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Panwar P, Allen MA, Williams TJ, Haque S, Brazendale S, Hancock AM, Paez-Espino D, Cavicchioli R. Remarkably coherent population structure for a dominant Antarctic Chlorobium species. Microbiome 2021; 9:231. [PMID: 34823595 PMCID: PMC8620254 DOI: 10.1186/s40168-021-01173-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 10/09/2021] [Indexed: 05/22/2023]
Abstract
BACKGROUND In Antarctica, summer sunlight enables phototrophic microorganisms to drive primary production, thereby "feeding" ecosystems to enable their persistence through the long, dark winter months. In Ace Lake, a stratified marine-derived system in the Vestfold Hills of East Antarctica, a Chlorobium species of green sulphur bacteria (GSB) is the dominant phototroph, although its seasonal abundance changes more than 100-fold. Here, we analysed 413 Gb of Antarctic metagenome data including 59 Chlorobium metagenome-assembled genomes (MAGs) from Ace Lake and nearby stratified marine basins to determine how genome variation and population structure across a 7-year period impacted ecosystem function. RESULTS A single species, Candidatus Chlorobium antarcticum (most similar to Chlorobium phaeovibrioides DSM265) prevails in all three aquatic systems and harbours very little genomic variation (≥ 99% average nucleotide identity). A notable feature of variation that did exist related to the genomic capacity to biosynthesize cobalamin. The abundance of phylotypes with this capacity changed seasonally ~ 2-fold, consistent with the population balancing the value of a bolstered photosynthetic capacity in summer against an energetic cost in winter. The very high GSB concentration (> 108 cells ml-1 in Ace Lake) and seasonal cycle of cell lysis likely make Ca. Chlorobium antarcticum a major provider of cobalamin to the food web. Analysis of Ca. Chlorobium antarcticum viruses revealed the species to be infected by generalist (rather than specialist) viruses with a broad host range (e.g., infecting Gammaproteobacteria) that were present in diverse Antarctic lakes. The marked seasonal decrease in Ca. Chlorobium antarcticum abundance may restrict specialist viruses from establishing effective lifecycles, whereas generalist viruses may augment their proliferation using other hosts. CONCLUSION The factors shaping Antarctic microbial communities are gradually being defined. In addition to the cold, the annual variation in sunlight hours dictates which phototrophic species can grow and the extent to which they contribute to ecosystem processes. The Chlorobium population studied was inferred to provide cobalamin, in addition to carbon, nitrogen, hydrogen, and sulphur cycling, as critical ecosystem services. The specific Antarctic environmental factors and major ecosystem benefits afforded by this GSB likely explain why such a coherent population structure has developed in this Chlorobium species. Video abstract.
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Affiliation(s)
- Pratibha Panwar
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
| | - Michelle A Allen
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
| | - Timothy J Williams
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
| | - Sabrina Haque
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
- Present address: Department of Molecular Sciences, Macquarie University, Sydney, New South Wales, 2109, Australia
| | - Sarah Brazendale
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
- , Present address: Pegarah, Australia
| | - Alyce M Hancock
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
- Present address: Institute for Marine and Antarctic Studies, University of Tasmania, 20 Castray Esplanade, Battery Point, Tasmania, Australia
| | - David Paez-Espino
- Department of Energy Joint Genome Institute, Berkeley, CA, USA
- Present address: Mammoth Biosciences, Inc., 1000 Marina Blvd. Suite 600, Brisbane, CA, USA
| | - Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia.
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2
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Zimmermann M, Escrig S, Lavik G, Kuypers MMM, Meibom A, Ackermann M, Schreiber F. Substrate and electron donor limitation induce phenotypic heterogeneity in different metabolic activities in a green sulphur bacterium. Environ Microbiol Rep 2018; 10:179-183. [PMID: 29393582 DOI: 10.1111/1758-2229.12616] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 10/13/2017] [Accepted: 01/14/2018] [Indexed: 06/07/2023]
Abstract
Populations of genetically identical cells can display marked variation in phenotypic traits; such variation is termed phenotypic heterogeneity. Here, we investigate the effect of substrate and electron donor limitation on phenotypic heterogeneity in N2 and CO2 fixation in the green sulphur bacterium Chlorobium phaeobacteroides. We grew populations in chemostats and batch cultures and used stable isotope labelling combined with nanometer-scale secondary ion mass spectrometry (NanoSIMS) to quantify phenotypic heterogeneity. Experiments in H2 S (i.e. electron donor) limited chemostats show that varying levels of NH4+ limitation induce heterogeneity in N2 fixation. Comparison of phenotypic heterogeneity between chemostats and batch (unlimited for H2 S) populations indicates that electron donor limitation drives heterogeneity in N2 and CO2 fixation. Our results demonstrate that phenotypic heterogeneity in a certain metabolic activity can be driven by different modes of limitation and that heterogeneity can emerge in different metabolic processes upon the same mode of limitation. In conclusion, our data suggest that limitation is a general driver of phenotypic heterogeneity in microbial populations.
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Affiliation(s)
- M Zimmermann
- Department of Environmental Systems Science, ETH Zurich - Swiss Federal Institute of Technology, Zurich, Switzerland
- Department of Environmental Microbiology, Eawag - Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - S Escrig
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - G Lavik
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - M M M Kuypers
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - A Meibom
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Center for Advanced Surface Analysis, Institute of Earth Sciences, University of Lausanne, Lausanne, Switzerland
| | - M Ackermann
- Department of Environmental Systems Science, ETH Zurich - Swiss Federal Institute of Technology, Zurich, Switzerland
- Department of Environmental Microbiology, Eawag - Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - F Schreiber
- Department of Environmental Systems Science, ETH Zurich - Swiss Federal Institute of Technology, Zurich, Switzerland
- Department of Environmental Microbiology, Eawag - Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Division Biodeterioration and Reference Organisms, Department of Materials and Environment, Federal Institute for Materials Research and Testing (BAM), Berlin, Germany
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3
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Deyaert E, Wauters L, Guaitoli G, Konijnenberg A, Leemans M, Terheyden S, Petrovic A, Gallardo R, Nederveen-Schippers LM, Athanasopoulos PS, Pots H, Van Haastert PJM, Sobott F, Gloeckner CJ, Efremov R, Kortholt A, Versées W. A homologue of the Parkinson's disease-associated protein LRRK2 undergoes a monomer-dimer transition during GTP turnover. Nat Commun 2017; 8:1008. [PMID: 29044096 PMCID: PMC5714945 DOI: 10.1038/s41467-017-01103-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 08/18/2017] [Indexed: 11/24/2022] Open
Abstract
Mutations in LRRK2 are a common cause of genetic Parkinson's disease (PD). LRRK2 is a multi-domain Roco protein, harbouring kinase and GTPase activity. In analogy with a bacterial homologue, LRRK2 was proposed to act as a GTPase activated by dimerization (GAD), while recent reports suggest LRRK2 to exist under a monomeric and dimeric form in vivo. It is however unknown how LRRK2 oligomerization is regulated. Here, we show that oligomerization of a homologous bacterial Roco protein depends on the nucleotide load. The protein is mainly dimeric in the nucleotide-free and GDP-bound states, while it forms monomers upon GTP binding, leading to a monomer-dimer cycle during GTP hydrolysis. An analogue of a PD-associated mutation stabilizes the dimer and decreases the GTPase activity. This work thus provides insights into the conformational cycle of Roco proteins and suggests a link between oligomerization and disease-associated mutations in LRRK2.
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Affiliation(s)
- Egon Deyaert
- VIB-VUB Center for Structural Biology, Pleinlaan 2, 1050, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Lina Wauters
- VIB-VUB Center for Structural Biology, Pleinlaan 2, 1050, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
- Department of Cell Biochemistry, University of Groningen, Groningen, 9747 AG, The Netherlands
| | - Giambattista Guaitoli
- German Center for Neurodegenerative Diseases (DZNE), 72076, Tübingen, Germany
- Eberhard Karls University, Institute for Ophthalmic Research, Center for Ophthalmology, 72076, Tübingen, Germany
| | - Albert Konijnenberg
- Department of Chemistry, Biomolecular & Analytical Mass Spectrometry group, University of Antwerp, 2020, Antwerp, Belgium
| | - Margaux Leemans
- VIB-VUB Center for Structural Biology, Pleinlaan 2, 1050, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Susanne Terheyden
- Department of Cell Biochemistry, University of Groningen, Groningen, 9747 AG, The Netherlands
- Structural Biology Group, Max-Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
| | - Arsen Petrovic
- Department of Mechanistic Cell Biology, Max-Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
| | - Rodrigo Gallardo
- VIB Center for Brain & Disease Research, 3000, Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, PB 802, 3000, Leuven, Belgium
| | | | | | - Henderikus Pots
- Department of Cell Biochemistry, University of Groningen, Groningen, 9747 AG, The Netherlands
| | - Peter J M Van Haastert
- Department of Cell Biochemistry, University of Groningen, Groningen, 9747 AG, The Netherlands
| | - Frank Sobott
- Department of Chemistry, Biomolecular & Analytical Mass Spectrometry group, University of Antwerp, 2020, Antwerp, Belgium
- Astbury Centre for Structural Molecular Biology, University of Leeds, LS2 9JT, Leeds, UK
- School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, Leeds, UK
| | - Christian Johannes Gloeckner
- German Center for Neurodegenerative Diseases (DZNE), 72076, Tübingen, Germany
- Eberhard Karls University, Institute for Ophthalmic Research, Center for Ophthalmology, 72076, Tübingen, Germany
| | - Rouslan Efremov
- VIB-VUB Center for Structural Biology, Pleinlaan 2, 1050, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Arjan Kortholt
- Department of Cell Biochemistry, University of Groningen, Groningen, 9747 AG, The Netherlands
| | - Wim Versées
- VIB-VUB Center for Structural Biology, Pleinlaan 2, 1050, Brussels, Belgium.
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium.
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Abstract
One theory of bacterial speciation states that bacterial and animal species share the property of cohesion, meaning that diversity within a species is constrained. A new study provides direct evidence that genome-wide sweeps can limit diversity within bacterial species.
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Affiliation(s)
- Frederick M Cohan
- Department of Biology, Wesleyan University, Middletown, CT 06459, USA.
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5
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Dornfeld C, Weisberg AJ, K C R, Dudareva N, Jelesko JG, Maeda HA. Phylobiochemical characterization of class-Ib aspartate/prephenate aminotransferases reveals evolution of the plant arogenate phenylalanine pathway. Plant Cell 2014; 26:3101-14. [PMID: 25070637 PMCID: PMC4145135 DOI: 10.1105/tpc.114.127407] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 06/21/2014] [Accepted: 07/03/2014] [Indexed: 05/22/2023]
Abstract
The aromatic amino acid Phe is required for protein synthesis and serves as the precursor of abundant phenylpropanoid plant natural products. While Phe is synthesized from prephenate exclusively via a phenylpyruvate intermediate in model microbes, the alternative pathway via arogenate is predominant in plant Phe biosynthesis. However, the molecular and biochemical evolution of the plant arogenate pathway is currently unknown. Here, we conducted phylogenetically informed biochemical characterization of prephenate aminotransferases (PPA-ATs) that belong to class-Ib aspartate aminotransferases (AspAT Ibs) and catalyze the first committed step of the arogenate pathway in plants. Plant PPA-ATs and succeeding arogenate dehydratases (ADTs) were found to be most closely related to homologs from Chlorobi/Bacteroidetes bacteria. The Chlorobium tepidum PPA-AT and ADT homologs indeed efficiently converted prephenate and arogenate into arogenate and Phe, respectively. A subset of AspAT Ib enzymes exhibiting PPA-AT activity was further identified from both Plantae and prokaryotes and, together with site-directed mutagenesis, showed that Thr-84 and Lys-169 play key roles in specific recognition of dicarboxylic keto (prephenate) and amino (aspartate) acid substrates. The results suggest that, along with ADT, a gene encoding prephenate-specific PPA-AT was transferred from a Chlorobi/Bacteroidetes ancestor to a eukaryotic ancestor of Plantae, allowing efficient Phe and phenylpropanoid production via arogenate in plants today.
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Affiliation(s)
- Camilla Dornfeld
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Alexandra J Weisberg
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061
| | - Ritesh K C
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061
| | - Natalia Dudareva
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
| | - John G Jelesko
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061
| | - Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin 53706
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6
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Lunina ON, Savvichev AS, Kuznetsov BB, Pimenov NV, Gorlenko VM. [Anoxygenic phototrophic bacteria of the Kislo-Sladkoe Stratified Lake (White Sea, Kandalaksha Bay)]. Mikrobiologiia 2014; 83:90-108. [PMID: 25436251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The community of anoxygenic phototrophic bacteria (APB) in the water column of the Kislo-Sladkoe stratified lake recently isolated from the sea (White Sea, Kandalaksha Bay) was investigated in September 2010. The water of the sulfide-rich zone was greenish-brown due to intense development of green sulfur bacteria (GSB). Nine APB strains were isolated from the water samples: three belonging to GSB, five, to purple sulfur bacteria (PSB), and one, to purple nonsulfur bacteria (PNB). GSB predominated in the phototrophic community of the chemocline. Unexpectedly, two morphologically different green-colored GSB strains were found to be phylogenetically identical and related to the brown-colored @Chlorobium phaeovibrioides (99% similarity according to the 16S rRNA gene sequencing). Homology to the closest green-colored species (Chlorobium luteolum) was 98%. Two morphologically and physiologically similar PSB strains (TcrPS10 and AmPS10) had rounded cells containing okenonokenonee and gas vesicles. According to the 16S rRNA gene sequencing, these strains were most closely related (99%) to two different Thiocapsa species: Tca. marina (containing okenonokenonee and no gas vesicles) and Tca. rosea (containing spirilloxanthin and gas vesicles). The remaining isolates of purple bacteria were similar to the already described APB species.
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7
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Yu LJ, Unno M, Kimura Y, Yanagimoto K, Oh-oka H, Wang-Otomo ZY. Structure analysis and characterization of the cytochrome c-554 from thermophilic green sulfur photosynthetic bacterium Chlorobaculum tepidum. Photosynth Res 2013; 118:249-258. [PMID: 24052268 DOI: 10.1007/s11120-013-9922-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 09/03/2013] [Indexed: 06/02/2023]
Abstract
The cytochrome (Cyt) c-554 in thermophilic green photosynthetic bacterium Chlorobaculum tepidum serves as an intermediate electron carrier, transferring electrons to the membrane-bound Cyt c z from various enzymes involved in the oxidations of sulfide, thiosulfate, and sulfite compounds. Spectroscopically, this protein exhibits an asymmetric α-absorption band for the reduced form and particularly large paramagnetic (1)H NMR shifts for the heme methyl groups with an unusual shift pattern in the oxidized form. The crystal structure of the Cyt c-554 has been determined at high resolution. The overall fold consists of four α-helices and is characterized by a remarkably long and flexible loop between the α3 and α4 helices. The axial ligand methionine has S-chirality at the sulfur atom with its C(ε)H3 group pointing toward the heme pyrrole ring I. This configuration corresponds to an orientation of the lone-pair orbital of the sulfur atom directed at the pyrrole ring II and explains the lowest-field (1)H NMR shift arising from the 18(1) heme methyl protons. Differing from most other class I Cyts c, no hydrogen bond was formed between the methionine sulfur atom and polypeptide chain. Lack of this hydrogen bond may account for the observed large paramagnetic (1)H NMR shifts of the heme methyl protons. The surface-exposed heme pyrrole ring II edge is in a relatively hydrophobic environment surrounded by several electronically neutral residues. This portion is considered as an electron transfer gateway. The structure of the Cyt c-554 is compared with those of other Cyts c, and possible interactions of this protein with its electron transport partners are discussed.
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Affiliation(s)
- Long-Jiang Yu
- Faculty of Science, Ibaraki University, Bunkyo 2-1-1, Mito, 310-8512, Japan
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Nagy V, Pirakitikulr N, Zhou KI, Chillón I, Luo J, Pyle AM. Predicted group II intron lineages E and F comprise catalytically active ribozymes. RNA 2013; 19:1266-1278. [PMID: 23882113 PMCID: PMC3753933 DOI: 10.1261/rna.039123.113] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 06/12/2013] [Indexed: 06/02/2023]
Abstract
Group II introns are self-splicing, retrotransposable ribozymes that contribute to gene expression and evolution in most organisms. The ongoing identification of new group II introns and recent bioinformatic analyses have suggested that there are novel lineages, which include the group IIE and IIF introns. Because the function and biochemical activity of group IIE and IIF introns have never been experimentally tested and because these introns appear to have features that distinguish them from other introns, we set out to determine if they were indeed self-splicing, catalytically active RNA molecules. To this end, we transcribed and studied a set of diverse group IIE and IIF introns, quantitatively characterizing their in vitro self-splicing reactivity, ionic requirements, and reaction products. In addition, we used mutational analysis to determine the relative role of the EBS-IBS 1 and 2 recognition elements during splicing by these introns. We show that group IIE and IIF introns are indeed distinct active intron families, with different reactivities and structures. We show that the group IIE introns self-splice exclusively through the hydrolytic pathway, while group IIF introns can also catalyze transesterifications. Intriguingly, we observe one group IIF intron that forms circular intron. Finally, despite an apparent EBS2-IBS2 duplex in the sequences of these introns, we find that this interaction plays no role during self-splicing in vitro. It is now clear that the group IIE and IIF introns are functional ribozymes, with distinctive properties that may be useful for biotechnological applications, and which may contribute to the biology of host organisms.
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Affiliation(s)
- Vivien Nagy
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA
| | - Nathan Pirakitikulr
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA
| | - Katherine Ismei Zhou
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Isabel Chillón
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Jerome Luo
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Anna Marie Pyle
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
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Harada J, Mizoguchi T, Satoh S, Tsukatani Y, Yokono M, Noguchi M, Tanaka A, Tamiaki H. Specific gene bciD for C7-methyl oxidation in bacteriochlorophyll e biosynthesis of brown-colored green sulfur bacteria. PLoS One 2013; 8:e60026. [PMID: 23560066 PMCID: PMC3613366 DOI: 10.1371/journal.pone.0060026] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Accepted: 02/20/2013] [Indexed: 11/18/2022] Open
Abstract
The gene named bciD, which encodes the enzyme involved in C7-formylation in bacteriochlorophyll e biosynthesis, was found and investigated by insertional inactivation in the brown-colored green sulfur bacterium Chlorobaculum limnaeum (previously called Chlorobium phaeobacteroides). The bciD mutant cells were green in color, and accumulated bacteriochlorophyll c homologs bearing the 7-methyl group, compared to C7-formylated BChl e homologs in the wild type. BChl-c homolog compositions in the mutant were further different from those in Chlorobaculum tepidum which originally produced BChl c: (3(1) S)-8-isobutyl-12-ethyl-BChl c was unusually predominant.
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Affiliation(s)
- Jiro Harada
- Department of Medical Biochemistry, Kurume University School of Medicine, Kurume, Fukuoka, Japan
- * E-mail: (JH); (HT)
| | - Tadashi Mizoguchi
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Souichirou Satoh
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Yusuke Tsukatani
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
- Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
| | - Makio Yokono
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Masato Noguchi
- Department of Medical Biochemistry, Kurume University School of Medicine, Kurume, Fukuoka, Japan
| | - Ayumi Tanaka
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Hokkaido, Japan
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Sapporo, Hokkaido, Japan
| | - Hitoshi Tamiaki
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
- * E-mail: (JH); (HT)
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Bradbury LMT, Shumskaya M, Tzfadia O, Wu SB, Kennelly EJ, Wurtzel ET. Lycopene cyclase paralog CruP protects against reactive oxygen species in oxygenic photosynthetic organisms. Proc Natl Acad Sci U S A 2012; 109:E1888-97. [PMID: 22706644 PMCID: PMC3390835 DOI: 10.1073/pnas.1206002109] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In photosynthetic organisms, carotenoids serve essential roles in photosynthesis and photoprotection. A previous report designated CruP as a secondary lycopene cyclase involved in carotenoid biosynthesis [Maresca J, et al. (2007) Proc Natl Acad Sci USA 104:11784-11789]. However, we found that cruP KO or cruP overexpression plants do not exhibit correspondingly reduced or increased production of cyclized carotenoids, which would be expected if CruP was a lycopene cyclase. Instead, we show that CruP aids in preventing accumulation of reactive oxygen species (ROS), thereby reducing accumulation of β-carotene-5,6-epoxide, a ROS-catalyzed autoxidation product, and inhibiting accumulation of anthocyanins, which are known chemical indicators of ROS. Plants with a nonfunctional cruP accumulate substantially higher levels of ROS and β-carotene-5,6-epoxide in green tissues. Plants overexpressing cruP show reduced levels of ROS, β-carotene-5,6-epoxide, and anthocyanins. The observed up-regulation of cruP transcripts under photoinhibitory and lipid peroxidation-inducing conditions, such as high light stress, cold stress, anoxia, and low levels of CO(2), fits with a role for CruP in mitigating the effects of ROS. Phylogenetic distribution of CruP in prokaryotes showed that the gene is only present in cyanobacteria that live in habitats characterized by large variation in temperature and inorganic carbon availability. Therefore, CruP represents a unique target for developing resilient plants and algae needed to supply food and biofuels in the face of global climate change.
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Affiliation(s)
- Louis M. T. Bradbury
- Department of Biological Sciences, Lehman College, City University of New York, West, Bronx, NY 10468; and
| | - Maria Shumskaya
- Department of Biological Sciences, Lehman College, City University of New York, West, Bronx, NY 10468; and
| | - Oren Tzfadia
- Department of Biological Sciences, Lehman College, City University of New York, West, Bronx, NY 10468; and
- Graduate School and University Center, City University of New York, New York, NY 10016-4309
| | - Shi-Biao Wu
- Department of Biological Sciences, Lehman College, City University of New York, West, Bronx, NY 10468; and
| | - Edward J. Kennelly
- Department of Biological Sciences, Lehman College, City University of New York, West, Bronx, NY 10468; and
- Graduate School and University Center, City University of New York, New York, NY 10016-4309
| | - Eleanore T. Wurtzel
- Department of Biological Sciences, Lehman College, City University of New York, West, Bronx, NY 10468; and
- Graduate School and University Center, City University of New York, New York, NY 10016-4309
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11
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Gomez Maqueo Chew A, Frigaard NU, Bryant DA. Mutational analysis of three bchH paralogs in (bacterio-)chlorophyll biosynthesis in Chlorobaculum tepidum. Photosynth Res 2009; 101:21-34. [PMID: 19568953 DOI: 10.1007/s11120-009-9460-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2009] [Accepted: 06/10/2009] [Indexed: 05/28/2023]
Abstract
The first committed step in the biosynthesis of (bacterio-)chlorophyll is the insertion of Mg2+ into protoporphyrin IX by Mg-chelatase. In all known (B)Chl-synthesizing organisms, Mg-chelatase is encoded by three genes that are homologous to bchH, bchD, and bchI of Rhodobacter spp. The genomes of all sequenced strains of green sulfur bacteria (Chlorobi) encode multiple bchH paralogs, and in the genome of Chlorobaculum tepidum, there are three bchH paralogs, denoted CT1295 (bchT), CT1955 (bchS), and CT1957 (bchH). Cba. tepidum mutants lacking one or two of these paralogs were constructed and characterized. All of the mutants lacking only one of these BchH homologs, as well as bchS bchT and bchH bchT double mutants, which can only produce BchH or BchS, respectively, were viable. However, attempts to construct a bchH bchS double mutant, in which only BchT was functional, were consistently unsuccessful. This result suggested that BchT alone is unable to support the minimal (B)Chl synthesis requirements of cells required for viability. The pigment compositions of the various mutant strains varied significantly. The BChl c content of the bchS mutant was only approximately 10% of that of the wild type, and this mutant excreted large amounts of protoporphyrin IX into the growth medium. The observed differences in BChl c production of the mutant strains were consistent with the hypothesis that the three BchH homologs function in end product regulation and/or substrate channeling of intermediates in the BChl c biosynthetic pathway.
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Affiliation(s)
- Aline Gomez Maqueo Chew
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, S-235 Frear Building, PA 16802, University Park, USA
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12
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Liang CW, Zhang XW, Tian L, Qin S. Functional characterization of sll0659 from Synechocystis sp. PCC 6803. Indian J Biochem Biophys 2008; 45:275-277. [PMID: 18788479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Synechocystis sp. PCC 6803 lacks a gene for the any known types of lycopene cyclase. Recently, we reported that Sll0659 (unknown for its function) from Synechocystis sp. PCC6803 shows similarity in sequence to a lycopene cyclase gene-CruA from Chlorobium tepidum. To test, whether sll0659 encoded protein serves as lycopene cyclase, in this study, we investigated the carotenoids of the wild types and mutants. In the sll0659 deleted mutant, there is no blockage at the lycopene cyclization step. Our results demonstrate that sll0659 does not affect lycopene cycilzation. However, the ultrastructure of mutants suggests the involvement or necessity of sll0659 in the cell division.
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Affiliation(s)
- Cheng-Wei Liang
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, P.R. China
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13
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Muraki N, Seo D, Shiba T, Sakurai T, Kurisu G. Crystallization and preliminary X-ray studies of ferredoxin-NAD(P)+ reductase from Chlorobium tepidum. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:186-9. [PMID: 18323604 PMCID: PMC2374157 DOI: 10.1107/s1744309108003667] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2007] [Accepted: 02/02/2008] [Indexed: 11/11/2022]
Abstract
Ferredoxin-NAD(P)(+) reductase (FNR) is a key enzyme that catalyzes the photoreduction of NAD(P)(+) to generate NAD(P)H during the final step of the photosynthetic electron-transport chain. FNR from the green sulfur bacterium Chlorobium tepidum is a homodimeric enzyme with a molecular weight of 90 kDa; it shares a high level of amino-acid sequence identity to thioredoxin reductase rather than to conventional plant-type FNRs. In order to understand the structural basis of the ferredoxin-dependency of this unique photosynthetic FNR, C. tepidum FNR has been heterologously expressed, purified and crystallized in two forms. Form I crystals belong to space group C222(1) and contain one dimer in the asymmetric unit, while form II crystals belong to space group P4(1)22 or P4(3)22. Diffraction data were collected from a form I crystal to 2.4 A resolution on the synchrotron-radiation beamline NW12 at the Photon Factory.
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Affiliation(s)
- Norifumi Muraki
- Department of Life Sciences, University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Daisuke Seo
- Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa 920-1192, Japan
| | - Tomoo Shiba
- Department of Life Sciences, University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Takeshi Sakurai
- Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa 920-1192, Japan
| | - Genji Kurisu
- Department of Life Sciences, University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8902, Japan
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14
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Nakamura Y, Tsuchiya M, Ohta H. Plastidic phosphatidic acid phosphatases identified in a distinct subfamily of lipid phosphate phosphatases with prokaryotic origin. J Biol Chem 2007. [PMID: 17652095 DOI: 10.1074/jbc.m70438520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Abstract
Plastidic phosphatidic acid phosphatase (PAP) dephosphorylates phosphatidic acid to yield diacylglycerol, which is a precursor for galactolipids, a primary and indispensable component of photosynthetic membranes. Despite its functional importance, the molecular characteristics and phylogenetic origin of plastidic PAP were unknown because no potential homologs have been found. Here, we report the isolation and characterization of plastidic PAPs in Arabidopsis that belong to a distinct lipid phosphate phosphatase (LPP) subfamily with prokaryotic origin. Because no homolog of mammalian LPP was found in cyanobacteria, we sought an LPP ortholog in a more primitive organism, Chlorobium tepidum, and its homologs in cyanobacteria. Arabidopsis had five homologs of cyanobacterial LPP, three of which (LPP gamma, LPP epsilon 1, and LPP epsilon 2) localized to chloroplasts. Complementation of yeast Delta dpp1 Delta lpp1 Delta pah1 by plastidic LPPs rescued the relevant phenotype in vitro and in vivo, suggesting that they function as PAPs. Of the three LPPs, LPP gamma activity best resembled the native activity. The three plastidic LPPs were differentially expressed both in green and nongreen tissues, with LPP gamma expressed the highest in shoots. A knock-out mutant for LPP gamma could not be obtained, although a lpp epsilon 1 lpp epsilon 2 double knock-out showed no significant changes in lipid composition. However, lpp gamma homozygous mutant was isolated only under ectopic overexpression of LPP gamma, suggesting that loss of LPP gamma may cause lethal effect on plant viability. Thus, in Arabidopsis, there are three isoforms of plastidic PAP that belong to a distinct subfamily of LPP, and LPP gamma may be the primary plastidic PAP.
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Affiliation(s)
- Yuki Nakamura
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259-B-65 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Mami Tsuchiya
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259-B-65 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Hiroyuki Ohta
- Center for Biological Resources and Informatics, Tokyo Institute of Technology, 4259-B-65 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan; Research Center for the Evolving Earth and Planets, Tokyo Institute of Technology, 4259-B-65 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan.
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15
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Nakamura Y, Tsuchiya M, Ohta H. Plastidic phosphatidic acid phosphatases identified in a distinct subfamily of lipid phosphate phosphatases with prokaryotic origin. J Biol Chem 2007; 282:29013-29021. [PMID: 17652095 DOI: 10.1074/jbc.m704385200] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Plastidic phosphatidic acid phosphatase (PAP) dephosphorylates phosphatidic acid to yield diacylglycerol, which is a precursor for galactolipids, a primary and indispensable component of photosynthetic membranes. Despite its functional importance, the molecular characteristics and phylogenetic origin of plastidic PAP were unknown because no potential homologs have been found. Here, we report the isolation and characterization of plastidic PAPs in Arabidopsis that belong to a distinct lipid phosphate phosphatase (LPP) subfamily with prokaryotic origin. Because no homolog of mammalian LPP was found in cyanobacteria, we sought an LPP ortholog in a more primitive organism, Chlorobium tepidum, and its homologs in cyanobacteria. Arabidopsis had five homologs of cyanobacterial LPP, three of which (LPP gamma, LPP epsilon 1, and LPP epsilon 2) localized to chloroplasts. Complementation of yeast Delta dpp1 Delta lpp1 Delta pah1 by plastidic LPPs rescued the relevant phenotype in vitro and in vivo, suggesting that they function as PAPs. Of the three LPPs, LPP gamma activity best resembled the native activity. The three plastidic LPPs were differentially expressed both in green and nongreen tissues, with LPP gamma expressed the highest in shoots. A knock-out mutant for LPP gamma could not be obtained, although a lpp epsilon 1 lpp epsilon 2 double knock-out showed no significant changes in lipid composition. However, lpp gamma homozygous mutant was isolated only under ectopic overexpression of LPP gamma, suggesting that loss of LPP gamma may cause lethal effect on plant viability. Thus, in Arabidopsis, there are three isoforms of plastidic PAP that belong to a distinct subfamily of LPP, and LPP gamma may be the primary plastidic PAP.
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Affiliation(s)
- Yuki Nakamura
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259-B-65 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Mami Tsuchiya
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259-B-65 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Hiroyuki Ohta
- Center for Biological Resources and Informatics, Tokyo Institute of Technology, 4259-B-65 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan; Research Center for the Evolving Earth and Planets, Tokyo Institute of Technology, 4259-B-65 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan.
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Maresca JA, Graham JE, Wu M, Eisen JA, Bryant DA. Identification of a fourth family of lycopene cyclases in photosynthetic bacteria. Proc Natl Acad Sci U S A 2007; 104:11784-9. [PMID: 17606904 PMCID: PMC1905924 DOI: 10.1073/pnas.0702984104] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A fourth and large family of lycopene cyclases was identified in photosynthetic prokaryotes. The first member of this family, encoded by the cruA gene of the green sulfur bacterium Chlorobium tepidum, was identified in a complementation assay with a lycopene-producing strain of Escherichia coli. Orthologs of cruA are found in all available green sulfur bacterial genomes and in all cyanobacterial genomes that lack genes encoding CrtL- or CrtY-type lycopene cyclases. The cyanobacterium Synechococcus sp. PCC 7002 has two homologs of CruA, denoted CruA and CruP, and both were shown to have lycopene cyclase activity. Although all characterized lycopene cyclases in plants are CrtL-type proteins, genes orthologous to cruP also occur in plant genomes. The CruA- and CruP-type carotenoid cyclases are members of the FixC dehydrogenase superfamily and are distantly related to CrtL- and CrtY-type lycopene cyclases. Identification of these cyclases fills a major gap in the carotenoid biosynthetic pathways of green sulfur bacteria and cyanobacteria.
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Affiliation(s)
- Julia A. Maresca
- *Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802; and
| | - Joel E. Graham
- *Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802; and
| | - Martin Wu
- The Institute for Genomic Research (TIGR), Rockville, MD 20850
| | | | - Donald A. Bryant
- *Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802; and
- To whom correspondence should be addressed at:
Department of Biochemistry and Molecular Biology, Pennsylvania State University, S-235 Frear Building, University Park, PA 16802. E-mail:
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17
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Ikonen TP, Li H, Pšenčík J, Laurinmäki PA, Butcher SJ, Frigaard NU, Serimaa RE, Bryant DA, Tuma R. X-ray scattering and electron cryomicroscopy study on the effect of carotenoid biosynthesis to the structure of Chlorobium tepidum chlorosomes. Biophys J 2007; 93:620-8. [PMID: 17468163 PMCID: PMC1896238 DOI: 10.1529/biophysj.106.101444] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chlorosomes, the main antenna complexes of green photosynthetic bacteria, were isolated from null mutants of Chlorobium tepidum, each of which lacked one enzyme involved in the biosynthesis of carotenoids. The effects of the altered carotenoid composition on the structure of the chlorosomes were studied by means of x-ray scattering and electron cryomicroscopy. The chlorosomes from each mutant strain exhibited a lamellar arrangement of the bacteriochlorophyll c aggregates, which are the major constituents of the chlorosome interior. However, the carotenoid content and composition had a pronounced effect on chlorosome biogenesis and structure. The results indicate that carotenoids with a sufficiently long conjugated system are important for the biogenesis of the chlorosome baseplate. Defects in the baseplate structure affected the shape of the chlorosomes and were correlated with differences in the arrangement of lamellae and spacing between the lamellar planes of bacteriochlorophyll aggregates. In addition, comparisons among the various mutants enabled refinement of the assignments of the x-ray scattering peaks. While the main scattering peaks come from the lamellar structure of bacteriochlorophyll c aggregates, some minor peaks may originate from the paracrystalline arrangement of CsmA in the baseplate.
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Affiliation(s)
- T. P. Ikonen
- Department of Physical Sciences, University of Helsinki, Helsinki, Finland; Department of Biochemistry and Molecular Biology, Pennsylvania State University, State College, Pennsylvania; Department of Chemical Physics and Optics, Charles University, Prague, Czech Republic; Institute of Biotechnology and Department of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland; and Department of Molecular Biology, University of Copenhagen, Denmark
| | - H. Li
- Department of Physical Sciences, University of Helsinki, Helsinki, Finland; Department of Biochemistry and Molecular Biology, Pennsylvania State University, State College, Pennsylvania; Department of Chemical Physics and Optics, Charles University, Prague, Czech Republic; Institute of Biotechnology and Department of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland; and Department of Molecular Biology, University of Copenhagen, Denmark
| | - J. Pšenčík
- Department of Physical Sciences, University of Helsinki, Helsinki, Finland; Department of Biochemistry and Molecular Biology, Pennsylvania State University, State College, Pennsylvania; Department of Chemical Physics and Optics, Charles University, Prague, Czech Republic; Institute of Biotechnology and Department of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland; and Department of Molecular Biology, University of Copenhagen, Denmark
| | - P. A. Laurinmäki
- Department of Physical Sciences, University of Helsinki, Helsinki, Finland; Department of Biochemistry and Molecular Biology, Pennsylvania State University, State College, Pennsylvania; Department of Chemical Physics and Optics, Charles University, Prague, Czech Republic; Institute of Biotechnology and Department of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland; and Department of Molecular Biology, University of Copenhagen, Denmark
| | - S. J. Butcher
- Department of Physical Sciences, University of Helsinki, Helsinki, Finland; Department of Biochemistry and Molecular Biology, Pennsylvania State University, State College, Pennsylvania; Department of Chemical Physics and Optics, Charles University, Prague, Czech Republic; Institute of Biotechnology and Department of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland; and Department of Molecular Biology, University of Copenhagen, Denmark
| | - N.-U. Frigaard
- Department of Physical Sciences, University of Helsinki, Helsinki, Finland; Department of Biochemistry and Molecular Biology, Pennsylvania State University, State College, Pennsylvania; Department of Chemical Physics and Optics, Charles University, Prague, Czech Republic; Institute of Biotechnology and Department of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland; and Department of Molecular Biology, University of Copenhagen, Denmark
| | - R. E. Serimaa
- Department of Physical Sciences, University of Helsinki, Helsinki, Finland; Department of Biochemistry and Molecular Biology, Pennsylvania State University, State College, Pennsylvania; Department of Chemical Physics and Optics, Charles University, Prague, Czech Republic; Institute of Biotechnology and Department of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland; and Department of Molecular Biology, University of Copenhagen, Denmark
| | - D. A. Bryant
- Department of Physical Sciences, University of Helsinki, Helsinki, Finland; Department of Biochemistry and Molecular Biology, Pennsylvania State University, State College, Pennsylvania; Department of Chemical Physics and Optics, Charles University, Prague, Czech Republic; Institute of Biotechnology and Department of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland; and Department of Molecular Biology, University of Copenhagen, Denmark
| | - R. Tuma
- Department of Physical Sciences, University of Helsinki, Helsinki, Finland; Department of Biochemistry and Molecular Biology, Pennsylvania State University, State College, Pennsylvania; Department of Chemical Physics and Optics, Charles University, Prague, Czech Republic; Institute of Biotechnology and Department of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland; and Department of Molecular Biology, University of Copenhagen, Denmark
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18
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Abstract
The green sulfur bacterium Chlorobium tepidum produces chlorobactene as its primary carotenoid. Small amounts of chlorobactene are hydroxylated by the enzyme CrtC and then glucosylated and acylated to produce chlorobactene glucoside laurate. The genes encoding the enzymes responsible for these modifications of chlorobactene, CT1987, and CT0967, have been identified by comparative genomics, and these genes were insertionally inactivated in C. tepidum to verify their predicted function. The gene encoding chlorobactene glucosyltransferase (CT1987) has been named cruC, and the gene encoding chlorobactene lauroyltransferase (CT0967) has been named cruD. Homologs of these genes are found in the genomes of all sequenced green sulfur bacteria and filamentous anoxygenic phototrophs as well as in the genomes of several nonphotosynthetic bacteria that produce similarly modified carotenoids. The other bacteria in which these genes are found are not closely related to green sulfur bacteria or to one another. This suggests that the ability to synthesize modified carotenoids has been a frequently transferred trait.
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Affiliation(s)
- Julia A Maresca
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, S-235 Frear Building, PA 16802, USA
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19
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Li H, Frigaard NU, Bryant DA. Molecular Contacts for Chlorosome Envelope Proteins Revealed by Cross-Linking Studies with Chlorosomes from Chlorobium tepidum. Biochemistry 2006; 45:9095-103. [PMID: 16866355 DOI: 10.1021/bi060776y] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chlorosomes are unique light-harvesting antennae found in two phyla of green bacteria: Chlorobi and Chloroflexi. In the green sulfur bacterium Chlorobium tepidum, 10 proteins (CsmA, CsmB, CsmC, CsmD, CsmE, CsmF, CsmH, CsmI, CsmJ, and CsmX) exist in the chlorosome envelope. Chlorosomes from the wild type and mutants lacking a single chlorosome protein were cross-linked with the zero-length cross-linker 1-ethyl-3-[3-(dimethylamino)propyl]carbodiimide (EDC) and analyzed by gel electrophoresis. Similar cross-linking products were observed when the time and temperature were varied or when EDC was replaced with glutaraldehyde. Specific interactions between chlorosome proteins in cross-linked products were identified by immunoblotting with polyclonal antibodies raised against recombinant chlorosome proteins. We confirmed these interactions by demonstrating that these products were missing in appropriate mutants. Confirming the location of CsmA in the paracrystalline baseplate, cross-linking showed that CsmA forms dimers, trimers, and homomultimers as large as dodecamers and that CsmA directly interacts with the Fenna-Matthews-Olson protein. Cross-linking further suggests that the precursor form of CsmA is inserted near the edges of the baseplate, where CsmA and pre-CsmA interact with CsmB and CsmF. Several chlorosome proteins, including CsmA, CsmC, CsmD, CsmH, CsmI, CsmJ, and CsmX, were shown to exist as homomultimers in the chlorosome envelope. On the basis of the structural information obtained from these cross-linking experiments, a model for the locations and interactions of the proteins of the chlorosome envelope is proposed.
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Affiliation(s)
- Hui Li
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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20
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Saga Y, Wazawa T, Ishii Y, Yanagida T, Tamiaki H. Single supramolecule spectroscopy of natural and alkaline-treated chlorosomes from green sulfur photosynthetic bacteria. J Nanosci Nanotechnol 2006; 6:1750-7. [PMID: 17025079 DOI: 10.1166/jnn.2006.223] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Fluorescence emission properties of intact and alkaline-treated chlorosomes containing bacteriochlorophyll(BChl)-c, d, and e, which were isolated from four species of green sulfur photosynthetic bacteria, were successfully studied at the single-unit level using a total internal reflection fluorescence microscope. Single intact chlorosomes containing BChl-c from Chlorobium (Chl.) tepidum exhibited heterogeneous emission bands of BChl-c self-aggregates. In contrast, fluorescence spectra of chlorosomal BChl self-aggregates in single intact chlorosomes from the other three Chlorobium species were less heterogeneous than those from Chi. tepidum. Removal of energy-accepting BChl-a/protein complexes called baseplates from the intact chlorosomes by treatments with alkaline media hardly changed spectral shapes of BChl aggregates and their peak distributions at the single-chlorosome level. The similarity of spectral properties at the single-unit level between intact and alkaline-treated chlorosomes of four Chlorobium species clearly indicated that the removal of base-plates from intact chlorosomes by the alkaline-treatment did not affect BChl self-aggregates inside single chlorosomes.
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Affiliation(s)
- Yoshitaka Saga
- Department of Bioscience and Biotechnology, Faculty of Science and Engineering, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
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21
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Kakitani Y, Nagae H, Mizoguchi T, Egawa A, Akiba K, Fujiwara T, Akutsu H, Koyama Y. Assembly of a Mixture of Isomeric BChl c from Chlorobium limicola As Determined by Intermolecular 13C−13C Dipolar Correlations: Coexistence of Dimer-Based and Pseudo-Monomer-Based Stackings. Biochemistry 2006; 45:7574-85. [PMID: 16768453 DOI: 10.1021/bi0525728] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A mixture of bacteriochlorophyll (BChl) c isomers was extracted from the cells of Chlorobium limicola that were grown in the media of 13C-enriched and natural-abundance isotopic compositions. The magic-angle spinning 13C NMR proton-driven spin-diffusion spectra were recorded with mixing times of 50, 100, and 250 ms for two different kinds of in vitro aggregates, one consisting of pure [13C]BChl c and the other consisting of a 1:1 mixture of [13C]BChl c and [12C]BChl c; those peaks whose intensities were reduced to approximately 1/4 by this dilution were assigned to intermolecular 13C-13C dipolar correlation peaks. On the other hand, the nearest-neighbor intermolecular carbon-carbon close contacts with distances of 4-6 A were simulated, to predict observed correlation peaks, for six different models of BChl c assembly. They include weakly overlapped monomers forming structure 1 and structure 2, strongly overlapped dimers forming straight and inclined columns, and weakly overlapped dimers forming aligned and displaced layers. Comparison between the observed correlation peaks and the predicted carbon-carbon close contacts, for both the macrocycles and the side chains, led us to a conclusion that the weakly overlapped dimers forming displaced layers are most likely the assembly of the BChl c molecules in the aggregate.
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Affiliation(s)
- Yoshinori Kakitani
- Faculty of Science and Technology, Kwansei Gakuin University, Gakuen, Sanda 669-1337, Japan
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22
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Tsukatani Y, Miyamoto R, Itoh S, Oh-oka H. Soluble cytochrome c-554, CycA, is not essential for photosynthetic electron transfer in Chlorobium tepidum. FEBS Lett 2006; 580:2191-4. [PMID: 16579991 DOI: 10.1016/j.febslet.2006.03.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2006] [Revised: 03/02/2006] [Accepted: 03/03/2006] [Indexed: 11/18/2022]
Abstract
We constructed a mutant lacking soluble cytochrome c-554 (CycA) by disruption of the cycA gene in the green sulfur bacterium Chlorobium tepidum. The mutant grew phototrophically with a growth rate slower than that of the wild type, suggesting that CycA is not essential for photosynthetic electron transfer even though CycA is known to work as an electron donor to the reaction center. The re-reduction of photo-oxidized cytochrome c(z) by quinol oxidoreductase was inhibited almost completely by the addition of stigmatellin in the mutant cells. This result indicates that, in the mutant cells, the linear electron transfer can occur from the quinol oxidoreductase to cytochrome c(z), and to reaction center P840 with no participation of CycA.
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Affiliation(s)
- Yusuke Tsukatani
- Department of Biology, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
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23
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Kim JS, Shin DH, Pufan R, Huang C, Yokota H, Kim R, Kim SH. Crystal structure of ScpB from Chlorobium tepidum, a protein involved in chromosome partitioning. Proteins 2005; 62:322-8. [PMID: 16294331 DOI: 10.1002/prot.20751] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Structural maintenance of chromosome (SMC) proteins are essential in chromosome condensation and interact with non-SMC proteins in eukaryotes and with segregation and condensation proteins (ScpA and ScpB) in prokaryotes. The highly conserved gene in Chlorobium tepidum gi 21646405 encodes ScpB (ScpB_ChTe). The high resolution crystal structure of ScpB_ChTe shows that the monomeric structure consists of two similarly shaped globular domains composed of three helices sided by beta-strands [a winged helix-turn-helix (HTH)], a motif observed in the C-terminal domain of Scc1, a functionally related eukaryotic ScpA homolog, as well as in many DNA binding proteins.
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Affiliation(s)
- Jeong-Sun Kim
- Department of Chemistry, University of California, Berkeley, California 94720, USA
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Frigaard NU, Li H, Martinsson P, Das SK, Frank HA, Aartsma TJ, Bryant DA. Isolation and characterization of carotenosomes from a bacteriochlorophyll c-less mutant of Chlorobium tepidum. Photosynth Res 2005; 86:101-11. [PMID: 16172929 DOI: 10.1007/s11120-005-1331-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2004] [Accepted: 01/27/2005] [Indexed: 05/04/2023]
Abstract
Chlorosomes are the light-harvesting organelles in photosynthetic green bacteria and typically contain large amounts of bacteriochlorophyll (BChl) c in addition to smaller amounts of BChl a, carotenoids, and several protein species. We have isolated vestigial chlorosomes, denoted carotenosomes, from a BChl c-less, bchK mutant of the green sulfur bacterium Chlorobium tepidum. The physical shape of the carotenosomes (86 +/- 17 nm x 66 +/- 13 nm x 4.3 +/- 0.8 nm on average) was reminiscent of a flattened chlorosome. The carotenosomes contained carotenoids, BChl a, and the proteins CsmA and CsmD in ratios to each other comparable to their ratios in wild-type chlorosomes, but all other chlorosome proteins normally found in wild-type chlorosomes were found only in trace amounts or were not detected. Similar to wild-type chlorosomes, the CsmA protein in the carotenosomes formed oligomers at least up to homo-octamers as shown by chemical cross-linking and immunoblotting. The absorption spectrum of BChl a in the carotenosomes was also indistinguishable from that in wild-type chlorosomes. Energy transfer from the bulk carotenoids to BChl a in carotenosomes was poor. The results indicate that the carotenosomes have an intact baseplate made of remarkably stable oligomeric CsmA-BChl a complexes but are flattened in structure due to the absence of BChl c. Carotenosomes thus provide a valuable material for studying the biogenesis, structure, and function of the photosynthetic antennae in green bacteria.
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Affiliation(s)
- Niels-Ulrik Frigaard
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
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Abstract
Population analyses in water samples obtained from the chemocline of crenogenic, meromictic Lake Cadagno, Switzerland, in October for the years 1994 to 2003 were studied using in situ hybridization with specific probes. During this 10-year period, large shifts in abundance between purple and green sulfur bacteria and among different populations were obtained. Purple sulfur bacteria were the numerically most prominent phototrophic sulfur bacteria in samples obtained from 1994 to 2001, when they represented between 70 and 95% of the phototrophic sulfur bacteria. All populations of purple sulfur bacteria showed large fluctuations in time with populations belonging to the genus Lamprocystis being numerically much more important than those of the genera Chromatium and Thiocystis. Green sulfur bacteria were initially represented by Chlorobium phaeobacteroides but were replaced by Chlorobium clathratiforme by the end of the study. C. clathratiforme was the only green sulfur bacterium detected during the last 2 years of the analysis, when a shift in dominance from purple sulfur bacteria to green sulfur bacteria was observed in the chemocline. At this time, numbers of purple sulfur bacteria had decreased and those of green sulfur bacteria increased by about 1 order of magnitude and C. clathratiforme represented about 95% of the phototrophic sulfur bacteria. This major change in community structure in the chemocline was accompanied by changes in profiles of turbidity and photosynthetically available radiation, as well as for sulfide concentrations and light intensity. Overall, these findings suggest that a disruption of the chemocline in 2000 may have altered environmental niches and populations in subsequent years.
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Affiliation(s)
- Mauro Tonolla
- Cantonal Institute of Microbiology, Via Mirasole 22A, CH-6500 Bellinzona, Switzerland
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Abstract
Background Dekapentagonal maps depict the phylogenetic relationships of five genomes in a visually appealing diagram and can be viewed as an alternative to a single evolutionary consensus tree. In particular, the generated maps focus attention on those gene families that significantly deviate from the consensus or plurality phylogeny. PentaPlot is a software tool that computes such dekapentagonal maps given an appropriate probability support matrix. Results The visualization with dekapentagonal maps critically depends on the optimal layout of unrooted tree topologies representing different evolutionary relationships among five organisms along the vertices of the dekapentagon. This is a difficult optimization problem given the large number of possible layouts. At its core our tool utilizes a genetic algorithm with demes and a local search strategy to search for the optimal layout. The hybrid genetic algorithm performs satisfactorily even in those cases where the chosen genomes are so divergent that little phylogenetic information has survived in the individual gene families. Conclusion PentaPlot is being made publicly available as an open source project at .
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Affiliation(s)
- Lutz Hamel
- Department of Computer Science and Statistics, University of Rhode Island, Kingston, RI 02881, USA
| | - Olga Zhaxybayeva
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, 06269-3125, USA
- Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College Street, Halifax, NS B3H 1X5, Canada
| | - J Peter Gogarten
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, 06269-3125, USA
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Harada J, Saga Y, Yaeda Y, Oh-Oka H, Tamiaki H. In vitro activity of C-20 methyltransferase, BchU, involved in bacteriochlorophyllcbiosynthetic pathway in green sulfur bacteria. FEBS Lett 2005; 579:1983-7. [PMID: 15792807 DOI: 10.1016/j.febslet.2005.01.087] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2005] [Revised: 02/14/2005] [Accepted: 02/14/2005] [Indexed: 11/21/2022]
Abstract
The activity of a methyltransferase, BchU, which catalyzes methylation at the C-20 position of chlorin ring in the biosynthetic pathway of bacteriochlorophyll c, was investigated in vitro. The bchU gene derived from the photosynthetic green sulfur bacterium, Chlorobium tepidum, was overexpressed in Escherichia coli as a His-tagged protein (His(6)-BchU), and the enzyme was purified. In the presence of S-adenosylmethionine, His(6)-BchU methylated zinc bacteriopheophorbide d at the C-20 position to give zinc bacteriopheophorbide c. Metal-free bacteriopheophorbide d could not be methylated by the BchU, indicating that the central metal in the chlorin should be required for the recognition by the BchU.
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Affiliation(s)
- Jiro Harada
- Department of Bioscience and Biotechnology, Faculty of Science and Engineering, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
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Choi YK, Jun SR, Cha EY, Park JS, Park YS. Sepiapterin reductases from Chlorobium tepidum and Chlorobium limicola catalyze the synthesis of L-threo-tetrahydrobiopterin from 6-pyruvoyltetrahydropterin. FEMS Microbiol Lett 2005; 242:95-9. [PMID: 15621425 DOI: 10.1016/j.femsle.2004.10.044] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2004] [Revised: 10/20/2004] [Accepted: 10/25/2004] [Indexed: 11/21/2022] Open
Abstract
The ORF sequences of the gene encoding sepiapterin reductase were cloned from the genomic DNAs of Chlorobium tepidum and Chlorobium limicola, which are known to produce L-threo- and L-erythro-tetrahydrobiopterin (BH4)-N-acetylglucosamine, respectively. The deduced amino acid sequence of C. limicola consists of 241 residues, while C. tepidum SR has three residues more at the C-terminal. The overall protein sequence identity was 87.7%. Both recombinant proteins generated from Escherichia coli were identified to catalyze reduction of diketo compound 6-pyruvoyltetrahydropterin to L-threo-BH4. This result suggests that C. limicola needs an additional enzyme for L-erythro-BH4 synthesis to yield its glycoside. The catalytic activity of Chlorobium SRs also supports the previously proposed mechanism of two consecutive reductions of C1' carbonyl group of 6-pyruvoyltetrahydropterin via isomerization reaction.
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Affiliation(s)
- Yong Kee Choi
- School of Biotechnology and Biomedical Science, Inje University, Kimhae 621-749, Republic of Korea
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Frigaard NU, Sakuragi Y, Bryant DA. Gene inactivation in the cyanobacterium Synechococcus sp. PCC 7002 and the green sulfur bacterium Chlorobium tepidum using in vitro-made DNA constructs and natural transformation. Methods Mol Biol 2004; 274:325-40. [PMID: 15187290 DOI: 10.1385/1-59259-799-8:325] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Inactivation of a chromosomal gene is a useful approach to study the function of the gene in question and can be used to produce a desired phenotype in the organism. This chapter describes how to generate such mutants of the cyanobacterium Synechococcus sp. PCC 7002 and the green sulfur bacterium Chlorobium tepidum by natural transformation with synthetic DNA constructs. Two alternative methods to generate the DNA constructs, both performed entirely in vitro and based on the polymerase chain reaction (PCR), are also presented. These methods are ligation of DNA fragments with T4 DNA ligase, and megaprimer PCR.
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Affiliation(s)
- Niels-Ulrik Frigaard
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, USA
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Blankenship RE. Identification of a key step in the biosynthetic pathway of bacteriochlorophyll c and its implications for other known and unknown green sulfur bacteria. J Bacteriol 2004; 186:5187-8. [PMID: 15292118 PMCID: PMC490940 DOI: 10.1128/jb.186.16.5187-5188.2004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Robert E Blankenship
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287-1604, USA.
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Frigaard NU, Bryant DA. Seeing green bacteria in a new light: genomics-enabled studies of the photosynthetic apparatus in green sulfur bacteria and filamentous anoxygenic phototrophic bacteria. Arch Microbiol 2004; 182:265-76. [PMID: 15340781 DOI: 10.1007/s00203-004-0718-9] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2004] [Revised: 07/21/2004] [Accepted: 07/22/2004] [Indexed: 10/26/2022]
Abstract
Based upon their photosynthetic nature and the presence of a unique light-harvesting antenna structure, the chlorosome, the photosynthetic green bacteria are defined as a distinctive group in the Bacteria. However, members of the two taxa that comprise this group, the green sulfur bacteria (Chlorobi) and the filamentous anoxygenic phototrophic bacteria ("Chloroflexales"), are otherwise quite different, both physiologically and phylogenetically. This review summarizes how genome sequence information facilitated studies of the biosynthesis and function of the photosynthetic apparatus and the oxidation of inorganic sulfur compounds in two model organisms that represent these taxa, Chlorobium tepidum and Chloroflexus aurantiacus. The genes involved in bacteriochlorophyll (BChl) c and carotenoid biosynthesis in these two organisms were identified by sequence homology with known BChl a and carotenoid biosynthesis enzymes, gene cluster analysis in Cfx. aurantiacus, and gene inactivation studies in Chl. tepidum. Based on these results, BChl a and BChl c biosynthesis is similar in the two organisms, whereas carotenoid biosynthesis differs significantly. In agreement with its facultative anaerobic nature, Cfx. aurantiacus in some cases apparently produces structurally different enzymes for heme and BChl biosynthesis, in which one enzyme functions under anoxic conditions and the other performs the same reaction under oxic conditions. The Chl. tepidum mutants produced with modified BChl c and carotenoid species also allow the functions of these pigments to be studied in vivo.
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Affiliation(s)
- Niels-Ulrik Frigaard
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16801, USA.
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Frigaard NU, Maresca JA, Yunker CE, Jones AD, Bryant DA. Genetic manipulation of carotenoid biosynthesis in the green sulfur bacterium Chlorobium tepidum. J Bacteriol 2004; 186:5210-20. [PMID: 15292122 PMCID: PMC490927 DOI: 10.1128/jb.186.16.5210-5220.2004] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2004] [Accepted: 05/14/2004] [Indexed: 11/20/2022] Open
Abstract
The green sulfur bacterium Chlorobium tepidum is a strict anaerobe and an obligate photoautotroph. On the basis of sequence similarity with known enzymes or sequence motifs, nine open reading frames encoding putative enzymes of carotenoid biosynthesis were identified in the genome sequence of C. tepidum, and all nine genes were inactivated. Analysis of the carotenoid composition in the resulting mutants allowed the genes encoding the following six enzymes to be identified: phytoene synthase (crtB/CT1386), phytoene desaturase (crtP/CT0807), zeta-carotene desaturase (crtQ/CT1414), gamma-carotene desaturase (crtU/CT0323), carotenoid 1',2'-hydratase (crtC/CT0301), and carotenoid cis-trans isomerase (crtH/CT0649). Three mutants (CT0180, CT1357, and CT1416 mutants) did not exhibit a discernible phenotype. The carotenoid biosynthetic pathway in C. tepidum is similar to that in cyanobacteria and plants by converting phytoene into lycopene using two plant-like desaturases (CrtP and CrtQ) and a plant-like cis-trans isomerase (CrtH) and thus differs from the pathway known in all other bacteria. In contrast to the situation in cyanobacteria and plants, the construction of a crtB mutant completely lacking carotenoids demonstrates that carotenoids are not essential for photosynthetic growth of green sulfur bacteria. However, the bacteriochlorophyll a contents of mutants lacking colored carotenoids (crtB, crtP, and crtQ mutants) were decreased from that of the wild type, and these mutants exhibited a significant growth rate defect under all light intensities tested. Therefore, colored carotenoids may have both structural and photoprotection roles in green sulfur bacteria. The ability to manipulate the carotenoid composition so dramatically in C. tepidum offers excellent possibilities for studying the roles of carotenoids in the light-harvesting chlorosome antenna and iron-sulfur-type (photosystem I-like) reaction center. The phylogeny of carotenogenic enzymes in green sulfur bacteria and green filamentous bacteria is also discussed.
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Affiliation(s)
- Niels-Ulrik Frigaard
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
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Maresca JA, Gomez Maqueo Chew A, Ponsatí MR, Frigaard NU, Ormerod JG, Bryant DA. The bchU gene of Chlorobium tepidum encodes the c-20 methyltransferase in bacteriochlorophyll c biosynthesis. J Bacteriol 2004; 186:2558-66. [PMID: 15090495 PMCID: PMC387796 DOI: 10.1128/jb.186.9.2558-2566.2004] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacteriochlorophylls (BChls) c and d, two of the major light-harvesting pigments in photosynthetic green sulfur bacteria, differ only by the presence of a methyl group at the C-20 methine bridge position in BChl c. A gene potentially encoding the C-20 methyltransferase, bchU, was identified by comparative analysis of the Chlorobium tepidum and Chloroflexus aurantiacus genome sequences. Homologs of this gene were amplified and sequenced from Chlorobium phaeobacteroides strain 1549, Chlorobium vibrioforme strain 8327d, and C. vibrioforme strain 8327c, which produce BChls e, d, and c, respectively. A single nucleotide insertion in the bchU gene of C. vibrioforme strain 8327d was found to cause a premature, in-frame stop codon and thus the formation of a truncated, nonfunctional gene product. The spontaneous mutant of this strain that produces BChl c (strain 8327c) has a second frameshift mutation that restores the correct reading frame in bchU. The bchU gene was inactivated in C. tepidum, a BChl c-producing species, and the resulting mutant produced only BChl d. Growth rate measurements showed that BChl c- and d-producing strains of the same organism (C. tepidum or C. vibrioforme) have similar growth rates at high and intermediate light intensities but that strains producing BChl c grow faster than those with BChl d at low light intensities. Thus, the bchU gene encodes the C-20 methyltransferase for BChl c biosynthesis in Chlorobium species, and methylation at the C-20 position to produce BChl c rather than BChl d confers a significant competitive advantage to green sulfur bacteria living at limiting red and near-infrared light intensities.
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Affiliation(s)
- Julia A Maresca
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
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Frigaard NU, Li H, Milks KJ, Bryant DA. Nine mutants of Chlorobium tepidum each unable to synthesize a different chlorosome protein still assemble functional chlorosomes. J Bacteriol 2004; 186:646-53. [PMID: 14729689 PMCID: PMC321489 DOI: 10.1128/jb.186.3.646-653.2004] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Chlorosomes of the green sulfur bacterium Chlorobium tepidum comprise mostly bacteriochlorophyll c (BChl c), small amounts of BChl a, carotenoids, and quinones surrounded by a lipid-protein envelope. These structures contain 10 different protein species (CsmA, CsmB, CsmC, CsmD, CsmE, CsmF, CsmH, CsmI, CsmJ, and CsmX) but contain relatively little total protein compared to other photosynthetic antenna complexes. Except for CsmA, which has been suggested to bind BChl a, the functions of the chlorosome proteins are not known. Nine mutants in which a single csm gene was inactivated were created; these mutants included genes encoding all chlorosome proteins except CsmA. All mutants had BChl c contents similar to that of the wild-type strain and had growth rates indistinguishable from or within approximately 90% (CsmC(-) and CsmJ(-)) of those of the wild-type strain. Chlorosomes isolated from the mutants lacked only the protein whose gene had been inactivated and were generally similar to those from the wild-type strain with respect to size, shape, and BChl c, BChl a, and carotenoid contents. However, chlorosomes from the csmC mutant were about 25% shorter than those from the wild-type strain, and the BChl c absorbance maximum was blue-shifted about 8 nm, indicating that the structure of the BChl c aggregates in these chlorosomes is altered. The results of the present study establish that, except with CsmA, when the known chlorosome proteins are eliminated individually, none of them are essential for the biogenesis, light harvesting, or structural organization of BChl c and BChl a within the chlorosome. These results demonstrate that chlorosomes are remarkably robust structures that can tolerate considerable changes in protein composition.
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Affiliation(s)
- Niels-Ulrik Frigaard
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
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