biochemical fractionation for proteomics. Proximity-based proteomics relies on spatiotemporal protein labeling followed by mass spectrometry of the labeled proteins to determine the proteome of the region of interest. We performed proximity-based proteomics in the cyanobacterium Synechococcus sp. PCC 7002 with the APEX2 enzyme, an engineered ascorbate peroxidase. We determined the proteome of the thylakoid lumen, a region of the cell that has remained challenging to study with existing methods, using a translational fusion between APEX2 and PsbU, a lumenal subunit of photosystem II. Our results demonstrate the power of APEX2 as a tool to study the cell biology of intracellular features and processes, including photosystem II assembly in cyanobacteria, with enhanced spatiotemporal resolution.
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Affiliation(s)
- Kelsey K Dahlgren
- Department of Biochemistry, University of Colorado, Boulder, CO, 80309, USA
- Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO, 80309, USA
- BioFrontiers Institute, University of Colorado, Boulder, CO, 80309, USA
- Interdisciplinary Quantitative Biology Program (IQ Biology), BioFrontiers Institute, University of Colorado, Boulder, CO, 80309, USA
| | - Colin Gates
- Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO, 80309, USA
| | - Thomas Lee
- Department of Biochemistry, University of Colorado, Boulder, CO, 80309, USA
| | - Jeffrey C Cameron
- Department of Biochemistry, University of Colorado, Boulder, CO, 80309, USA.
- Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO, 80309, USA.
- National Renewable Energy Laboratory, Golden, CO, 80401, USA.
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30
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Miles JA, Davies TA, Hayman RD, Lorenzen G, Taylor J, Anjarwalla M, Allen SJR, Graham JWD, Taylor PC. A Case Study of Eukaryogenesis: The Evolution of Photoreception by Photolyase/Cryptochrome Proteins. J Mol Evol 2020; 88:662-673. [PMID: 32979052 PMCID: PMC7560933 DOI: 10.1007/s00239-020-09965-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 09/05/2020] [Indexed: 11/23/2022]
Abstract
Eukaryogenesis, the origin of the eukaryotes, is still poorly understood. Herein, we show how a detailed all-kingdom phylogenetic analysis overlaid with a map of key biochemical features can provide valuable clues. The photolyase/cryptochrome family of proteins are well known to repair DNA in response to potentially harmful effects of sunlight and to entrain circadian rhythms. Phylogenetic analysis of photolyase/cryptochrome protein sequences from a wide range of prokaryotes and eukaryotes points to a number of horizontal gene transfer events between ancestral bacteria and ancestral eukaryotes. Previous experimental research has characterised patterns of tryptophan residues in these proteins that are important for photoreception, specifically a tryptophan dyad, a canonical tryptophan triad, an alternative tryptophan triad, a tryptophan tetrad and an alternative tetrad. Our results suggest that the spread of the different triad and tetrad motifs across the kingdoms of life accompanied the putative horizontal gene transfers and is consistent with multiple bacterial contributions to eukaryogenesis.
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Affiliation(s)
- Jennifer A Miles
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Thomas A Davies
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Robert D Hayman
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Georgia Lorenzen
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Jamie Taylor
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Mubeena Anjarwalla
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Sammie J R Allen
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - John W D Graham
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Paul C Taylor
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK.
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK.
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31
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Popović S, Krizmanić J, Vidaković D, Karadžić V, Milovanović Ž, Pećić M, Subakov Simić G. Biofilms in caves: easy method for the assessment of dominant phototrophic groups/taxa in situ. ENVIRONMENTAL MONITORING AND ASSESSMENT 2020; 192:720. [PMID: 33089398 DOI: 10.1007/s10661-020-08686-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 10/15/2020] [Indexed: 06/11/2023]
Abstract
Domination of certain aerophytic phototrophic group or specific taxon in biofilms is connected with biofilm features recognised in situ. Well-developed, gelatinous, olive to dark-green biofilms are composed mostly of coccoid cyanobacterial forms. The same features, characterised biofilms dominated by one coccoid taxon, except the latter were vividly coloured. Gloeobacter caused the appearance of purple, Gloeocapsa representatives yellow and Chroococcidiopsis black biofilm. The brown to the dark colour of heterocytous biofilms was mainly caused by Nostoc. Simple trichal Cyanobacteria were occasionally present in biofilm, except in one blue-coloured sample. According to the principal component analysis (PCA), well-developed and gelatinous biofilms were correlated with Cyanobacteria, while scanning electron microscopy (SEM) revealed richness of extracellular polymeric substances (EPS) in such biofilms. Biofilm with calcified cyanobacterium (Geitleria cf. calcarea) was also found. Chlorophyta-abundant biofilms (many rich in Desmococcus), thinner than cyanobacterial, were predominantly green and occasionally yellow and blue. Many were dry when observed in situ (confirmed with PCA), with few being moistened (i.e. Klebsormidium-dominant). Diatom biofilms were usually developed on sediment, mosses or near seeping water (demonstrated by PCA) and were also thinner than cyanobacterial ones. Compared to cyanobacterial biofilms, SEM showed less developed EPS in those rich in diatoms and green algae, where microorganisms are more exposed to the environment. The study demonstrates an easy method for biofilm assessment based on visual characterisation and provides encouragement for more frequent biofilm investigation in caves that can be important from an ecological, biological, biotechnological point of view and which assessment can have an irreplaceable role in potential monitoring and protection.
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Affiliation(s)
- Slađana Popović
- Center for Ecology and Technoeconomics, Institute of Chemistry, Technology and Metallurgy, National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia.
| | - Jelena Krizmanić
- Faculty of Biology, Institute of Botany and Botanical Garden 'Jevremovac', University of Belgrade, Belgrade, Serbia
| | - Danijela Vidaković
- Department of Chemistry, Institute of Chemistry, Technology and Metallurgy, National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Vesna Karadžić
- Institute of Public Health of Serbia Dr. Milan Jovanovic Batut, Belgrade, Serbia
| | - Željka Milovanović
- Center for Ecology and Technoeconomics, Institute of Chemistry, Technology and Metallurgy, National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Marija Pećić
- Faculty of Biology, Institute of Botany and Botanical Garden 'Jevremovac', University of Belgrade, Belgrade, Serbia
| | - Gordana Subakov Simić
- Faculty of Biology, Institute of Botany and Botanical Garden 'Jevremovac', University of Belgrade, Belgrade, Serbia
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32
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Raven JA. Chloride involvement in the synthesis, functioning and repair of the photosynthetic apparatus in vivo. THE NEW PHYTOLOGIST 2020; 227:334-342. [PMID: 32170958 DOI: 10.1111/nph.16541] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 03/05/2020] [Indexed: 06/10/2023]
Abstract
Cl- has long been known as a micronutrient for oxygenic photosynthetic resulting from its role an essential cofactor for photosystem II (PSII). Evidence on the in vivo Cl- distribution in Spinacia oleracea leaves and chloroplasts shows that sufficient Cl- is present for the involvement in PSII function, as indicated by in vitro studies on, among other organisms, S. oleracea PsII. There is also sufficient Cl- to function, with K+ , in parsing the H+ electrochemical potential difference (proton motive force) across the illuminated thylakoid membrane into electrical potential difference and pH difference components. However, recent in vitro work on PSII from S. oleracea shows that oxygen evolving complex (OEC) synthesis, and resynthesis after photodamage, requires significantly higher Cl- concentrations than would satisfy the function of assembled PSII O2 evolution of the synthesised PSII with the OEC. The low Cl- affinity of OEC (re-)assembly could be a component limiting the rate of OEC (re-)assembly.
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Affiliation(s)
- John A Raven
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
- Climate Change Cluster, University of Technology, Ultimo, Sydney, NSW, 2007, Australia
- School of Biological Science, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
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33
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Cavalier-Smith T, Chao EEY. Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria). PROTOPLASMA 2020. [PMID: 31900730 DOI: 10.1007/s00709-019-01442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Palaeontologically, eubacteria are > 3× older than neomura (eukaryotes, archaebacteria). Cell biology contrasts ancestral eubacterial murein peptidoglycan walls and derived neomuran N-linked glycoprotein coats/walls. Misinterpreting long stems connecting clade neomura to eubacteria on ribosomal sequence trees (plus misinterpreted protein paralogue trees) obscured this historical pattern. Universal multiprotein ribosomal protein (RP) trees, more accurate than rRNA trees, are taxonomically undersampled. To reduce contradictions with genically richer eukaryote trees and improve eubacterial phylogeny, we constructed site-heterogeneous and maximum-likelihood universal three-domain, two-domain, and single-domain trees for 143 eukaryotes (branching now congruent with 187-protein trees), 60 archaebacteria, and 151 taxonomically representative eubacteria, using 51 and 26 RPs. Site-heterogeneous trees greatly improve eubacterial phylogeny and higher classification, e.g. showing gracilicute monophyly, that many 'rDNA-phyla' belong in Proteobacteria, and reveal robust new phyla Synthermota and Aquithermota. Monoderm Posibacteria and Mollicutes (two separate wall losses) are both polyphyletic: multiple outer membrane losses in Endobacteria occurred separately from Actinobacteria; neither phylum is related to Chloroflexi, the most divergent prokaryotes, which originated photosynthesis (new model proposed). RP trees support an eozoan root for eukaryotes and are consistent with archaebacteria being their sisters and rooted between Filarchaeota (=Proteoarchaeota, including 'Asgardia') and Euryarchaeota sensu-lato (including ultrasimplified 'DPANN' whose long branches often distort trees). Two-domain trees group eukaryotes within Planctobacteria, and archaebacteria with Planctobacteria/Sphingobacteria. Integrated molecular/palaeontological evidence favours negibacterial ancestors for neomura and all life. Unique presence of key pre-neomuran characters favours Planctobacteria only as ancestral to neomura, which apparently arose by coevolutionary repercussions (explained here in detail, including RP replacement) of simultaneous outer membrane and murein loss. Planctobacterial C-1 methanotrophic enzymes are likely ancestral to archaebacterial methanogenesis and β-propeller-α-solenoid proteins to eukaryotic vesicle coats, nuclear-pore-complexes, and intraciliary transport. Planctobacterial chaperone-independent 4/5-protofilament microtubules and MamK actin-ancestors prepared for eukaryote intracellular motility, mitosis, cytokinesis, and phagocytosis. We refute numerous wrong ideas about the universal tree.
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Affiliation(s)
| | - Ema E-Yung Chao
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
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34
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Cavalier-Smith T, Chao EEY. Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria). PROTOPLASMA 2020; 257:621-753. [PMID: 31900730 PMCID: PMC7203096 DOI: 10.1007/s00709-019-01442-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 09/19/2019] [Indexed: 05/02/2023]
Abstract
Palaeontologically, eubacteria are > 3× older than neomura (eukaryotes, archaebacteria). Cell biology contrasts ancestral eubacterial murein peptidoglycan walls and derived neomuran N-linked glycoprotein coats/walls. Misinterpreting long stems connecting clade neomura to eubacteria on ribosomal sequence trees (plus misinterpreted protein paralogue trees) obscured this historical pattern. Universal multiprotein ribosomal protein (RP) trees, more accurate than rRNA trees, are taxonomically undersampled. To reduce contradictions with genically richer eukaryote trees and improve eubacterial phylogeny, we constructed site-heterogeneous and maximum-likelihood universal three-domain, two-domain, and single-domain trees for 143 eukaryotes (branching now congruent with 187-protein trees), 60 archaebacteria, and 151 taxonomically representative eubacteria, using 51 and 26 RPs. Site-heterogeneous trees greatly improve eubacterial phylogeny and higher classification, e.g. showing gracilicute monophyly, that many 'rDNA-phyla' belong in Proteobacteria, and reveal robust new phyla Synthermota and Aquithermota. Monoderm Posibacteria and Mollicutes (two separate wall losses) are both polyphyletic: multiple outer membrane losses in Endobacteria occurred separately from Actinobacteria; neither phylum is related to Chloroflexi, the most divergent prokaryotes, which originated photosynthesis (new model proposed). RP trees support an eozoan root for eukaryotes and are consistent with archaebacteria being their sisters and rooted between Filarchaeota (=Proteoarchaeota, including 'Asgardia') and Euryarchaeota sensu-lato (including ultrasimplified 'DPANN' whose long branches often distort trees). Two-domain trees group eukaryotes within Planctobacteria, and archaebacteria with Planctobacteria/Sphingobacteria. Integrated molecular/palaeontological evidence favours negibacterial ancestors for neomura and all life. Unique presence of key pre-neomuran characters favours Planctobacteria only as ancestral to neomura, which apparently arose by coevolutionary repercussions (explained here in detail, including RP replacement) of simultaneous outer membrane and murein loss. Planctobacterial C-1 methanotrophic enzymes are likely ancestral to archaebacterial methanogenesis and β-propeller-α-solenoid proteins to eukaryotic vesicle coats, nuclear-pore-complexes, and intraciliary transport. Planctobacterial chaperone-independent 4/5-protofilament microtubules and MamK actin-ancestors prepared for eukaryote intracellular motility, mitosis, cytokinesis, and phagocytosis. We refute numerous wrong ideas about the universal tree.
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Affiliation(s)
| | - Ema E-Yung Chao
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
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Strašková A, Steinbach G, Konert G, Kotabová E, Komenda J, Tichý M, Kaňa R. Pigment-protein complexes are organized into stable microdomains in cyanobacterial thylakoids. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:148053. [PMID: 31344362 DOI: 10.1016/j.bbabio.2019.07.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 06/28/2019] [Accepted: 07/18/2019] [Indexed: 02/03/2023]
Abstract
Thylakoids are the place of the light-photosynthetic reactions. To gain maximal efficiency, these reactions are conditional to proper pigment-pigment and protein-protein interactions. In higher plants thylakoids, the interactions lead to a lateral asymmetry in localization of protein complexes (i.e. granal/stromal thylakoids) that have been defined as a domain-like structures characteristic by different biochemical composition and function (Albertsson P-Å. 2001,Trends Plant Science 6: 349-354). We explored this complex organization of thylakoid pigment-proteins at single cell level in the cyanobacterium Synechocystis sp. PCC 6803. Our 3D confocal images captured heterogeneous distribution of all main photosynthetic pigment-protein complexes (PPCs), Photosystem I (fluorescently tagged by YFP), Photosystem II and Phycobilisomes. The acquired images depicted cyanobacterial thylakoid membrane as a stable, mosaic-like structure formed by microdomains (MDs). These microcompartments are of sub-micrometer in sizes (~0.5-1.5 μm), typical by particular PPCs ratios and importantly without full segregation of observed complexes. The most prevailing MD is represented by MD with high Photosystem I content which allows also partial separation of Photosystems like in higher plants thylakoids. We assume that MDs stability (in minutes) provides optimal conditions for efficient excitation/electron transfer. The cyanobacterial MDs thus define thylakoid membrane organization as a system controlled by co-localization of three main PPCs leading to formation of thylakoid membrane mosaic. This organization might represent evolutional and functional precursor for the granal/stromal spatial heterogeneity in photosystems that is typical for higher plant thylakoids.
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Affiliation(s)
- A Strašková
- Institute of Microbiology, Czech Academy of Sciences, Centre Algatech, Novohradská 237, 379 81 Třeboň, Czech Republic
| | - G Steinbach
- Institute of Microbiology, Czech Academy of Sciences, Centre Algatech, Novohradská 237, 379 81 Třeboň, Czech Republic
| | - G Konert
- Institute of Microbiology, Czech Academy of Sciences, Centre Algatech, Novohradská 237, 379 81 Třeboň, Czech Republic
| | - E Kotabová
- Institute of Microbiology, Czech Academy of Sciences, Centre Algatech, Novohradská 237, 379 81 Třeboň, Czech Republic
| | - J Komenda
- Institute of Microbiology, Czech Academy of Sciences, Centre Algatech, Novohradská 237, 379 81 Třeboň, Czech Republic
| | - M Tichý
- Institute of Microbiology, Czech Academy of Sciences, Centre Algatech, Novohradská 237, 379 81 Třeboň, Czech Republic
| | - R Kaňa
- Institute of Microbiology, Czech Academy of Sciences, Centre Algatech, Novohradská 237, 379 81 Třeboň, Czech Republic.
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Herrmann AJ, Gehringer MM. An investigation into the effects of increasing salinity on photosynthesis in freshwater unicellular cyanobacteria during the late Archaean. GEOBIOLOGY 2019; 17:343-359. [PMID: 30874335 DOI: 10.1111/gbi.12339] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 02/04/2019] [Accepted: 02/10/2019] [Indexed: 06/09/2023]
Abstract
The oldest species of bacteria capable of oxygenic photosynthesis today are the freshwater Cyanobacteria Gloeobacter spp., belonging to the class Oxyphotobacteria. Several modern molecular evolutionary studies support the freshwater origin of cyanobacteria during the Archaean and their subsequent acquisition of salt tolerance mechanisms necessary for their expansion into the marine environment. This study investigated the effect of a sudden washout event from a freshwater location into either a brackish or marine environment on the photosynthetic efficiency of two unicellular freshwater cyanobacteria: the salt-tolerant Chroococcidiopsis thermalis PCC7203 and the cyanobacterial phylogenetic root species, Gloeobacter violaceus PCC7421. Strains were cultured under present atmospheric levels (PAL) of CO2 or an atmosphere containing elevated levels of CO2 and reduced O2 (eCO2 rO2 ) in simulated shallow water or terrestrial environmental conditions. Both strains exhibited a reduction in growth rates and gross photosynthesis, accompanied by significant reductions in chlorophyll a content, in brackish water, with only C. thermalis able to grow at marine salinity levels. While the experimental atmosphere caused a significant increase in gross photosynthesis rates in both strains, it did not increase their growth rates, nor the amount of O2 released. The differences in growth responses to increasing salinities could be attributed to genetic differences, with C. thermalis carrying additional genes for trehalose synthesis. This study demonstrates that, if cyanobacteria did evolve in a freshwater environment, they would have been capable of withstanding a sudden washout into increasingly saline environments. Both C. thermalis and G. violaceus continued to grow and photosynthesise, albeit at diminished rates, in brackish water, thereby providing a route for the evolution of open ocean-dwelling strains, necessary for the oxygenation of the Earth's atmosphere.
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Affiliation(s)
- Achim J Herrmann
- Department of Microbiology, Technical University of Kaiserslautern, Kaiserslautern, Germany
| | - Michelle M Gehringer
- Department of Microbiology, Technical University of Kaiserslautern, Kaiserslautern, Germany
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Mareš J, Johansen JR, Hauer T, Zima J, Ventura S, Cuzman O, Tiribilli B, Kaštovský J. Taxonomic resolution of the genus Cyanothece (Chroococcales, Cyanobacteria), with a treatment on Gloeothece and three new genera, Crocosphaera, Rippkaea, and Zehria. JOURNAL OF PHYCOLOGY 2019; 55:578-610. [PMID: 30830691 DOI: 10.1111/jpy.12853] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 12/06/2018] [Indexed: 06/09/2023]
Abstract
The systematics of single-celled cyanobacteria represents a major challenge due to morphological convergence and application of various taxonomic concepts. The genus Cyanothece is one of the most problematic cases, as the name has been applied to oval-shaped coccoid cyanobacteria lacking sheaths with little regard to their phylogenetic position and details of morphology and ultrastructure. Hereby we analyze an extensive set of complementary genetic and phenotypic evidence to disentangle the relationships among these cyanobacteria. We provide diagnostic characters to separate the known genera Cyanothece, Gloeothece, and Aphanothece, and provide a valid description for Crocosphaera gen. nov. We describe two new genera, Rippkaea and Zehria, to characterize two distinct phylogenetic lineages outside the previously known genera. We further describe 13 new species in total including Cyanothece svehlovae, Gloeothece aequatorialis, G. aurea, G. bryophila, G. citriformis, G. reniformis, Gloeothece tonkinensis, G. verrucosa, Crocosphaera watsonii, C. subtropica, C. chwakensis, Rippkaea orientalis, and Zehria floridana to recognize the intrageneric diversity as rendered by polyphasic analysis. We discuss the close relationship of free-living cyanobacteria from the Crocosphaera lineage to nitrogen-fixing endosymbionts of marine algae. The current study includes several experimental strains (Crocosphaera and "Cyanothece") important for the study of diazotrophy and the global oceanic nitrogen cycle, and provides evidence suggesting ancestral N2 -fixing capability in the chroococcalean lineage.
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Affiliation(s)
- Jan Mareš
- Institute of Hydrobiology, Biology Centre, The Czech Academy of Sciences, Na Sádkách 7, CZ-37005, České Budějovice, Czech Republic
- Department of Botany, University of South Bohemia, Faculty of Science, Branišovská 1760, CZ-37005, České Budějovice, Czech Republic
| | - Jeffrey R Johansen
- Department of Botany, University of South Bohemia, Faculty of Science, Branišovská 1760, CZ-37005, České Budějovice, Czech Republic
- John Carroll University, Department of Biology, University Heights, Ohio, 44118, USA
| | - Tomáš Hauer
- Department of Botany, University of South Bohemia, Faculty of Science, Branišovská 1760, CZ-37005, České Budějovice, Czech Republic
- Institute of Botany, Academy of Sciences of the Czech Republic, Dukelská 135, CZ-37982, Třeboň, Czech Republic
| | - Jan Zima
- Institute of Botany, Academy of Sciences of the Czech Republic, Dukelská 135, CZ-37982, Třeboň, Czech Republic
- Department of Parasitology, Faculty of Science, University of South Bohemia, Branišovská 1760, CZ-37005, České Budějovice
| | - Stefano Ventura
- Firenze Unit, Institute of Ecosystem Study, National Research Council of Italy, via Madonna del Piano 10, I-500 19, Sesto Fiorentino, Italy
| | - Oana Cuzman
- Institute for the Conservation and Valorization of Cultural Heritage, National Research Council of Italy, via Madonna del Piano 10, I-500 19, Sesto Fiorentino, Italy
| | - Bruno Tiribilli
- Firenze Unit, Institute for Complex Systems, National Research Council of Italy, via Madonna del Piano 10, I-500 19, Sesto Fiorentino, Italy
| | - Jan Kaštovský
- Department of Botany, University of South Bohemia, Faculty of Science, Branišovská 1760, CZ-37005, České Budějovice, Czech Republic
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Mareš J, Strunecký O, Bučinská L, Wiedermannová J. Evolutionary Patterns of Thylakoid Architecture in Cyanobacteria. Front Microbiol 2019; 10:277. [PMID: 30853950 PMCID: PMC6395441 DOI: 10.3389/fmicb.2019.00277] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 02/01/2019] [Indexed: 01/28/2023] Open
Abstract
While photosynthetic processes have become increasingly understood in cyanobacterial model strains, differences in the spatial distribution of thylakoid membranes among various lineages have been largely unexplored. Cyanobacterial cells exhibit an intriguing diversity in thylakoid arrangements, ranging from simple parietal to radial, coiled, parallel, and special types. Although metabolic background of their variability remains unknown, it has been suggested that thylakoid patterns are stable in certain phylogenetic clades. For decades, thylakoid arrangements have been used in cyanobacterial classification as one of the crucial characters for definition of taxa. The last comprehensive study addressing their evolutionary history in cyanobacteria was published 15 years ago. Since then both DNA sequence and electron microscopy data have grown rapidly. In the current study, we map ultrastructural data of >200 strains onto the SSU rRNA gene tree, and the resulting phylogeny is compared to a phylogenomic tree. Changes in thylakoid architecture in general follow the phylogeny of housekeeping loci. Parietal arrangement is resolved as the original thylakoid organization, evolving into complex arrangement in the most derived group of heterocytous cyanobacteria. Cyanobacteria occupying intermediate phylogenetic positions (greater filamentous, coccoid, and baeocytous types) exhibit fascicular, radial, and parallel arrangements, partly tracing the reconstructed course of phylogenetic branching. Contrary to previous studies, taxonomic value of thylakoid morphology seems very limited. Only special cases such as thylakoid absence or the parallel arrangement could be used as taxonomically informative apomorphies. The phylogenetic trees provide evidence of both paraphyly and reversion from more derived architectures in the simple parietal thylakoid pattern. Repeated convergent evolution is suggested for the radial and fascicular architectures. Moreover, thylakoid arrangement is constrained by cell size, excluding the occurrence of complex architectures in cyanobacteria smaller than 2 μm in width. It may further be dependent on unknown (eco)physiological factors as suggested by recurrence of the radial type in unrelated but morphologically similar cyanobacteria, and occurrence of special features throughout the phylogeny. No straightforward phylogenetic congruences have been found between proteins involved in photosynthesis and thylakoid formation, and the thylakoid patterns. Remarkably, several postulated thylakoid biogenesis factors are partly or completely missing in cyanobacteria, challenging their proposed essential roles.
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Affiliation(s)
- Jan Mareš
- Center Algatech, Institute of Microbiology, Czech Academy of Sciences, Třeboň, Czechia
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia
- Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Otakar Strunecký
- Faculty of Science, University of South Bohemia, České Budějovice, Czechia
- Institute of Aquaculture, Faculty of Fisheries and Protection of Waters, University of South Bohemia, České Budějovice, Czechia
| | - Lenka Bučinská
- Center Algatech, Institute of Microbiology, Czech Academy of Sciences, Třeboň, Czechia
- Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Jana Wiedermannová
- Laboratory of Molecular Genetics of Bacteria, Institute of Microbiology, Czech Academy of Sciences, Prague, Czechia
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Radioprotective role of cyanobacterial phycobilisomes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1860:121-128. [PMID: 30465750 DOI: 10.1016/j.bbabio.2018.11.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 11/07/2018] [Accepted: 11/18/2018] [Indexed: 11/20/2022]
Abstract
Cyanobacteria are thought to be responsible for pioneering dioxygen production and the so-called "Great Oxygenation Event" that determined the formation of the ozone layer and the ionosphere restricting ionizing radiation levels reaching our planet, which increased biological diversity but also abolished the necessity of radioprotection. We speculated that ancient protection mechanisms could still be present in cyanobacteria and studied the effect of ionizing radiation and space flight during the Foton-M4 mission on Synechocystis sp. PCC6803. Spectral and functional characteristics of photosynthetic membranes revealed numerous similarities of the effects of α-particles and space flight, which both interrupted excitation energy transfer from phycobilisomes to the photosystems and significantly reduced the concentration of phycobiliproteins. Although photosynthetic activity was severely suppressed, the effect was reversible, and the cells could rapidly recover from the stress. We suggest that the actual existence and the uncoupling of phycobilisomes may play a specific role not only in photo-, but also in radioprotection, which could be crucial for the early evolution of Life on Earth.
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Strunecký O, Kopejtka K, Goecke F, Tomasch J, Lukavský J, Neori A, Kahl S, Pieper DH, Pilarski P, Kaftan D, Koblížek M. High diversity of thermophilic cyanobacteria in Rupite hot spring identified by microscopy, cultivation, single-cell PCR and amplicon sequencing. Extremophiles 2018; 23:35-48. [PMID: 30284641 DOI: 10.1007/s00792-018-1058-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 09/24/2018] [Indexed: 10/28/2022]
Abstract
Genotypic and morphological diversity of cyanobacteria in the Rupite hot spring (Bulgaria) was investigated by means of optical microscopy, cultivation, single-cell PCR, and 16S rRNA gene amplicon sequencing. Altogether, 34 sites were investigated along the 71-39 °C temperature gradient. Analysis of samples from eight representative sites shown that Illumina, optical microscopy, and Roche 454 identified 72, 45 and 19% respective occurrences of all cumulatively present taxa. Optical microscopy failed to detect species of minor occurrence; whereas, amplicon sequencing technologies suffered from failed primer annealing and the presence of species with extensive extracellular polysaccharides production. Amplicon sequencing of the 16S rRNA gene V5-V6 region performed by Illumina identified the cyanobacteria most reliably to the generic level. Nevertheless, only the combined use of optical microscopy, cultivation and sequencing methods allowed for reliable estimate of the cyanobacterial diversity. Here, we show that Rupite hot-spring system hosts one of the richest cyanobacterial flora reported from a single site above 50 °C. Chlorogloeopsis sp. was the most abundant at the highest temperature (68 °C), followed by Leptolyngbya boryana, Thermoleptolyngbya albertanoae, Synechococcus bigranulatus, Oculatella sp., and Desertifilum sp. thriving above 60 °C, while Leptolyngbya geysericola, Geitlerinema splendidum, and Cyanobacterium aponinum were found above 50 °C.
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Affiliation(s)
- Otakar Strunecký
- Institute of Aquaculture, CENAKVA, Faculty of Fisheries and Protection of Waters, University of South Bohemia, 37005, České Budějovice, Czech Republic. .,Faculty of Science, University of South Bohemia, 37005, České Budějovice, Czech Republic.
| | - Karel Kopejtka
- Center Algatech, Institute of Microbiology CAS, 37981, Třeboň, Czech Republic
| | - Franz Goecke
- Center Algatech, Institute of Microbiology CAS, 37981, Třeboň, Czech Republic.,Department of Plant and Environmental Science, Norwegian University of Life Sciences, 1432, Ås, Norway
| | - Jürgen Tomasch
- Group Microbial Communication, Helmholtz Centre for Infection Research, 38124, Brunswick, Germany
| | - Jaromír Lukavský
- Department of Plant Ecology, Institute of Botany CAS, 37901, Třeboň, Czech Republic
| | - Amir Neori
- Israel Oceanographic and Limnological Research Ltd., National Center for Mariculture, 88112, Eilat, Israel
| | - Silke Kahl
- Group Microbial Interactions and Processes, Helmholtz Centre for Infection Research, 38124, Brunswick, Germany
| | - Dietmar H Pieper
- Group Microbial Interactions and Processes, Helmholtz Centre for Infection Research, 38124, Brunswick, Germany
| | - Plamen Pilarski
- Institute of Plant Physiology and Genetics BAS, 1113, Sofia, Bulgaria
| | - David Kaftan
- Center Algatech, Institute of Microbiology CAS, 37981, Třeboň, Czech Republic.,Faculty of Science, University of South Bohemia, 37005, České Budějovice, Czech Republic
| | - Michal Koblížek
- Center Algatech, Institute of Microbiology CAS, 37981, Třeboň, Czech Republic
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Sluchanko NN, Slonimskiy YB, Maksimov EG. Features of Protein-Protein Interactions in the Cyanobacterial Photoprotection Mechanism. BIOCHEMISTRY (MOSCOW) 2018. [PMID: 29523061 DOI: 10.1134/s000629791713003x] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Photoprotective mechanisms of cyanobacteria are characterized by several features associated with the structure of their water-soluble antenna complexes - the phycobilisomes (PBs). During energy transfer from PBs to chlorophyll of photosystem reaction centers, the "energy funnel" principle is realized, which regulates energy flux due to the specialized interaction of the PBs core with a quenching molecule capable of effectively dissipating electron excitation energy into heat. The role of the quencher is performed by ketocarotenoid within the photoactive orange carotenoid protein (OCP), which is also a sensor for light flux. At a high level of insolation, OCP is reversibly photoactivated, and this is accompanied by a significant change in its structure and spectral characteristics. Such conformational changes open the possibility for protein-protein interactions between OCP and the PBs core (i.e., activation of photoprotection mechanisms) or the fluorescence recovery protein. Even though OCP was discovered in 1981, little was known about the conformation of its active form until recently, as well as about the properties of homologs of its N and C domains. Studies carried out during recent years have made a breakthrough in understanding of the structural-functional organization of OCP and have enabled discovery of new aspects of the regulation of photoprotection processes in cyanobacteria. This review focuses on aspects of protein-protein interactions between the main participants of photoprotection reactions and on certain properties of representatives of newly discovered families of OCP homologs.
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Affiliation(s)
- N N Sluchanko
- Bach Institute of Biochemistry, Federal Research Center "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, 119071, Russia.
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Raven JA, Beardall J, Sánchez-Baracaldo P. The possible evolution and future of CO2-concentrating mechanisms. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:3701-3716. [PMID: 28505361 DOI: 10.1093/jxb/erx110] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
CO2-concentrating mechanisms (CCMs), based either on active transport of inorganic carbon (biophysical CCMs) or on biochemistry involving supplementary carbon fixation into C4 acids (C4 and CAM), play a major role in global primary productivity. However, the ubiquitous CO2-fixing enzyme in autotrophs, Rubisco, evolved at a time when atmospheric CO2 levels were very much higher than today and O2 was very low and, as CO2 and O2 approached (by no means monotonically), today's levels, at some time subsequently many organisms evolved a CCM that increased the supply of CO2 and decreased Rubisco oxygenase activity. Given that CO2 levels and other environmental factors have altered considerably between when autotrophs evolved and the present day, and are predicted to continue to change into the future, we here examine the drivers for, and possible timing of, evolution of CCMs. CCMs probably evolved when CO2 fell to 2-16 times the present atmospheric level, depending on Rubisco kinetics. We also assess the effects of other key environmental factors such as temperature and nutrient levels on CCM activity and examine the evidence for evolutionary changes in CCM activity and related cellular processes as well as limitations on continuity of CCMs through environmental variations.
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Affiliation(s)
- John A Raven
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
- Functional Plant Biology and Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - John Beardall
- School of Biological Sciences, Monash University, Building 18, Clayton Campus, Vic 3800, Australia
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Voráčová K, Hájek J, Mareš J, Urajová P, Kuzma M, Cheel J, Villunger A, Kapuscik A, Bally M, Novák P, Kabeláč M, Krumschnabel G, Lukeš M, Voloshko L, Kopecký J, Hrouzek P. The cyanobacterial metabolite nocuolin a is a natural oxadiazine that triggers apoptosis in human cancer cells. PLoS One 2017; 12:e0172850. [PMID: 28253280 PMCID: PMC5333925 DOI: 10.1371/journal.pone.0172850] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 02/11/2017] [Indexed: 12/22/2022] Open
Abstract
Oxadiazines are heterocyclic compounds containing N-N-O or N-N-C-O system within a six membered ring. These structures have been up to now exclusively prepared via organic synthesis. Here, we report the discovery of a natural oxadiazine nocuolin A (NoA) that has a unique structure based on 1,2,3-oxadiazine. We have identified this compound in three independent cyanobacterial strains of genera Nostoc, Nodularia, and Anabaena and recognized the putative gene clusters for NoA biosynthesis in their genomes. Its structure was characterized using a combination of NMR, HRMS and FTIR methods. The compound was first isolated as a positive hit during screening for apoptotic inducers in crude cyanobacterial extracts. We demonstrated that NoA-induced cell death has attributes of caspase-dependent apoptosis. Moreover, NoA exhibits a potent anti-proliferative activity (0.7-4.5 μM) against several human cancer lines, with p53-mutated cell lines being even more sensitive. Since cancers bearing p53 mutations are resistant to several conventional anti-cancer drugs, NoA may offer a new scaffold for the development of drugs that have the potential to target tumor cells independent of their p53 status. As no analogous type of compound was previously described in the nature, NoA establishes a novel class of bioactive secondary metabolites.
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Affiliation(s)
- Kateřina Voráčová
- Centre Algatech, Institute of Microbiology, The Czech Academy of Sciences (CAS) v.v.i., Třeboň, Czech Republic
- University of South Bohemia, Faculty of Science, České Budějovice, Czech Republic
| | - Jan Hájek
- Centre Algatech, Institute of Microbiology, The Czech Academy of Sciences (CAS) v.v.i., Třeboň, Czech Republic
- University of South Bohemia, Faculty of Science, České Budějovice, Czech Republic
- Biology Centre (CAS) v.v.i., Institute of Hydrobiology, České Budějovice, Czech Republic
| | - Jan Mareš
- Centre Algatech, Institute of Microbiology, The Czech Academy of Sciences (CAS) v.v.i., Třeboň, Czech Republic
- University of South Bohemia, Faculty of Science, České Budějovice, Czech Republic
- Biology Centre (CAS) v.v.i., Institute of Hydrobiology, České Budějovice, Czech Republic
- Centre for Phycology, Institute of Botany (CAS) v.v.i., Czech Republic
| | - Petra Urajová
- Centre Algatech, Institute of Microbiology, The Czech Academy of Sciences (CAS) v.v.i., Třeboň, Czech Republic
| | - Marek Kuzma
- Laboratory of Molecular Structure Characterization, Institute of Microbiology (CAS), Prague, Czech Republic
| | - José Cheel
- Centre Algatech, Institute of Microbiology, The Czech Academy of Sciences (CAS) v.v.i., Třeboň, Czech Republic
| | - Andreas Villunger
- Medical University Innsbruck, Division of Developmental Immunology, Biocenter Innsbruck, Innsbruck, Austria
- Tyrolean Cancer Research Institute, Innsbruck, Austria
| | - Alexandra Kapuscik
- Centre Algatech, Institute of Microbiology, The Czech Academy of Sciences (CAS) v.v.i., Třeboň, Czech Republic
| | - Marcel Bally
- British Columbia Cancer Agency, Department of Experimental Therapeutics, Vancouver, BC Canada
| | - Petr Novák
- Laboratory of Molecular Structure Characterization, Institute of Microbiology (CAS), Prague, Czech Republic
| | - Martin Kabeláč
- University of South Bohemia, Faculty of Science, České Budějovice, Czech Republic
| | - Gerhard Krumschnabel
- Medical University Innsbruck, Division of Developmental Immunology, Biocenter Innsbruck, Innsbruck, Austria
| | - Martin Lukeš
- Centre Algatech, Institute of Microbiology, The Czech Academy of Sciences (CAS) v.v.i., Třeboň, Czech Republic
| | | | - Jiří Kopecký
- Centre Algatech, Institute of Microbiology, The Czech Academy of Sciences (CAS) v.v.i., Třeboň, Czech Republic
| | - Pavel Hrouzek
- Centre Algatech, Institute of Microbiology, The Czech Academy of Sciences (CAS) v.v.i., Třeboň, Czech Republic
- University of South Bohemia, Faculty of Science, České Budějovice, Czech Republic
- * E-mail:
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The current status of cyanobacterial nomenclature under the "prokaryotic" and the "botanical" code. Antonie Van Leeuwenhoek 2017; 110:1257-1269. [PMID: 28243951 DOI: 10.1007/s10482-017-0848-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 02/21/2017] [Indexed: 10/20/2022]
Abstract
Cyanobacterial taxonomy developed in the botanical world because Cyanobacteria/Cyanophyta have traditionally been identified as algae. However, they possess a prokaryotic cell structure, and phylogenetically they belong to the Bacteria. This caused nomenclature problems as the provisions of the International Code of Nomenclature for algae, fungi, and plants (ICN; the "Botanical Code") differ from those of the International Code of Nomenclature of Prokaryotes (ICNP; the "Prokaryotic Code"). While the ICN recognises names validly published under the ICNP, Article 45(1) of the ICN has not yet been reciprocated in the ICNP. Different solutions have been proposed to solve the current problems. In 2012 a Special Committee on the harmonisation of the nomenclature of Cyanobacteria was appointed, but its activity has been minimal. Two opposing proposals to regulate cyanobacterial nomenclature were recently submitted, one calling for deletion of the cyanobacteria from the groups of organisms whose nomenclature is regulated by the ICNP, the second to consistently apply the rules of the ICNP to all cyanobacteria. Following a general overview of the current status of cyanobacterial nomenclature under the two codes we present five case studies of genera for which nomenclatural aspects have been discussed in recent years: Microcystis, Planktothrix, Halothece, Gloeobacter and Nostoc.
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Genome-wide comparative analysis of codon usage bias and codon context patterns among cyanobacterial genomes. Mar Genomics 2016; 32:31-39. [PMID: 27733306 DOI: 10.1016/j.margen.2016.10.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 09/11/2016] [Accepted: 10/03/2016] [Indexed: 11/20/2022]
Abstract
With the increasing accumulation of genomic sequence information of prokaryotes, the study of codon usage bias has gained renewed attention. The purpose of this study was to examine codon selection pattern within and across cyanobacterial species belonging to diverse taxonomic orders and habitats. We performed detailed comparative analysis of cyanobacterial genomes with respect to codon bias. Our analysis reflects that in cyanobacterial genomes, A- and/or T-ending codons were used predominantly in the genes whereas G- and/or C-ending codons were largely avoided. Variation in the codon context usage of cyanobacterial genes corresponded to the clustering of cyanobacteria as per their GC content. Analysis of codon adaptation index (CAI) and synonymous codon usage order (SCUO) revealed that majority of genes are associated with low codon bias. Codon selection pattern in cyanobacterial genomes reflected compositional constraints as major influencing factor. It is also identified that although, mutational constraint may play some role in affecting codon usage bias in cyanobacteria, compositional constraint in terms of genomic GC composition coupled with environmental factors affected codon selection pattern in cyanobacterial genomes.
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Williams L, Loewen-Schneider K, Maier S, Büdel B. Cyanobacterial diversity of western European biological soil crusts along a latitudinal gradient. FEMS Microbiol Ecol 2016; 92:fiw157. [PMID: 27411981 PMCID: PMC4970567 DOI: 10.1093/femsec/fiw157] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2016] [Indexed: 01/26/2023] Open
Abstract
Cyanobacteria associated with biological soil crusts (BSCs) have important attributes, such as nitrogen fixation and soil stabilisation. However, research on these organisms has been minimal, and their diversity and distribution throughout temperate Europe is currently unknown. The SCIN (Soil Crust International) project is a multidisciplinary research initiative that aims to achieve improved understanding of the BSCs of Europe, one facet being an investigation into the cyanobacterial communities of BSCs across a latitudinal gradient. Cyanobacteria assemblages were analysed by both morphological and molecular analysis. Two treatments were applied prior to DNA extraction, continued sample wetting and a dry sample process, and 16S ribosomal RNA (rRNA) amplicons were processed by Illumina MiSeq sequencing. The results reveal high and variable cyanobacterial diversity with each site showing a unique assemblage. Many common cyanobacterial genera, for example Nostoc and Microcoleus, were found in all sites but the abundances of different genera varied considerably. The polyphasic approach was found to be essential in recording the presence of important cyanobacteria that a single method itself did not highlight. The wet and dry treatments showed some differences in diversity, but mainly in abundance, this may suggest how cyanobacterial composition of BSCs changes with seasonal variability. Investigating the diversity and community composition of cyanobacteria associated with biological soil crusts in climatically different regions of Europe.
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Affiliation(s)
- Laura Williams
- Plant Ecology and Systematics, Biology Institute, University of Kaiserslautern, PO Box 3049, 67653 Kaiserslautern, Germany
| | - Katharina Loewen-Schneider
- Plant Ecology and Systematics, Biology Institute, University of Kaiserslautern, PO Box 3049, 67653 Kaiserslautern, Germany
| | - Stefanie Maier
- Institute of Plant Sciences, University of Graz, 8010 Graz, Austria
| | - Burkhard Büdel
- Plant Ecology and Systematics, Biology Institute, University of Kaiserslautern, PO Box 3049, 67653 Kaiserslautern, Germany
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Bohunická M, Mareš J, Hrouzek P, Urajová P, Lukeš M, Šmarda J, Komárek J, Gaysina LA, Strunecký O. A combined morphological, ultrastructural, molecular, and biochemical study of the peculiar family Gomontiellaceae (Oscillatoriales) reveals a new cylindrospermopsin-producing clade of cyanobacteria. JOURNAL OF PHYCOLOGY 2015; 51:1040-54. [PMID: 26987000 DOI: 10.1111/jpy.12354] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Accepted: 09/12/2015] [Indexed: 05/11/2023]
Abstract
Members of the morphologically unusual cyanobacterial family Gomontiellaceae were studied using a polyphasic approach. Cultured strains of Hormoscilla pringsheimii, Starria zimbabweënsis, Crinalium magnum, and Crinalium epipsammum were thoroughly examined, and the type specimen of the family, Gomontiella subtubulosa, was investigated. The results of morphological observations using both light microscopy and transmission electron microscopy were consistent with previous reports and provided evidence for the unique morphological and ultrastructural traits of this family. Analysis of the 16S rRNA gene confirmed the monophyletic origin of non-marine repre-sentatives of genera traditionally classified into this family. The family was phylogenetically placed among other groups of filamentous cyanobacterial taxa. The presence of cellulose in the cell wall was analyzed and confirmed in all cultured Gomontiellaceae members using Fourier transform infrared spectroscopy and fluorescence microscopy. Evaluation of toxins produced by the studied strains revealed the hepatotoxin cylindrospermopsin (CYN) in available strains of the genus Hormoscilla. Production of this compound in both Hormoscilla strains was detected using high-performance liquid chromatography in tandem with high resolution mass spectrometry and confirmed by positive PCR amplification of the cyrJ gene from the CYN biosynthetic cluster. To our knowledge, this is the first report of CYN production by soil cyanobacteria, establishing a previously unreported CYN-producing lineage. This study indicates that cyanobacteria of the family Gomontiellaceae form a separate but coherent cluster defined by numerous intriguing morphological, ultrastructural, and biochemical features, and exhibiting a toxic potential worthy of further investigation.
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Affiliation(s)
- Markéta Bohunická
- Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice, CZ-370 05, Czech Republic
- Centre for Phycology, Institute of Botany of the CAS, v.v.i., Dukelská 135, Třeboň, CZ-379 82, Czech Republic
| | - Jan Mareš
- Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice, CZ-370 05, Czech Republic
- Centre for Phycology, Institute of Botany of the CAS, v.v.i., Dukelská 135, Třeboň, CZ-379 82, Czech Republic
- Institute of Hydrobiology, Biology Centre of the CAS, v.v.i., Na Sádkách 7, České Budějovice, CZ-370 05, Czech Republic
| | - Pavel Hrouzek
- Center Algatech, Institute of Microbiology of the CAS, v.v.i., Opatovický mlýn, Třeboň, CZ-379 81, Czech Republic
| | - Petra Urajová
- Center Algatech, Institute of Microbiology of the CAS, v.v.i., Opatovický mlýn, Třeboň, CZ-379 81, Czech Republic
| | - Martin Lukeš
- Center Algatech, Institute of Microbiology of the CAS, v.v.i., Opatovický mlýn, Třeboň, CZ-379 81, Czech Republic
| | - Jan Šmarda
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Brno-Bohunice, CZ-625 00, Czech Republic
| | - Jiří Komárek
- Centre for Phycology, Institute of Botany of the CAS, v.v.i., Dukelská 135, Třeboň, CZ-379 82, Czech Republic
| | - Lira A Gaysina
- Department of Bioecology and Biological Education, M. Akmullah Bashkir State Pedagogical University, 450000 Ufa, Okt'yabrskoi revolucii 3a, Republic of Bashkortostan, Russian Federation
| | - Otakar Strunecký
- Centre for Phycology, Institute of Botany of the CAS, v.v.i., Dukelská 135, Třeboň, CZ-379 82, Czech Republic
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Steinbach G, Schubert F, Kaňa R. Cryo-imaging of photosystems and phycobilisomes in Anabaena sp. PCC 7120 cells. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2015; 152:395-9. [DOI: 10.1016/j.jphotobiol.2015.10.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 10/02/2015] [Accepted: 10/05/2015] [Indexed: 01/03/2023]
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50
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Chrismas NAM, Anesio AM, Sánchez-Baracaldo P. Multiple adaptations to polar and alpine environments within cyanobacteria: a phylogenomic and Bayesian approach. Front Microbiol 2015; 6:1070. [PMID: 26528250 PMCID: PMC4602134 DOI: 10.3389/fmicb.2015.01070] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 09/17/2015] [Indexed: 01/15/2023] Open
Abstract
Cyanobacteria are major primary producers in the polar and alpine regions contributing significantly to nitrogen and carbon cycles in the cryosphere. Recent advancements in environmental sequencing techniques have revealed great molecular diversity of microorganisms in cold environments. However, there are no comprehensive phylogenetic analyses including the entire known diversity of cyanobacteria from these extreme environments. We present here a global phylogenetic analysis of cyanobacteria including an extensive dataset comprised of available small subunit (SSU) rRNA gene sequences of cyanobacteria from polar and high altitude environments. Furthermore, we used a large-scale multi-gene (135 proteins and 2 ribosomal RNAs) genome constraint including 57 cyanobacterial genomes. Our analyses produced the first phylogeny of cold cyanobacteria exhibiting robust deep branching relationships implementing a phylogenomic approach. We recovered several clades common to Arctic, Antarctic and alpine sites suggesting that the traits necessary for survival in the cold have been acquired by a range of different mechanisms in all major cyanobacteria lineages. Bayesian ancestral state reconstruction revealed that 20 clades each have common ancestors with high probabilities of being capable of surviving in cold environments.
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Affiliation(s)
- Nathan A M Chrismas
- Bristol Glaciology Centre, School of Geographical Sciences, University of Bristol Bristol, UK
| | - Alexandre M Anesio
- Bristol Glaciology Centre, School of Geographical Sciences, University of Bristol Bristol, UK
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