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DNA Gyrase Inhibitors Increase the Frequency of Bacteriophage-like RcGTA-Mediated Gene Transfer in Rhodobacter capsulatus. Genes (Basel) 2022; 13:genes13112071. [DOI: 10.3390/genes13112071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 10/31/2022] [Accepted: 11/04/2022] [Indexed: 11/10/2022] Open
Abstract
Rhodobacter capsulatus produces a bacteriophage-like particle called the gene transfer agent (RcGTA) that mediates horizontal gene transfer. RcGTA particles transfer random ~4.5-kb fragments of genomic DNA that integrate into recipient genomes by allelic replacement. This work addresses the effect of sub-inhibitory concentrations of antibiotics on gene transfer by RcGTA. A transduction assay was developed to test the effects of various substances on gene transfer. Using this assay, low concentrations of DNA gyrase inhibitors were found to increase the frequency of gene transfer. Novobiocin was studied in more detail, and it was found that this antibiotic did not influence the production or release of RcGTA but instead appeared to act on the recipient cells. The target of novobiocin in other species has been shown to be the GyrB subunit of DNA gyrase (a heterotetramer of 2GyrA and 2GyrB). R. capsulatus encodes GyrA and GyrB homologues, and a GyrB overexpression plasmid was created and found to confer resistance to novobiocin. The presence of the overexpression plasmid in recipient cells greatly diminished the novobiocin-mediated increase in gene transfer, confirming that this effect is due to the binding of novobiocin by GyrB. The results of this work show that antibiotics affect gene transfer in R. capsulatus and may be relevant to microbial genetic exchange in natural ecosystems.
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Proctor MS, Sutherland GA, Canniffe DP, Hitchcock A. The terminal enzymes of (bacterio)chlorophyll biosynthesis. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211903. [PMID: 35573041 PMCID: PMC9066304 DOI: 10.1098/rsos.211903] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 03/29/2022] [Indexed: 05/03/2023]
Abstract
(Bacterio)chlorophylls are modified tetrapyrroles that are used by phototrophic organisms to harvest solar energy, powering the metabolic processes that sustain most of the life on Earth. Biosynthesis of these pigments involves enzymatic modification of the side chains and oxidation state of a porphyrin precursor, modifications that differ by species and alter the absorption properties of the pigments. (Bacterio)chlorophylls are coordinated by proteins that form macromolecular assemblies to absorb light and transfer excitation energy to a special pair of redox-active (bacterio)chlorophyll molecules in the photosynthetic reaction centre. Assembly of these pigment-protein complexes is aided by an isoprenoid moiety esterified to the (bacterio)chlorin macrocycle, which anchors and stabilizes the pigments within their protein scaffolds. The reduction of the isoprenoid 'tail' and its addition to the macrocycle are the final stages in (bacterio)chlorophyll biosynthesis and are catalysed by two enzymes, geranylgeranyl reductase and (bacterio)chlorophyll synthase. These enzymes work in conjunction with photosynthetic complex assembly factors and the membrane biogenesis machinery to synchronize delivery of the pigments to the proteins that coordinate them. In this review, we summarize current understanding of the catalytic mechanism, substrate recognition and regulation of these crucial enzymes and their involvement in thylakoid biogenesis and photosystem repair in oxygenic phototrophs.
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Affiliation(s)
- Matthew S. Proctor
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - George A. Sutherland
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Daniel P. Canniffe
- Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
| | - Andrew Hitchcock
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
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Zoolkefli FIRM, Moriguchi K, Cho Y, Kiyokawa K, Yamamoto S, Suzuki K. Isolation and Analysis of Donor Chromosomal Genes Whose Deficiency Is Responsible for Accelerating Bacterial and Trans-Kingdom Conjugations by IncP1 T4SS Machinery. Front Microbiol 2021; 12:620535. [PMID: 34093458 PMCID: PMC8174662 DOI: 10.3389/fmicb.2021.620535] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 04/06/2021] [Indexed: 11/13/2022] Open
Abstract
Conjugal transfer is a major driving force of genetic exchange in eubacteria, and the system in IncP1-type broad-host-range plasmids transfers DNA even to eukaryotes and archaea in a process known as trans-kingdom conjugation (TKC). Although conjugation factors encoded on plasmids have been extensively analyzed, those on the donor chromosome have not. To identify the potential conjugation factor(s), a genome-wide survey on a comprehensive collection of Escherichia coli gene knockout mutants (Keio collection) as donors to Saccharomyces cerevisiae recipients was performed using a conjugal transfer system mediated by the type IV secretion system (T4SS) of the IncP1α plasmid. Out of 3,884 mutants, three mutants (ΔfrmR, ΔsufA, and ΔiscA) were isolated, which showed an increase by one order of magnitude in both E. coli-E. coli and E. coli-yeast conjugations without an increase in the mRNA accumulation level for the conjugation related genes examined. The double-knockout mutants for these genes (ΔfrmRΔsufA and ΔiscAΔfrmR) did not show synergistic effects on the conjugation efficiency, suggesting that these factors affect a common step in the conjugation machinery. The three mutants demonstrated increased conjugation efficiency in IncP1β-type but not in IncN- and IncW-type broad-host-range plasmid transfers, and the homologous gene knockout mutants against the three genes in Agrobacterium tumefaciens also showed increased TKC efficiency. These results suggest the existence of a specific regulatory system in IncP1 plasmids that enables the control of conjugation efficiency in different hosts, which could be utilized for the development of donor strains as gene introduction tools into bacteria, eukaryotes, and archaea.
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Affiliation(s)
| | - Kazuki Moriguchi
- Department of Biological Science, Graduate School of Science, Hiroshima University, Higashihiroshima, Japan.,Program of Basic Biology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Japan
| | - Yunjae Cho
- Department of Biological Science, Faculty of Science, Hiroshima University, Higashihiroshima, Japan
| | - Kazuya Kiyokawa
- Program of Basic Biology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Japan
| | - Shinji Yamamoto
- Department of Biological Science, Graduate School of Science, Hiroshima University, Higashihiroshima, Japan
| | - Katsunori Suzuki
- Department of Biological Science, Graduate School of Science, Hiroshima University, Higashihiroshima, Japan.,Program of Basic Biology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Japan
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4
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Pallegar P, Canuti M, Langille E, Peña-Castillo L, Lang AS. A Two-Component System Acquired by Horizontal Gene Transfer Modulates Gene Transfer and Motility via Cyclic Dimeric GMP. J Mol Biol 2020; 432:4840-4855. [PMID: 32634380 DOI: 10.1016/j.jmb.2020.07.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/08/2020] [Accepted: 07/01/2020] [Indexed: 10/23/2022]
Abstract
Bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) is an important intracellular signaling molecule that affects diverse physiological processes in bacteria. The intracellular levels of c-di-GMP are controlled by proteins acting as diguanylate cyclase (DGC) and phosphodiesterase (PDE) enzymes that synthesize and degrade c-di-GMP, respectively. In the alphaproteobacterium Rhodobacter capsulatus, flagellar motility and gene exchange via production of the gene transfer agent RcGTA are regulated by c-di-GMP. One of the R. capsulatus proteins involved in this regulation is Rcc00620, which contains an N-terminal two-component system response regulator receiver (REC) domain and C-terminal DGC and PDE domains. We demonstrate that the enzymatic activity of Rcc00620 is regulated through the phosphorylation status of its REC domain, which is controlled by a cognate histidine kinase protein, Rcc00621. In this system, the phosphorylated form of Rcc00620 is active as a PDE enzyme and stimulates gene transfer and motility. In addition, we discovered that the rcc00620 and rcc00621 genes are present in only one lineage within the genus Rhodobacter and were acquired via horizontal gene transfer from a distantly related alphaproteobacterium in the order Sphingomonadales. Therefore, a horizontally acquired regulatory system regulates gene transfer in the recipient organism.
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Affiliation(s)
- Purvikalyan Pallegar
- Department of Biology, Memorial University of Newfoundland, St. John's, NL A1B 3X9, Canada.
| | - Marta Canuti
- Department of Biology, Memorial University of Newfoundland, St. John's, NL A1B 3X9, Canada.
| | - Evan Langille
- Department of Chemistry, Memorial University of Newfoundland, St. John's, NL A1B 3X7, Canada.
| | - Lourdes Peña-Castillo
- Department of Biology, Memorial University of Newfoundland, St. John's, NL A1B 3X9, Canada; Department of Computer Science, Memorial University of Newfoundland, St. John's, NL A1B 3X5, Canada.
| | - Andrew S Lang
- Department of Biology, Memorial University of Newfoundland, St. John's, NL A1B 3X9, Canada.
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Pallegar P, Peña-Castillo L, Langille E, Gomelsky M, Lang AS. Cyclic di-GMP-Mediated Regulation of Gene Transfer and Motility in Rhodobacter capsulatus. J Bacteriol 2020; 202:e00554-19. [PMID: 31659012 PMCID: PMC6941535 DOI: 10.1128/jb.00554-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 10/19/2019] [Indexed: 02/08/2023] Open
Abstract
Gene transfer agents (GTAs) are bacteriophage-like particles produced by several bacterial and archaeal lineages that contain small pieces of the producing cells' genomes that can be transferred to other cells in a process similar to transduction. One well-studied GTA is RcGTA, produced by the alphaproteobacterium Rhodobacter capsulatus RcGTA gene expression is regulated by several cellular regulatory systems, including the CckA-ChpT-CtrA phosphorelay. The transcription of multiple other regulator-encoding genes is affected by the response regulator CtrA, including genes encoding putative enzymes involved in the synthesis and hydrolysis of the second messenger bis-(3'-5')-cyclic dimeric GMP (c-di-GMP). To investigate whether c-di-GMP signaling plays a role in RcGTA production, we disrupted the CtrA-affected genes potentially involved in this process. We found that disruption of four of these genes affected RcGTA gene expression and production. We performed site-directed mutagenesis of key catalytic residues in the GGDEF and EAL domains responsible for diguanylate cyclase (DGC) and c-di-GMP phosphodiesterase (PDE) activities and analyzed the functions of the wild-type and mutant proteins. We also measured RcGTA production in R. capsulatus strains where intracellular levels of c-di-GMP were altered by the expression of either a heterologous DGC or a heterologous PDE. This adds c-di-GMP signaling to the collection of cellular regulatory systems controlling gene transfer in this bacterium. Furthermore, the heterologous gene expression and the four gene disruptions had similar effects on R. capsulatus flagellar motility as found for gene transfer, and we conclude that c-di-GMP inhibits both RcGTA production and flagellar motility in R. capsulatusIMPORTANCE Gene transfer agents (GTAs) are virus-like particles that move cellular DNA between cells. In the alphaproteobacterium Rhodobacter capsulatus, GTA production is affected by the activities of multiple cellular regulatory systems, to which we have now added signaling via the second messenger dinucleotide molecule bis-(3'-5')-cyclic dimeric GMP (c-di-GMP). Similar to the CtrA phosphorelay, c-di-GMP also affects R. capsulatus flagellar motility in addition to GTA production, with lower levels of intracellular c-di-GMP favoring increased flagellar motility and gene transfer. These findings further illustrate the interconnection of GTA production with global systems of regulation in R. capsulatus, providing additional support for the notion that the production of GTAs has been maintained in this and related bacteria because it provides a benefit to the producing organisms.
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Affiliation(s)
- Purvikalyan Pallegar
- Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
| | - Lourdes Peña-Castillo
- Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
- Department of Computer Science, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
| | - Evan Langille
- Department of Chemistry, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
| | - Mark Gomelsky
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming, USA
| | - Andrew S Lang
- Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
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6
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Characterization of a Glycyl Radical Enzyme Bacterial Microcompartment Pathway in Rhodobacter capsulatus. J Bacteriol 2019; 201:JB.00343-18. [PMID: 30510145 DOI: 10.1128/jb.00343-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 11/15/2018] [Indexed: 11/20/2022] Open
Abstract
Bacterial microcompartments (BMCs) are large (∼100-nm) protein shells that encapsulate enzymes, their substrates, and cofactors for the purposes of increasing metabolic reaction efficiency and protecting cells from toxic intermediates. The best-studied microcompartment is the carbon-fixing carboxysome that encapsulates ribulose-1,5-bisphosphate carboxylase and carbonic anhydrase. Other well-known BMCs include the Pdu and Eut BMCs, which metabolize 1,2-propanediol and ethanolamine, respectively, with vitamin B12-dependent diol dehydratase enzymes. Recent bioinformatic analyses identified a new prevalent type of BMC, hypothesized to utilize vitamin B12-independent glycyl radical enzymes to metabolize substrates. Here we use genetic and metabolic analyses to undertake in vivo characterization of the newly identified glycyl radical enzyme microcompartment 3 (GRM3) class of microcompartment clusters. Transcriptome sequencing analyses showed that the microcompartment gene cluster in the genome of the purple photosynthetic bacterium Rhodobacter capsulatus was expressed under dark anaerobic respiratory conditions in the presence of 1,2-propanediol. High-performance liquid chromatography and gas chromatography-mass spectrometry analyses showed that enzymes coded by this cluster metabolized 1,2-propanediol into propionaldehyde, propanol, and propionate. Surprisingly, the microcompartment pathway did not protect these cells from toxic propionaldehyde under the conditions used in this study, with buildup of this intermediate contributing to arrest of cell growth. We further show that expression of microcompartment genes is regulated by a two-component system located downstream of the microcompartment cluster.IMPORTANCE BMCs are protein shells that are designed to compartmentalize enzymatic reactions that require either sequestration of a substrate or the sequestration of toxic intermediates. Due to their ability to compartmentalize reactions, BMCs have also become attractive targets for bioengineering novel enzymatic reactions. Despite these useful features, little is known about the biochemistry of newly identified classes of BMCs. In this study, we have undertaken genetic and in vivo metabolic analyses of the newly identified GRM3 gene cluster.
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7
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The Protease ClpXP and the PAS Domain Protein DivL Regulate CtrA and Gene Transfer Agent Production in Rhodobacter capsulatus. Appl Environ Microbiol 2018; 84:AEM.00275-18. [PMID: 29625982 DOI: 10.1128/aem.00275-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 03/29/2018] [Indexed: 01/01/2023] Open
Abstract
Several members of the Rhodobacterales (Alphaproteobacteria) produce a conserved horizontal gene transfer vector, called the gene transfer agent (GTA), that appears to have evolved from a bacteriophage. The model system used to study GTA biology is the Rhodobacter capsulatus GTA (RcGTA), a small, tailed bacteriophage-like particle produced by a subset of the cells in a culture. The response regulator CtrA is conserved in the Alphaproteobacteria and is an essential regulator of RcGTA production: it controls the production and maturation of the RcGTA particle and RcGTA release from cells. CtrA also controls the natural transformation-like system required for cells to receive RcGTA-donated DNA. Here, we report that dysregulation of the CckA-ChpT-CtrA phosphorelay either by the loss of the PAS domain protein DivL or by substitution of the autophosphorylation residue of the hybrid histidine kinase CckA decreased CtrA phosphorylation and greatly increased RcGTA protein production in R. capsulatus We show that the loss of the ClpXP protease or the three C-terminal residues of CtrA results in increased CtrA levels in R. capsulatus and identify ClpX(P) to be essential for the maturation of RcGTA particles. Furthermore, we show that CtrA phosphorylation is important for head spike production. Our results provide novel insight into the regulation of CtrA and GTAs in the RhodobacteralesIMPORTANCE Members of the Rhodobacterales are abundant in ocean and freshwater environments. The conserved GTA produced by many Rhodobacterales may have an important role in horizontal gene transfer (HGT) in aquatic environments and provide a significant contribution to their adaptation. GTA production is controlled by bacterial regulatory systems, including the conserved CckA-ChpT-CtrA phosphorelay; however, several questions about GTA regulation remain. Our identification that a short DivL homologue and ClpXP regulate CtrA in R. capsulatus extends the model of CtrA regulation from Caulobacter crescentus to a member of the Rhodobacterales We found that the magnitude of RcGTA production greatly depends on DivL and CckA kinase activity, adding yet another layer of regulatory complexity to RcGTA. RcGTA is known to undergo CckA-dependent maturation, and we extend the understanding of this process by showing that the ClpX chaperone is required for formation of tailed, DNA-containing particles.
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8
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Westbye AB, O'Neill Z, Schellenberg-Beaver T, Beatty JT. The Rhodobacter capsulatus gene transfer agent is induced by nutrient depletion and the RNAP omega subunit. Microbiology (Reading) 2017; 163:1355-1363. [DOI: 10.1099/mic.0.000519] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Alexander B. Westbye
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC, Canada
- Present address: Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 't Horntje (Texel), Netherlands
| | - Zoe O'Neill
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC, Canada
| | - Tegan Schellenberg-Beaver
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC, Canada
| | - J. Thomas Beatty
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC, Canada
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9
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Fixen KR, Harwood CS. A polymorphism in the oxygen-responsive repressor PpsR2 confers a growth advantage to Rhodopseudomonas palustris under low light. PHOTOSYNTHESIS RESEARCH 2016; 129:199-204. [PMID: 27344652 DOI: 10.1007/s11120-016-0288-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 06/15/2016] [Indexed: 06/06/2023]
Abstract
The purple nonsulfur bacterium Rhodopseudomonas palustris grows aerobically using oxidative phosphorylation or anaerobically using photophosphorylation. The oxygen-responsive transcription regulator, PpsR2, regulates the transition to a phototrophic lifestyle by repressing transcription of photosynthesis genes during aerobic growth. Whereas most R. palustris strains have an arginine (Arg) at position 439 in the helix-turn-helix DNA-binding domain of this protein, some strains, including the well-studied strain CGA009, have a cysteine (Cys) at this position. Using allelic exchange, we found that the Cys439 in PpsR2 resulted in increased pigmentation and photosynthetic gene expression under both aerobic and anaerobic conditions. The Cys439 substitution also conferred a growth advantage to R. palustris at low light intensities. This indicates that variation in the PpsR2 protein results in R. palustris strains that have two different thresholds for derepressing photosynthesis genes in response to oxygen and light.
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Affiliation(s)
- Kathryn R Fixen
- Department of Microbiology, University of Washington, Box 375573, HSB K-340B, 1705 NE Pacific Street, Seattle, WA, 98195, USA
| | - Caroline S Harwood
- Department of Microbiology, University of Washington, Box 375573, HSB K-340B, 1705 NE Pacific Street, Seattle, WA, 98195, USA.
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10
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Hynes AP, Shakya M, Mercer RG, Grüll MP, Bown L, Davidson F, Steffen E, Matchem H, Peach ME, Berger T, Grebe K, Zhaxybayeva O, Lang AS. Functional and Evolutionary Characterization of a Gene Transfer Agent's Multilocus "Genome". Mol Biol Evol 2016; 33:2530-43. [PMID: 27343288 PMCID: PMC5026251 DOI: 10.1093/molbev/msw125] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Gene transfer agents (GTAs) are phage-like particles that can package and transfer a random piece of the producing cell’s genome, but are unable to transfer all the genes required for their own production. As such, GTAs represent an evolutionary conundrum: are they selfish genetic elements propagating through an unknown mechanism, defective viruses, or viral structures “repurposed” by cells for gene exchange, as their name implies? In Rhodobacter capsulatus, production of the R. capsulatus GTA (RcGTA) particles is associated with a cluster of genes resembling a small prophage. Utilizing transcriptomic, genetic and biochemical approaches, we report that the RcGTA “genome” consists of at least 24 genes distributed across five distinct loci. We demonstrate that, of these additional loci, two are involved in cell recognition and binding and one in the production and maturation of RcGTA particles. The five RcGTA “genome” loci are widespread within Rhodobacterales, but not all loci have the same evolutionary histories. Specifically, two of the loci have been subject to frequent, probably virus-mediated, gene transfer events. We argue that it is unlikely that RcGTA is a selfish genetic element. Instead, our findings are compatible with the scenario that RcGTA is a virus-derived element maintained by the producing organism due to a selective advantage of within-population gene exchange. The modularity of the RcGTA “genome” is presumably a result of selection on the host organism to retain GTA functionality.
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Affiliation(s)
- Alexander P Hynes
- Department of Biology, Memorial University of Newfoundland, St John's, NL, Canada
| | - Migun Shakya
- Department of Biological Sciences, Dartmouth College
| | - Ryan G Mercer
- Department of Biology, Memorial University of Newfoundland, St John's, NL, Canada
| | - Marc P Grüll
- Department of Biology, Memorial University of Newfoundland, St John's, NL, Canada
| | - Luke Bown
- Department of Biology, Memorial University of Newfoundland, St John's, NL, Canada
| | - Fraser Davidson
- Department of Biology, Memorial University of Newfoundland, St John's, NL, Canada
| | - Ekaterina Steffen
- Department of Biology, Memorial University of Newfoundland, St John's, NL, Canada
| | - Heidi Matchem
- Department of Biology, Memorial University of Newfoundland, St John's, NL, Canada
| | - Mandy E Peach
- Department of Biology, Memorial University of Newfoundland, St John's, NL, Canada
| | - Tim Berger
- Department of Biology, Memorial University of Newfoundland, St John's, NL, Canada
| | - Katherine Grebe
- Department of Biology, Memorial University of Newfoundland, St John's, NL, Canada
| | - Olga Zhaxybayeva
- Department of Biological Sciences, Dartmouth College Department of Computer Science, Dartmouth College
| | - Andrew S Lang
- Department of Biology, Memorial University of Newfoundland, St John's, NL, Canada
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11
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Westbye AB, Kuchinski K, Yip CK, Beatty JT. The Gene Transfer Agent RcGTA Contains Head Spikes Needed for Binding to the Rhodobacter capsulatus Polysaccharide Cell Capsule. J Mol Biol 2015; 428:477-91. [PMID: 26711507 DOI: 10.1016/j.jmb.2015.12.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 11/25/2015] [Accepted: 12/06/2015] [Indexed: 11/15/2022]
Abstract
Viruses and bacteriophages recognize cell surface proteins using receptor-binding proteins. In most tailed bacteriophages, receptor-binding proteins are located on the bacteriophage tail. The gene transfer agent of Rhodobacter capsulatus, RcGTA, morphologically resembles a tailed bacteriophage and binds to a capsular polysaccharide covering R. capsulatus cells. Here, we report that the RcGTA capsid (head) is decorated by spikes that are needed for binding to the capsule. The triangular spikes measured ~12nm and appeared to be attached at the capsid vertices. Head spike production required the putative carbohydrate-binding protein ghsB (rcc01080) previously thought to encode a side tail fiber protein. We found that ghsB is likely co-transcribed with ghsA (rcc01079) and that ghsA/ghsB is regulated by the CckA-ChpT-CtrA phosphorelay homologues and a quorum-sensing system. GhsA and GhsB were found to be CckA-dependent RcGTA maturation factors, as GhsA- and GhsB-deficient particles were found to have altered native-gel electrophoresis migration. Additionally, we provide electron microscopy images showing that RcGTA contains side tail fibers and a baseplate-like structure near the tip of the tail, which are independent of ghsB.
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Affiliation(s)
- Alexander B Westbye
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Kevin Kuchinski
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Calvin K Yip
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - J Thomas Beatty
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC, Canada V6T 1Z3.
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12
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Lange C, Kiesel S, Peters S, Virus S, Scheer H, Jahn D, Moser J. Broadened Substrate Specificity of 3-Hydroxyethyl Bacteriochlorophyllide a Dehydrogenase (BchC) Indicates a New Route for the Biosynthesis of Bacteriochlorophyll a. J Biol Chem 2015; 290:19697-709. [PMID: 26088139 PMCID: PMC4528133 DOI: 10.1074/jbc.m115.660555] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 06/18/2015] [Indexed: 11/06/2022] Open
Abstract
Bacteriochlorophyll a biosynthesis requires formation of a 3-hydroxyethyl group on pyrrole ring A that gets subsequently converted into a 3-acetyl group by 3-vinyl bacteriochlorophyllide a hydratase (BchF) followed by 3-hydroxyethyl bacteriochlorophyllide a dehydrogenase (BchC). Heterologous overproduction of Chlorobaculum tepidum BchF revealed an integral transmembrane protein that was efficiently isolated by detergent solubilization. Recombinant C. tepidum BchC was purified as a soluble protein-NAD(+) complex. Substrate recognition of BchC was investigated using six artificial substrate molecules. Modification of the isocyclic E ring, omission of the central magnesium ion, zinc as an alternative metal ion, and a non-reduced B ring system were tolerated by BchC. According to this broadened in vitro activity, the chlorin 3-hydroxyethyl chlorophyllide a was newly identified as a natural substrate of BchC in a reconstituted pathway consisting of dark-operative protochlorophyllide oxidoreductase, BchF, and BchC. The established reaction sequence would allow for an additional new branching point for the synthesis of bacteriochlorophyll a. Biochemical and site-directed mutagenesis analyses revealed, in contrast to theoretical predictions, a zinc-independent BchC catalysis that requires NAD(+) as a cofactor. Based on these results, we are designating a new medium-chain dehydrogenase/reductase family (MDR057 BchC) as theoretically proposed from a recent bioinformatics analysis.
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Affiliation(s)
- Christiane Lange
- From the Institute of Microbiology, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig, Germany and
| | - Svenja Kiesel
- From the Institute of Microbiology, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig, Germany and
| | - Sabine Peters
- From the Institute of Microbiology, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig, Germany and
| | - Simone Virus
- From the Institute of Microbiology, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig, Germany and
| | - Hugo Scheer
- Department Biology I, Botany, Ludwig-Maximilians-Universität München, Menzingerstrasse 67, D-80638 München, Germany
| | - Dieter Jahn
- From the Institute of Microbiology, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig, Germany and
| | - Jürgen Moser
- From the Institute of Microbiology, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig, Germany and
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13
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Homologues of Genetic Transformation DNA Import Genes Are Required for Rhodobacter capsulatus Gene Transfer Agent Recipient Capability Regulated by the Response Regulator CtrA. J Bacteriol 2015; 197:2653-63. [PMID: 26031909 DOI: 10.1128/jb.00332-15] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 05/27/2015] [Indexed: 01/23/2023] Open
Abstract
UNLABELLED Gene transfer agents (GTAs) morphologically resemble small, double-stranded DNA (dsDNA) bacteriophages; however, their only known role is to package and transfer random pieces of the producing cell genome to recipient cells. The best understood GTA is that of Rhodobacter capsulatus, termed RcGTA. We discovered that homologues of three genes involved in natural transformation in other bacteria, comEC, comF, and comM, are essential for RcGTA-mediated gene acquisition. This paper gives genetic and biochemical evidence that RcGTA-borne DNA entry into cells requires the ComEC and ComF putative DNA transport proteins and genetic evidence that putative cytoplasmic ComM protein of unknown function is required for recipient capability. Furthermore, the master regulator of RcGTA production in <1% of a cell population, CtrA, which is also required for gene acquisition in recipient cells, is expressed in the vast majority of the population. Our results indicate that RcGTA-mediated gene transfer combines key aspects of two bacterial horizontal gene transfer mechanisms, where donor DNA is packaged in transducing phage-like particles and recipient cells take up DNA using natural transformation-related machinery. Both of these differentiated subsets of a culture population, donors and recipients, are dependent on the same response regulator, CtrA. IMPORTANCE Horizontal gene transfer (HGT) is a major driver of bacterial evolution and adaptation to environmental stresses. Traits such as antibiotic resistance or metabolic properties can be transferred between bacteria via HGT; thus, HGT can have a tremendous effect on the fitness of a bacterial population. The three classically described HGT mechanisms are conjugation, transformation, and phage-mediated transduction. More recently, the HGT factor GTA was described, where random pieces of producing cell genome are packaged into phage-like particles that deliver DNA to recipient cells. In this report, we show that transport of DNA borne by the R. capsulatus RcGTA into recipient cells requires key genes previously thought to be specific to natural transformation pathways. These findings indicate that RcGTA combines central aspects of phage-mediated transduction and natural transformation in an efficient, regulated mode of HGT.
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14
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Tsukatani Y, Harada J, Nomata J, Yamamoto H, Fujita Y, Mizoguchi T, Tamiaki H. Rhodobacter sphaeroides mutants overexpressing chlorophyllide a oxidoreductase of Blastochloris viridis elucidate functions of enzymes in late bacteriochlorophyll biosynthetic pathways. Sci Rep 2015; 5:9741. [PMID: 25978726 PMCID: PMC4432870 DOI: 10.1038/srep09741] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 03/12/2015] [Indexed: 01/27/2023] Open
Abstract
In previous studies we have demonstrated that chlorophyllide a oxidoreductases (CORs) from bacteriochlorophyll (BChl) a-producing Rhodobacter species and BChl b-producing Blastochloris viridis show distinct substrate recognition and different catalytic hydrogenation reactions, and that these two types of CORs therefore cause committed steps for BChls a and b biosynthesis. In this study, COR genes from B. viridis were incorporated and overexpressed in a series of Rhodobacter sphaeroides mutants. We found that the following two factors are essential in making R. sphaeroides produce BChl b: the loss of functions of both intrinsic COR and 8-vinyl reductase (BciA) in the host R. sphaeroides strain; and expression of the BchYZ catalytic components of COR from B. viridis, not the complete set of COR (BchXYZ), in the host strain. In addition, we incorporated bchYZ of B. viridis into the R. sphaeroides mutant lacking BchJ and BciA, resulting in the strain accumulating both BChl a and BChl b. This is the first example of an anoxygenic photosynthetic bacterium producing BChls a and b together. The results suggest that BchJ enhances activity of the intrinsic COR. The physiological significance of BchJ in pigment biosynthetic pathways will be discussed.
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Affiliation(s)
- Yusuke Tsukatani
- 1] Graduate School of Life Sciences, Ritsumeikan University, Shiga 525-8577, Japan [2] PRESTO, Japan Science and Technology Agency, Saitama 332-0012, Japan [3] Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Jiro Harada
- Department of Medical Biochemistry, Kurume University School of Medicine, Fukuoka 830-0011, Japan
| | - Jiro Nomata
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Haruki Yamamoto
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Yuichi Fujita
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Tadashi Mizoguchi
- Graduate School of Life Sciences, Ritsumeikan University, Shiga 525-8577, Japan
| | - Hitoshi Tamiaki
- Graduate School of Life Sciences, Ritsumeikan University, Shiga 525-8577, Japan
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15
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Canniffe DP, Hunter CN. Engineered biosynthesis of bacteriochlorophyll b in Rhodobacter sphaeroides. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:1611-6. [PMID: 25058304 PMCID: PMC4331041 DOI: 10.1016/j.bbabio.2014.07.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 07/11/2014] [Accepted: 07/15/2014] [Indexed: 12/03/2022]
Abstract
Bacteriochlorophyll b has the most red-shifted absorbance maximum of all naturally occurring photopigments. It has a characteristic ethylidene group at the C8 position in place of the more common ethyl group, the product of a C8-vinyl reductase, which is carried by the majority of chlorophylls and bacteriochlorophylls used in photosynthesis. The subsequent and first step exclusive to bacteriochlorophyll biosynthesis, the reduction of the C7 = C8 bond, is catalyzed by chlorophyllide oxidoreductase. It has been demonstrated that the enzyme from bacteriochlorophyll a-utilizing bacteria can catalyze the formation of compounds carrying an ethyl group at C8 from both ethyl- and vinyl-carrying substrates, indicating a surprising additional C8-vinyl reductase function, while the enzyme from organisms producing BChl b could only catalyze C7 = C8 reduction with a vinyl substrate, but this product carried an ethylidene group at the C8 position. We have replaced the native chlorophyllide oxidoreductase-encoding genes of Rhodobacter sphaeroides with those from Blastochloris viridis, but the switch from bacteriochlorophyll a to b biosynthesis is only detected when the native conventional C8-vinyl reductase is absent. We propose a non-enzymatic mechanism for ethylidene group formation based on the absence of cellular C8-vinyl reductase activity. We engineer the production of a foreign photopigment in Rhodobacter sphaeroides. Native COR-encoding genes are replaced with those from Blastochloris viridis. Bacteriochlorophyll b is produced upon additional deletion of conventional 8VR. We propose that loss of 8VR activity by COR leads to ethylidene bond formation.
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Affiliation(s)
- Daniel P Canniffe
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK.
| | - C Neil Hunter
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
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16
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Cheng Z, Li K, Hammad LA, Karty JA, Bauer CE. Vitamin B12 regulates photosystem gene expression via the CrtJ antirepressor AerR in Rhodobacter capsulatus. Mol Microbiol 2014; 91:649-64. [PMID: 24329562 DOI: 10.1111/mmi.12491] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/08/2013] [Indexed: 12/29/2022]
Abstract
The tetrapyrroles haem, bacteriochlorophyll and cobalamin (B12 ) exhibit a complex interrelationship regarding their synthesis. In this study, we demonstrate that AerR functions as an antirepressor of the tetrapyrrole regulator CrtJ. We show that purified AerR contains B12 that is bound to a conserved histidine (His145) in AerR. The interaction of AerR to CrtJ was further demonstrated in vitro by pull down experiments using AerR as bait and quantified using microscale thermophoresis. DNase I DNA footprint assays show that AerR containing B12 inhibits CrtJ binding to the bchC promoter. We further show that bchC expression is greatly repressed in a B12 auxotroph of Rhodobacter capsulatus and that B12 regulation of gene expression is mediated by AerR's ability to function as an antirepressor of CrtJ. This study thus provides a mechanism for how the essential tetrapyrrole, cobalamin controls the synthesis of bacteriochlorophyll, an essential component of the photosystem.
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Affiliation(s)
- Zhuo Cheng
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, 47405, USA
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17
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Shiraki M, Okura H, Saito T. Transcriptional repression of the poly(3-hydroxybutyrate) depolymerase in Ralstonia pickettii T1 by a tetR-like gene. Antonie van Leeuwenhoek 2013; 105:89-98. [PMID: 24146107 DOI: 10.1007/s10482-013-0056-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 10/12/2013] [Indexed: 11/24/2022]
Abstract
Ralstonia pickettii T1 secretes a poly(3-hydroxybutyrate) (PHB) depolymerase (PhaZ) and a 3-hydroxybutyrate (3HB)-oligomer hydrolase, and extracellularly degrades PHB to produce 3HB. However, it is not clear how the expression of phaZ is regulated. In this study, the mechanism by which phaZ expression is controlled in R. pickettii T1 was examined using a mutant made by the random insertion of a transposon, Tn5. The mutant produced a larger amount of PhaZ than the wild type in nutrient broth or a minimal salt (SM) medium supplemented with succinate. However, there was essentially no difference in the activity or amount of PhaZ in the culture supernatant between the wild type and mutant when the two were grown on 3HB. The gene disrupted by the insertion of Tn5 (epdR) was cloned and its nucleotide sequence was determined. In a BLAST search, epdR showed a high degree of similarity to genes for TetR transcriptional regulators of several bacteria. The introduction of epdR into the wild type and mutant grown on the three media described above decreased the amount of PhaZ. These results indicated EpdR to be involved in the repression of phaZ in R. pickettii T1. A quantitative RT-PCR analysis indicated that mRNA levels corresponded with the activity detected and the amounts of PhaZ in the wild type and mutant. Furthermore, the amount of epdR transcript was inversely proportional to the amount of phaZ transcript. In addition, the existence of a positive element acting on phaZ expression was suggested, because in the mutant lacking EpdR, the amount of phaZ transcript varied in cells grown in SM-3HB, SM-succinate or nutrient broth. Based on the above results, a model for the regulation of PhaZ expression in R. pickettii T1 is proposed.
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Affiliation(s)
- Mari Shiraki
- Laboratory of Molecular Microbiology, Department of Biological Sciences, Faculty of Science, Kanagawa University, 2946 Tsuchiya, Hiratsuka, Kanagawa, 259-1293, Japan
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18
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Phosphate concentration and the putative sensor kinase protein CckA modulate cell lysis and release of the Rhodobacter capsulatus gene transfer agent. J Bacteriol 2013; 195:5025-40. [PMID: 23995641 DOI: 10.1128/jb.00669-13] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The gene transfer agent of Rhodobacter capsulatus (RcGTA) is a bacteriophage-like genetic element with the sole known function of horizontal gene transfer. Homologues of RcGTA genes are present in many members of the alphaproteobacteria and may serve an important role in microbial evolution. Transcription of RcGTA genes is induced as cultures enter the stationary phase; however, little is known about cis-active sequences. In this work, we identify the promoter of the first gene in the RcGTA structural gene cluster. Additionally, gene transduction frequency depends on the growth medium, and the reason for this is not known. We report that millimolar concentrations of phosphate posttranslationally inhibit the lysis-dependent release of RcGTA from cells in both a complex medium and a defined medium. Furthermore, we found that cell lysis requires the genes rcc00555 and rcc00556, which were expressed and studied in Escherichia coli to determine their predicted functions as an endolysin and holin, respectively. Production of RcGTA is regulated by host systems, including a putative histidine kinase, CckA, and we found that CckA is required for maximal expression of rcc00555 and for maturation of RcGTA to yield gene transduction-functional particles.
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19
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Hollingshead S, Kopecná J, Jackson PJ, Canniffe DP, Davison PA, Dickman MJ, Sobotka R, Hunter CN. Conserved chloroplast open-reading frame ycf54 is required for activity of the magnesium protoporphyrin monomethylester oxidative cyclase in Synechocystis PCC 6803. J Biol Chem 2012; 287:27823-33. [PMID: 22711541 DOI: 10.1074/jbc.m112.352526] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The cyclase step in chlorophyll (Chl) biosynthesis has not been characterized biochemically, although there are some plausible candidates for cyclase subunits. Two of these, Sll1214 and Sll1874 from the cyanobacterium Synechocystis 6803, were FLAG-tagged in vivo and used as bait in separate pulldown experiments. Mass spectrometry identified Ycf54 as an interaction partner in each case, and this interaction was confirmed by a reciprocal pulldown using FLAG-tagged Ycf54 as bait. Inactivation of the ycf54 gene (slr1780) in Synechocystis 6803 resulted in a strain that exhibited significantly reduced Chl levels. A detailed analysis of Chl precursors in the ycf54 mutant revealed accumulation of very high levels of Mg-protoporphyrin IX methyl ester and only traces of protochlorophyllide, the product of the cyclase, were detected. Western blotting demonstrated that levels of the cyclase component Sll1214 and the Chl biosynthesis enzymes Mg-protoporphyrin IX methyltransferase and protochlorophyllide reductase are significantly impaired in the ycf54 mutant. Ycf54 is, therefore, essential for the activity and stability of the oxidative cyclase. We discuss a possible role of Ycf54 as an auxiliary factor essential for the assembly of a cyclase complex or even a large multienzyme catalytic center.
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Affiliation(s)
- Sarah Hollingshead
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, United Kingdom
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20
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Hynes AP, Mercer RG, Watton DE, Buckley CB, Lang AS. DNA packaging bias and differential expression of gene transfer agent genes within a population during production and release of the Rhodobacter capsulatus gene transfer agent, RcGTA. Mol Microbiol 2012; 85:314-25. [PMID: 22640804 DOI: 10.1111/j.1365-2958.2012.08113.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Rhodobacter capsulatus produces a gene transfer agent (GTA) called RcGTA. RcGTA is a phage-like particle that packages R. capsulatus DNA and transfers it to other R. capsulatus cells. We quantified the relative frequency of packaging for each gene in the genome by hybridization of DNA from RcGTA particles to an R. capsulatus microarray. All genes were found within the RcGTA particles. However, the genes encoding the RcGTA particle were under-packaged compared with other regions. Gene transfer bioassays confirmed that the transfer of genes within the RcGTA structural cluster is reduced relative to those of other genes. Single-cell expression analysis, by flow cytometry analysis of cells containing RcGTA-reporter gene fusion constructs, demonstrated that RcGTA gene expression is not uniform within a culture. This phenomenon was accentuated when the constructs were placed in a strain lacking a putative lysis gene involved in RcGTA release; a small subpopulation was found to be responsible for ∼ 95% of RcGTA activity. We propose a mechanism whereby high levels of RcGTA gene transcription in the most active RcGTA-producing cells cause a reduction in their packaging frequency. This subpopulation's role in producing and releasing the RcGTA particles explains the lack of observed cell lysis in cultures.
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Affiliation(s)
- Alexander P Hynes
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave., St John's, NL, A1B 3X9, Canada
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21
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Mercer RG, Quinlan M, Rose AR, Noll S, Beatty JT, Lang AS. Regulatory systems controlling motility and gene transfer agent production and release in Rhodobacter capsulatus. FEMS Microbiol Lett 2012; 331:53-62. [PMID: 22443140 DOI: 10.1111/j.1574-6968.2012.02553.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Revised: 03/14/2012] [Accepted: 03/16/2012] [Indexed: 11/30/2022] Open
Abstract
Production of the gene transfer agent of Rhodobacter capsulatus, RcGTA, is dependent upon several cellular regulatory systems, including a putative phosphorelay involving the CtrA and CckA proteins. These proteins are also involved in flagellar motility in R. capsulatus. The interactions of proteins in this system are best understood in Caulobacter crescentus where CtrA is activated by phosphorylation by the CckA-ChpT phosphorelay. CtrA~P activity is further controlled by SciP, which represses ctrA transcription and CtrA activation of transcription. We show that R. capsulatus chpT and cckA mutants both have greatly reduced motility and RcGTA activity. Unlike the ctrA mutant where RcGTA gene transcription is absent, the decrease in RcGTA activity is because of reduced release of RcGTA from the cells. The sciP mutant is not affected for RcGTA production but our results support the C. crescentus model of SciP repression of flagellar motility genes. We show that both unphosphorylated and phosphorylated CtrA can activate RcGTA gene expression, while CtrA~P seems to be required for release of the particle and expression of motility genes. This has led us to a new model of how this regulatory system controls motility and production of RcGTA in R. capsulatus.
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Affiliation(s)
- Ryan G Mercer
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada
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22
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Bhaya D, Castelfranco PA. Chlorophyll biosynthesis and assembly into chlorophyll-protein complexes in isolated developing chloroplasts. Proc Natl Acad Sci U S A 2010; 82:5370-4. [PMID: 16593590 PMCID: PMC390570 DOI: 10.1073/pnas.82.16.5370] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Isolated developing plastids from greening cucumber cotyledons or from photoperiodically grown pea seedlings incorporated (14)C-labeled 5-aminolevulinic acid (ALA) into chlorophyll (Chl). Incorporation was light dependent, enhanced by S-adenosylmethionine, and linear for 1 hr. The in vitro rate of Chl synthesis from ALA was comparable to the in vivo rate of Chl accumulation. Levulinic acid and dioxoheptanoic acid strongly inhibited Chl synthesis but not plastid protein synthesis. Neither chloramphenicol nor spectinomycin affected Chl synthesis, although protein synthesis was strongly inhibited. Components of thylakoid membranes from plastids incubated with [(14)C]ALA were resolved by electrophoresis and then subjected to autoradiography. This work showed that (i) newly synthesized Chl was assembled into Chl-protein complexes and (ii) the inhibition of protein synthesis during the incubation did not alter the labeling pattern. Thus, there was no observable short-term coregulation between Chl synthesis (from ALA) and the synthesis of membrane proteins in isolated plastids.
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Affiliation(s)
- D Bhaya
- Department of Botany, University of California at Davis, Davis, CA 95616
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23
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Youvan DC, Alberti M, Begusch H, Bylina EJ, Hearst JE. Reaction center and light-harvesting I genes from Rhodopseudomonas capsulata. Proc Natl Acad Sci U S A 2010; 81:189-92. [PMID: 16593406 PMCID: PMC344636 DOI: 10.1073/pnas.81.1.189] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Five structural genes coding for the reaction center (RC) L, M, and H subunits and the two light-harvesting (LH) I polypeptides, B870alpha and B870beta, have been mapped on two restriction fragments from the R-prime plasmid pRPS404. It has been recently shown that enhanced near-infrared fluorescence mutants of Rhodopseudomonas capsulata typically lack RC or LH I polypeptides and that these lesions are marker-rescued by two restriction fragments from the R-prime plasmid: the 7.5-kilobase-pair EcoRI F fragment and the 4.75-kilobase-pair BamHI C-EcoRI fragment. We have now determined the nucleotide sequence of two restriction fragments and have found that the BamHI C-EcoRI B fragment carries the structural genes for the RC L and M subunits and both LH I polypeptides. Forty kilobase pairs away from this locus, the BamHI F fragment (within the EcoRI F fragment) carries the RC H subunit. The structural genes on the BamHI C-EcoRI B fragment are probably transcribed as part of a polycistronic mRNA. All of the structural genes begin with a consensus Shine-Dalgarno sequence and separate AUG start codons, indicating that the structural polypeptides are not cleaved from larger precursor polypeptides.
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Affiliation(s)
- D C Youvan
- Division of Chemical Biodynamics, Lawrence Berkeley Laboratory, University of California, Berkeley, CA 94720
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24
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Youvan DC, Ismail S. Light-harvesting II (B800-B850 complex) structural genes from Rhodopseudomonas capsulata. Proc Natl Acad Sci U S A 2010; 82:58-62. [PMID: 16593533 PMCID: PMC396970 DOI: 10.1073/pnas.82.1.58] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The light-harvesting II (LHII) structural genes coding for the (B800-B850 complex) beta- and alpha-polypeptides have been cloned and the nucleotide and deduced polypeptide sequences have been determined. This completes the sequencing of all seven structural genes coding for the structural polypeptides of the photosynthetic apparatus that bind the pigments and cofactors participating in the primary light reactions of photosynthesis. Unlike the structural genes coding for the reaction center L, M, and H subunits and the light-harvesting I (LHI) (B870 complex) structural polypeptides, the LHII structural genes are not within the 46-kilobase photosynthetic gene cluster carried by the R-prime plasmid pRPS404. Identical organization of the beta and alpha structural genes for both LHI and LHII and sequence homologies between the two beta-polypeptides and between the two alpha-polypeptides suggests that both complexes arose by gene duplication from a single ancestral light-harvesting complex and that the putative bacteriochlorophyll binding sequence Ala-X-X-X-His has been absolutely conserved.
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Affiliation(s)
- D C Youvan
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
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25
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Daldal F, Cheng S, Applebaum J, Davidson E, Prince RC. Cytochrome c(2) is not essential for photosynthetic growth of Rhodopseudomonas capsulata. Proc Natl Acad Sci U S A 2010; 83:2012-6. [PMID: 16593675 PMCID: PMC323220 DOI: 10.1073/pnas.83.7.2012] [Citation(s) in RCA: 167] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The structural gene for cytochrome c(2) (cycA) of the photosynthetic bacterium Rhodopseudomonas capsulata has been cloned, and the nucleotide and deduced polypeptide sequences have been determined. Compared with the known amino acid sequence of the purified cytochrome c(2), the nucleotide sequence corresponding to the N-terminal part of the cycA gene product indicates the presence of a putative 21 amino acid signal sequence. Thus, cytochrome c(2) may be synthesized as a precursor which is processed during its secretion to the periplasm. Insertion and insertion-deletion mutations were constructed in vitro and the chromosomal cycA(+) allele of a wild-type strain was replaced with these mutations by homologous recombination to yield c(2) (-) mutants of R. capsulata. The c(2) (-) mutants are stable, and they can grow by photosynthesis and by respiration. Since cytochrome c(2) is the primary electron donor to the reaction center during photosynthesis, the ability of these mutants to grow photosynthetically indicates that an alternative way(s) of reducing the oxidized reaction center must exist in R. capsulata. One candidate for this role may be the membrane-bound cytochrome c(1).
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Affiliation(s)
- F Daldal
- Cold Spring Harbor Laboratory, P.O. Box 100, Cold Spring Harbor, NY 11724
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26
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van Berkum P, Tully RE, Keister DL. Nonpigmented and Bacteriochlorophyll-Containing Bradyrhizobia Isolated from Aeschynomene indica. Appl Environ Microbiol 2010; 61:623-9. [PMID: 16534933 PMCID: PMC1388351 DOI: 10.1128/aem.61.2.623-629.1995] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The legume genus Aeschynomene is unusual, since many species develop stem nodules and the bradyrhizobia isolated from these nodules produce bacteriochlorophyll (Bchl). Evidence is presented that the bradyrhizobia of Aeschynomene indica have wide distribution throughout the world, since A. indica was nodulated when grown in 58 soils collected in 14 different countries. Only 38 of 79 isolates tested synthesized Bchl and carotenoids during heterotrophic growth. Nine isolates produced Bchl constitutively, and cultures were pigmented after growth in the dark. The other isolates required light for Bchl production. The DNA from seven pigmented and three nonpigmented bradyrhizobia hybridized with a DNA probe containing the genes for the photosynthetic apparatus of Rhodobacter capsulatus, but DNA from two other nonpigmented isolates did not hybridize with this probe. A relationship between pigmentation in culture and symbiotic phenotype was not evident, since bradyrhizobia of both Bchl phenotypes nodulated stems of A. indica and formed nitrogen-fixing symbioses. Several isolates, which were ineffective on A. indica, probably do belong to the proposed cross-inoculation group 3 (D. Alazard, Appl. Environ. Microbiol. 50:732-734, 1985), since they did not nodulate Aeschynomene americana or Macroptilium atropurpureum. Since it has been suggested that extant rhizobia arose from photosynthetic ancestors (J. I. Sprent, p. 45-54, in P. M. Gresshoff, L. E. Roth, G. Stacey, and W. E. Newton, ed., Nitrogen Fixation: Achievements and Objectives, 1990), we propose that the nonpigmented isolates may represent an extant lineage of an intermediate evolutionary stage.
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27
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Zappa S, Li K, Bauer CE. The tetrapyrrole biosynthetic pathway and its regulation in Rhodobacter capsulatus. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010; 675:229-50. [PMID: 20532744 PMCID: PMC2883787 DOI: 10.1007/978-1-4419-1528-3_13] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The purple anoxygenic photosynthetic bacterium Rhodobacter capsulatus is capable of growing in aerobic or anaerobic conditions, in the dark or using light, etc. Achieving versatile metabolic adaptations from respiration to photosynthesis requires the use of tetrapyrroles such as heme and bacteriochlorophyll, in order to carry oxygen, to transfer electrons, and to harvest light energy. A third tetrapyrrole, cobalamin (vitamin B(12)), is synthesized and used as a cofactor for many enzymes. Heme, bacteriochlorophyll, and vitamin B(12) constitute three major end products of the tetrapyrrole biosynthetic pathway in purple bacteria. Their respective synthesis involves a plethora of enzymes, several that have been characterized and several that are uncharacterized, as described in this review. To respond to changes in metabolic requirements, the pathway undergoes complex regulation to direct the flow of tetrapyrrole intermediates into a specific branch(s) at the expense of other branches of the pathway. Transcriptional regulation of the tetrapyrrole synthesizing enzymes by redox conditions and pathway intermediates is reviewed. In addition, we discuss the involvement of several transcription factors (RegA, CrtJ, FnrL, AerR, HbrL, Irr) as well as the role of riboswitches. Finally, the interdependence of the tetrapyrrole branches on each other synthesis is discussed.
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Affiliation(s)
- Sébastien Zappa
- Biology Department, Indiana University, Bloomington, IN 47405, USA.
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Sugimoto A, Shiraki M, Hatakeyama S, Saito T. Secretion pathway for the poly(3-hydroxybutyrate) depolymerase in Ralstonia pickettii T1. Antonie van Leeuwenhoek 2008; 94:223-32. [DOI: 10.1007/s10482-008-9235-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2007] [Accepted: 03/03/2008] [Indexed: 11/28/2022]
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Sawicki A, Willows R. S-adenosyl-L-methionine:magnesium-protoporphyrin IX O-methyltransferase from Rhodobacter capsulatus: mechanistic insights and stimulation with phospholipids. Biochem J 2007; 406:469-78. [PMID: 17594291 PMCID: PMC2049041 DOI: 10.1042/bj20070284] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2007] [Revised: 05/21/2007] [Accepted: 06/26/2007] [Indexed: 11/17/2022]
Abstract
The enzyme BchM (S-adenosyl-L-methionine:magnesium-protoporphyrin IX O-methyltransferase) from Rhodobacter capsulatus catalyses an intermediate reaction in the bacteriochlorophyll biosynthetic pathway. Overexpression of His(6)-tagged protein in Escherichia coli resulted in the majority of polypeptide existing as inclusion bodies. Purification from inclusion bodies was performed using metal-affinity chromatography after an elaborate wash step involving surfactant polysorbate-20. Initial enzymatic assays involved an in situ generation of S-adenosyl-L-methionine substrate using a crude preparation of S-adenosyl-L-methionine synthetase and this resulted in higher enzymatic activity compared with commercial S-adenosyl-L-methionine. A heat-stable stimulatory component present in the S-adenosyl-L-methionine synthetase was found to be a phospholipid, which increased enzymatic activity 3-4-fold. Purified phospholipids also stabilized enzymatic activity and caused a disaggregation of the protein to lower molecular mass forms, which ranged from monomeric to multimeric species as determined by size-exclusion chromatography. There was no stimulatory effect observed with magnesium-chelatase subunits on methyltransferase activity using His-BchM that had been stabilized with phospholipids. Substrate specificity of the enzyme was limited to 5-co-ordinate square-pyramidal metalloporphyrins, with magnesium-protoporphyrin IX being the superior substrate followed by zinc-protoporphyrin IX and magnesium-deuteroporphyrin. Kinetic analysis indicated a random sequential reaction mechanism. Three non-substrate metalloporphyrins acted as inhibitors with different modes of inhibition exhibited with manganese III-protoporphyrin IX (non-competitive or uncompetitive) compared with cobalt II-protoporphyrin IX (competitive).
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Key Words
- bacteriochlorophyll biosynthesis
- bchm
- magnesium–chelatase
- methyltransferase
- phosphatidylglycerol
- rhodobacter capsulatus
- bchm, s-adenosyl-l-methionine:magnesium-protoporphyrin ix o-methyltransferase
- dopg, dioleoyl (c18:1)2 phosphatidylglycerol
- dppg, dipalmitoyl (c16:0)2 phosphatidylglycerol
- dtt, dithiothreitol
- hisbchm, his16-tagged bchm
- mg-deutero, magnesium-deuteroporphyrin
- mg-proto, magnesium-protoporphyrin ix
- mgpe, magnesium-protoporphyrin ix monomethyl ester
- pe, phosphatidylethanolamine
- pg, phosphatidylglycerol
- popg, palmitoyl-oleoyl (c18:1,16:0) phosphatidylglycerol
- sah, s-adenosylhomocysteine
- sam, s-adenosyl-l-methionine
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Affiliation(s)
- Artur Sawicki
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Robert D. Willows
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
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Gregor J, Zeller T, Balzer A, Haberzettl K, Klug G. Bacterial Regulatory Networks Include Direct Contact of Response Regulator Proteins: Interaction of RegA and NtrX in Rhodobacter capsulatus. J Mol Microbiol Biotechnol 2007; 13:126-39. [PMID: 17693720 DOI: 10.1159/000103604] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The formation of photosynthetic complexes in facultatively photosynthetic bacteria is controlled by the oxygen tension in the environment. In Rhodobacter capsulatus the two-component system RegB/RegA plays a major role in the redox control of photosynthesis genes but also controls other redox-dependent systems. The response regulator RegA is phosphorylated under low oxygen tension and activates the puf and puc operons, which encode pigment binding proteins, by binding to their promoter regions. Data from a yeast two-hybrid analysis as well as an in vitroanalysis indicate that RegA interacts with the NtrX protein, the response regulator of the NtrY/NtrX two-component system which is believed to be involved in regulation of nitrogen fixation genes. Our further analysis revealed that NtrX is indeed involved in the regulation of the puf and puc operons. Furthermore, we showed that an altered NtrX protein, which is predicted to adopt the conformation of phosphorylated NtrX protein, binds within the puf promoter region close to the RegA binding sites. We conclude that a direct interaction of two response regulators connects the regulatory systems for redox control and nitrogen control.
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Affiliation(s)
- Jutta Gregor
- Institut für Mikrobiologie und Molekularbiologie, University of Giessen, Giessen, Germany
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Jäger A, Braatsch S, Haberzettl K, Metz S, Osterloh L, Han Y, Klug G. The AppA and PpsR proteins from Rhodobacter sphaeroides can establish a redox-dependent signal chain but fail to transmit blue-light signals in other bacteria. J Bacteriol 2007; 189:2274-82. [PMID: 17209035 PMCID: PMC1899404 DOI: 10.1128/jb.01699-06] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The AppA protein of Rhodobacter sphaeroides has the unique ability to sense and transmit redox and light signals. In response to decreasing oxygen tension, AppA antagonizes the transcriptional regulator PpsR, which represses the expression of photosynthesis genes, including the puc operon. This mechanism, which is based on direct protein-protein interaction, is prevented by blue-light absorption of the BLUF domain located in the N-terminal part of AppA. In order to test whether AppA and PpsR are sufficient to transmit redox and light signals, we expressed these proteins in three different bacterial species and monitored oxygen- and blue-light-dependent puc expression either directly or by using a luciferase-based reporter construct. The AppA/PpsR system could mediate redox-dependent gene expression in the alphaproteobacteria Rhodobacter capsulatus and Paracoccus denitrificans but not in the gammaproteobacterium Escherichia coli. Analysis of a prrA mutant strain of R. sphaeroides strongly suggests that light-dependent gene expression requires a balanced interplay of the AppA/PpsR system with the PrrA response regulator. Therefore, the AppA/PpsR system was unable to establish light signaling in other bacteria. Based on our data, we present a model for the interdependence of AppA/PpsR signaling and the PrrA transcriptional activator.
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Affiliation(s)
- Andreas Jäger
- Institut für Mikrobiologie und Molekularbiologie, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
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Aklujkar M, Prince RC, Beatty JT. The photosynthetic deficiency due to puhC gene deletion in Rhodobacter capsulatus suggests a PuhC protein-dependent process of RC/LH1/PufX complex reorganization. Arch Biochem Biophys 2006; 454:59-71. [PMID: 16949540 DOI: 10.1016/j.abb.2006.07.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2006] [Revised: 06/30/2006] [Accepted: 07/18/2006] [Indexed: 10/24/2022]
Abstract
Optimal photosynthetic reaction centre (RC) and core antenna (LH1) levels in the purple bacterium Rhodobacter capsulatus require the puhC gene. Deletion of puhC had little effect on RC and LH1 assembly individually, but significantly inhibited the photosynthetic growth of RC+ LH1- strains, suggesting that maximal RC catalytic activity is PuhC-dependent. Consistent with post-assembly reorganization of the RC/LH1/PufX core complex by PuhC to include latecomer proteins, spatial separation of pufX from the RC/LH1 genes inhibited PufX accumulation and photosynthetic growth only in PuhC- strains. Photosynthetic activity improved to different degrees when PuhC homologues from three other species were expressed in PuhC- R. capsulatus, indicating that PuhC homologues function similarly but may interact inefficiently with a heterologous core complex. Anaerobic photosynthetic growth of PuhC- strains was affected by the duration of prior semiaerobic growth, and by two genes that modulate bacteriochlorophyll production: pufQ and puhE. These observations agree with a speculative model in which reorganization of the core complex is an important regenerative process, accelerated by PuhC.
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Affiliation(s)
- Muktak Aklujkar
- Department of Microbiology and Immunology, University of British Columbia, 4556 - 2350 Health Sciences Mall, Vancouver, BC, Canada.
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Nomata J, Mizoguchi T, Tamiaki H, Fujita Y. A second nitrogenase-like enzyme for bacteriochlorophyll biosynthesis: reconstitution of chlorophyllide a reductase with purified X-protein (BchX) and YZ-protein (BchY-BchZ) from Rhodobacter capsulatus. J Biol Chem 2006; 281:15021-8. [PMID: 16571720 DOI: 10.1074/jbc.m601750200] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In most photosynthetic organisms, the chlorin ring structure of chlorophyll a is formed by the reduction of the porphyrin D-ring by the dark-operative nitrogenase-like enzyme, protochlorophyllide reductase (DPOR). Subsequently, the chlorin B-ring is reduced in bacteriochlorophyll biosynthesis to form a bacteriochlorin ring structure. Phenotypic analysis of mutants lacking one of three genes, bchX, bchY, or bchZ, which show significant sequence similarity to the structural genes of nitrogenase, suggests that a second nitrogenase-like enzyme is involved in the chlorin B-ring reduction. However, there is no biochemical evidence for this. Here, we report the reconstitution of chlorophyllide a reductase (COR) with purified proteins. Two Rhodobacter capsulatus strains that overexpressed Strep-tagged BchX and BchY were isolated. Strep-tagged BchX was purified as a single polypeptide, and BchZ was co-purified with Strep-tagged BchY. When BchX and BchY-BchZ components were incubated with chlorophyllide a, ATP, and dithionite under anaerobic conditions, chlorophyllide a was converted to a new pigment with a Qy band of longer wavelength at 734 nm (P734) in 80% acetone. The formation of P734 was dependent on ATP and dithionite. High performance liquid chromatography and mass spectroscopic analysis indicated that P734 is 3-vinyl bacteriochlorophyllide a, which is formed by the B-ring reduction of chlorophyllide a. These results demonstrate that the B-ring of chlorin is reduced by a second nitrogenase-like enzyme and that the sequential actions of two nitrogenase-like enzymes, DPOR and COR, convert porphyrin to bacteriochlorin. The evolutionary implications of nitrogenase-like enzymes to determine the ring structure of (bacterio)chlorophyll pigments are discussed.
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Affiliation(s)
- Jiro Nomata
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
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Aklujkar M, Prince RC, Beatty JT. The puhE gene of Rhodobacter capsulatus is needed for optimal transition from aerobic to photosynthetic growth and encodes a putative negative modulator of bacteriochlorophyll production. Arch Biochem Biophys 2005; 437:186-98. [PMID: 15850558 DOI: 10.1016/j.abb.2005.03.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2005] [Revised: 03/10/2005] [Accepted: 03/11/2005] [Indexed: 10/25/2022]
Abstract
A conserved orf of previously unknown function (herein designated as puhE) is located 3' of the reaction centre H (puhA) gene in purple photosynthetic bacteria, in the order puhABCE in Rhodobacter capsulatus. Disruptions of R. capsulatus puhE resulted in a long lag in the growth of photosynthetic cultures inoculated with cells grown under high aeration, and increased the level of the peripheral antenna, light-harvesting complex 2 (LH2). The amount of the photosynthetic reaction centre (RC) and its core antenna, light-harvesting complex 1 (LH1), was reduced; however, there was no decrease in expression of a lacZ reporter fused to the puf (RC and LH1) promoter, in RC assembly in the absence of LH1, or in LH1 assembly in the absence of the RC. In strains that lack LH2, disruption of puhE increased the in vivo absorption at 780 nm, which we attribute to excess bacteriochlorophyll a (BChl) pigment production. This effect was seen in the presence and absence of PufQ, a protein that stimulates BChl biosynthesis. Expression of puhE from a plasmid reduced A(780) production in puhE mutants. We suggest that PuhE modulates BChl biosynthesis independently of PufQ, and that the presence of excess BChl in PuhE(-)LH2(+) strains results in excess LH2 assembly and also interferes with the adaptation of cells during the transition from aerobic respiratory to anaerobic photosynthetic growth.
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Affiliation(s)
- Muktak Aklujkar
- Department of Microbiology and Immunology, University of British Columbia, 300-6174 University Blvd., Vancouver, BC, Canada V6T 1Z3
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Aklujkar M, Prince RC, Beatty JT. The PuhB protein of Rhodobacter capsulatus functions in photosynthetic reaction center assembly with a secondary effect on light-harvesting complex 1. J Bacteriol 2005; 187:1334-43. [PMID: 15687197 PMCID: PMC545628 DOI: 10.1128/jb.187.4.1334-1343.2005] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The core of the photosynthetic apparatus of purple photosynthetic bacteria such as Rhodobacter capsulatus consists of a reaction center (RC) intimately associated with light-harvesting complex 1 (LH1) and the PufX polypeptide. The abundance of the RC and LH1 components was previously shown to depend on the product of the puhB gene (formerly known as orf214). We report here that disruption of puhB diminishes RC assembly, with an indirect effect on LH1 assembly, and reduces the amount of PufX. Under semiaerobic growth conditions, the core complex was present at a reduced level in puhB mutants. After transfer of semiaerobically grown cultures to photosynthetic (anaerobic illuminated) conditions, the RC/LH1 complex became only slightly more abundant, and the amount of PufX increased as cells began photosynthetic growth. We discovered that the photosynthetic growth of puhB disruption strains of R. capsulatus starts after a long lag period, which is due to physiological adaptation rather than secondary mutations. Using a hybrid protein expression system, we determined that the three predicted transmembrane segments of PuhB are capable of spanning a cell membrane and that the second transmembrane segment could mediate self-association of PuhB. We discuss the possible function of PuhB as a dimeric RC assembly factor.
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Affiliation(s)
- Muktak Aklujkar
- Department of Microbiology and Immunology, University of British Columbia, 300-6174 University Blvd., Vancouver, British Columbia V6T 1Z3, Canada
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Nomata J, Swem LR, Bauer CE, Fujita Y. Overexpression and characterization of dark-operative protochlorophyllide reductase from Rhodobacter capsulatus. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2005; 1708:229-37. [PMID: 15953479 DOI: 10.1016/j.bbabio.2005.02.002] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2005] [Revised: 02/12/2005] [Accepted: 02/15/2005] [Indexed: 11/21/2022]
Abstract
Dark-operative protochlorophyllide oxidoreductase (DPOR) plays a crucial role in light-independent (bacterio)chlorophyll biosynthesis in most photosynthetic organisms. However, the biochemical properties of DPOR are still largely undefined. Here, we constructed an overexpression system of two separable components of DPOR, L-protein (BchL) and NB-protein (BchN-BchB), in the broad-host-range vector pJRD215 in Rhodobacter capsulatus. We established a stable DPOR assay system by mixing crude extracts from the two transconjugants under anaerobic conditions. Using this assay system, we demonstrated some basic properties of DPOR. The Km value for protochlorophyllide was 10.6 muM. Ferredoxin functioned as an electron donor to DPOR. Elution profiles in gel filtration chromatography indicated that L-protein and NB-protein are a homodimer [(BchL)(2)] and a heterotetramer [(BchN)(2)(BchB)(2)], respectively. These results provide a framework for the characterization of these components in detail, and further support a nitrogenase model of DPOR.
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Affiliation(s)
- Jiro Nomata
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
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Smart JL, Willett JW, Bauer CE. Regulation of hem gene expression in Rhodobacter capsulatus by redox and photosystem regulators RegA, CrtJ, FnrL, and AerR. J Mol Biol 2004; 342:1171-86. [PMID: 15351643 DOI: 10.1016/j.jmb.2004.08.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2004] [Revised: 08/02/2004] [Accepted: 08/03/2004] [Indexed: 11/18/2022]
Abstract
Biosynthetic pathways for heme and chlorophyll share common intermediates from 5-aminolevulinic acid through protoporphyrin IX. To obtain a better understanding of how photosynthetic organisms coordinate heme and chlorophyll biosynthesis, we have undertaken detailed analysis of the expression pattern of numerous heme biosynthesis genes in the purple photosynthetic bacterium Rhodobacter capsulatus. beta-Galactosidase reporter assays demonstrated that expression of hemA, hemB, hemC, hemE and hemZ genes is elevated under conditions that give rise to elevated bacteriochlorophyll synthesis. Heme gene expression is shown to be affected by mutations in previously identified transcriptional regulators RegA, FnrL, CrtJ, and AerR, which also control expression of genes involved in bacteriochlorophyll and carotenoid synthesis, and synthesis of the apoprotein subunits of the photosynthetic and electron transport apparatus. High-resolution primer extension analysis of hem mRNA reveals the presence of numerous putative RegA, FnrL and CrtJ binding sites in several hem promoter regions.
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Affiliation(s)
- James L Smart
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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Jäger S, Jäger A, Klug G. CIRCE is not involved in heat-dependent transcription of groESL but in stabilization of the mRNA 5'-end in Rhodobacter capsulatus. Nucleic Acids Res 2004; 32:386-96. [PMID: 14729923 PMCID: PMC373284 DOI: 10.1093/nar/gkh174] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The CIRCE element, an inverted DNA repeat, is known to be involved in the temperature-dependent regulation of genes for heat shock proteins in a variety of organisms. The CIRCE element was identified as the target for the HrcA protein, which represses transcription of heat shock genes under normal growth temperature. Our data reveal that the CIRCE element is not involved in the temperature-dependent transcription of the groESL genes in Rhodobacter capsulatus. Apparently, R.capsulatus does not harbour an HrcA protein. The mechanisms of heat shock regulation of the groESL genes in R.capsulatus therefore diverge significantly from the regulatory pathway identified in other organisms. A structural analysis of the CIRCE RNA element revealed a stem of 11 nt pairs and a loop of only 5 nt. This folding differs from a structure with a 9 nt loop suggested previously on the basis of computer analysis. The RNA structure leads to a slight stabilization of the groESL mRNA that is more pronounced at normal growth temperature than under heat shock conditions.
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Affiliation(s)
- Stephanie Jäger
- Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität Giessen, Heinrich-Buff-Ring 26, D-35392 Giessen, Germany
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Abstract
Control of the synthesis of the purple bacterial photosystem has been an active area of research for many decades. The period of the 1960s involved physiological characterization of photosystem synthesis under different growth conditions. In the 1970s Barry Marrs and coworkers developed genetic tools that were used to define and map genes needed for synthesis of photopigments. The 1980s was a period of cloning and physical mapping of photosynthesis genes onto the chromosome, the demonstration that regulation of photosystem synthesis involved transcriptional control of gene expression, and sequence analysis of photosynthesis genes. The 1990s was a period of the discovery and characterization of regulatory genes that control synthesis of the photosystem in response to alterations in oxygen tension and light intensity. Although several photosynthetic organisms are mentioned for comparison and contrast, the focus of this minireview is on Rhodobacter capsulatus.
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Affiliation(s)
- Carl Bauer
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA,
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Jackson WJ, Prince RC, Stewart GJ, Marrs BL. Energetic and topographic properties of a Rhodopseudomonas capsulata mutant deficient in the B870 complex. Biochemistry 2002. [DOI: 10.1021/bi00374a018] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Dong C, Elsen S, Swem LR, Bauer CE. AerR, a second aerobic repressor of photosynthesis gene expression in Rhodobacter capsulatus. J Bacteriol 2002; 184:2805-14. [PMID: 11976310 PMCID: PMC135018 DOI: 10.1128/jb.184.10.2805-2814.2002] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Open reading frame orf192, which is located immediately upstream of the aerobic repressor gene crtJ, was genetically and biochemically demonstrated to code for a second aerobic repressor (AerR) of photosynthesis gene expression in Rhodobacter capsulatus. Promoter-mapping studies indicate that crtJ has its own promoter but that a significant proportion of crtJ expression is promoted by read-through transcription of orf192 (aerR) transcripts through crtJ. Disruption of aerR resulted in increased photopigment biosynthesis during aerobic growth to a level similar to that of disruption of crtJ. Like that reported for CrtJ, beta-galactosidase assays of reporter gene expression indicated that disruption of aerR resulted in a two- to threefold increase in aerobic expression of the crtI and pucB operons. However, unlike CrtJ, AerR aerobically represses puf operon expression and does not aerobically repress bchC expression. Gel mobility shift analysis with purified AerR indicates that AerR does not bind to a bchC promoter probe but does bind to the crtI, puc, and puf promoter probes. These results indicate that AerR is a DNA-binding protein that targets genes partially overlapping a subset of genes that are also controlled by CrtJ. We also provide evidence for cooperative binding of AerR and CrtJ to the puc promoter region.
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Affiliation(s)
- Chen Dong
- Department of Biology, Jordan Hall, Indiana University, Bloomington, IN 47405, USA
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Biel AJ, Canada K, Huang D, Indest K, Sullivan K. Oxygen-mediated regulation of porphobilinogen formation in Rhodobacter capsulatus. J Bacteriol 2002; 184:1685-92. [PMID: 11872720 PMCID: PMC134899 DOI: 10.1128/jb.184.6.1685-1692.2002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2001] [Accepted: 12/05/2001] [Indexed: 11/20/2022] Open
Abstract
A Rhodobacter capsulatus hemC mutant has been isolated and used to show that oxygen regulates the intracellular levels of porphobilinogen. Experiments using a hemB-cat gene fusion demonstrated that oxygen does not transcriptionally regulate hemB transcription. Porphobilinogen synthase activity is not regulated by oxygen nor is the enzyme feedback inhibited by hemin or protoporphyrin IX. It was demonstrated that less than 20% of [(14)C]aminolevulinate was incorporated into bacteriochlorophyll, suggesting that the majority of the aminolevulinate is diverted from the common tetrapyrrole pathway. Porphobilinogen oxygenase activity was not observed in this organism; however, an NADPH-linked aminolevulinate dehydrogenase activity was demonstrated. The specific activity of this enzyme increased with increasing oxygen tension. The results presented here suggest that carbon flow over the common tetrapyrrole pathway is regulated by a combination of feedback inhibition of aminolevulinate synthase and diversion of aminolevulinate from the pathway by aminolevulinate dehydrogenase.
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Affiliation(s)
- Alan J Biel
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA.
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Abstract
The bacterium Rhodobacter capsulatus is capable of an unusual form of genetic exchange, mediated by a transducing bacteriophage-like particle called the gene transfer agent (GTA). GTA production by R. capsulatus is controlled at the level of transcription by a cellular two-component signal transduction system that includes a putative histidine kinase (CckA) and response regulator (CtrA). We found that, in addition to regulating genetic exchange by R. capsulatus, this signal transduction system controls motility. As with the regulation of GTA production, the control of motility by CckA and CtrA occurs through modulation of gene transcription. Disruptions of the cckA and ctrA genes resulted in a loss of class II, class III, and class IV flagellar gene transcripts, suggesting that cckA and ctrA function in motility as class I flagellar genes. We also found that, analogous to the GTA genes, transcription of R. capsulatus flagellar genes appears to be growth phase dependent: class II flagellar gene transcripts are maximal in the mid-log phase of the culture growth cycle, whereas class III gene transcripts are maximal in the late-log phase of growth. We speculate that coordinate regulation of motility and GTA-mediated genetic exchange in R. capsulatus exists because these two processes are complementary mechanisms for cells to cope with unfavorable conditions in natural environments.
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Affiliation(s)
- Andrew S Lang
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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Marrs BL. The early history of the genetics of photosynthetic bacteria: a personal account. PHOTOSYNTHESIS RESEARCH 2002; 73:55-8. [PMID: 16245103 DOI: 10.1023/a:1020483824314] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The development of genetics as a tool for the study of photosynthesis is recounted, beginning in the period when no genetic exchange mechanism was known for any photosynthetic microorganism, and ending with the sequencing of the key genes for photosynthesis.
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Affiliation(s)
- Barry L Marrs
- Fraunhofer USA Center for Molecular Biotechnology, 15 Innovation Way, Newark, DE, 19711, USA,
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Swem LR, Elsen S, Bird TH, Swem DL, Koch HG, Myllykallio H, Daldal F, Bauer CE. The RegB/RegA two-component regulatory system controls synthesis of photosynthesis and respiratory electron transfer components in Rhodobacter capsulatus. J Mol Biol 2001; 309:121-38. [PMID: 11491283 DOI: 10.1006/jmbi.2001.4652] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Recently, we demonstrated that the RegB/RegA two-component regulatory system from Rhodobacter capsulatus functions as a global regulator of metabolic processes that either generate or consume reducing equivalents. For example, the RegB/RegA system controls expression of such energy generating processes as photosynthesis and hydrogen utilization. In addition, RegB/RegA also control nitrogen and carbon fixation pathways that utilize reducing equivalents. Here, we use a combination of DNase I protection and plasmid-based reporter expression studies to demonstrate that RegA directly controls synthesis of cytochrome cbb3 and ubiquinol oxidases that function as terminal electron acceptors in a branched respiratory chain. We also demonstrate that RegA controls expression of cytochromes c2, c(y) and the cytochrome bc1 complex that are involved in both photosynthetic and respiratory electron transfer events. These data provide evidence that the RegB/RegA two-component system has a major role in controlling the synthesis of numerous processes that affect reducing equivalents in Rhodobacter capsulatus.
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Affiliation(s)
- L R Swem
- Department of Biology, Indiana University, Bloomington 47405, USA
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Saegusa H, Shiraki M, Kanai C, Saito T. Cloning of an intracellular Poly[D(-)-3-Hydroxybutyrate] depolymerase gene from Ralstonia eutropha H16 and characterization of the gene product. J Bacteriol 2001; 183:94-100. [PMID: 11114905 PMCID: PMC94854 DOI: 10.1128/jb.183.1.94-100.2001] [Citation(s) in RCA: 111] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2000] [Accepted: 10/10/2000] [Indexed: 11/20/2022] Open
Abstract
An intracellular poly[D(-)-3-hydroxybutyrate] (PHB) depolymerase gene (phaZ) has been cloned from Ralstonia eutropha H16 by the shotgun method, sequenced, and characterized. Nucleotide sequence analysis of a 2.3-kbp DNA fragment revealed an open reading frame of 1,260 bp, encoding a protein of 419 amino acids with a predicted molecular mass of 47,316 Da. The crude extract of Escherichia coli containing the PHB depolymerase gene digested artificial amorphous PHB granules and released mainly oligomeric D(-)-3-hydroxybutyrate, with some monomer. The gene product did not hydrolyze crystalline PHB or freeze-dried artificial amorphous PHB granules. The deduced amino acid sequence lacked sequence corresponding to a classical lipase box, Gly-X-Ser-X-Gly. The gene product was expressed in R. eutropha cells concomitant with the synthesis of PHB and localized in PHB granules. Although a mutant of R. eutropha whose phaZ gene was disrupted showed a higher PHB content compared to the wild type in a nutrient-rich medium, it accumulated PHB as much as the wild type did in a nitrogen-free, carbon-rich medium. These results indicate that the cloned phaZ gene encodes an intracellular PHB depolymerase in R. eutropha.
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Affiliation(s)
- H Saegusa
- Research Institute of Innovative Technology for the Earth Branch in Kanagawa University, Department of Biological Sciences, Faculty of Science, Kanagawa University, 2946 Tsuchiya, Hiratsuka, Kanagawa 259-1293, Japan
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Aklujkar M, Harmer AL, Prince RC, Beatty JT. The orf162b sequence of Rhodobacter capsulatus encodes a protein required for optimal levels of photosynthetic pigment-protein complexes. J Bacteriol 2000; 182:5440-7. [PMID: 10986247 PMCID: PMC110987 DOI: 10.1128/jb.182.19.5440-5447.2000] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2000] [Accepted: 07/10/2000] [Indexed: 11/20/2022] Open
Abstract
The orf162b sequence, the second open reading frame 3' of the reaction center (RC) H protein gene puhA in the Rhodobacter capsulatus photosynthesis gene cluster, is shown to be transcribed from a promoter located 5' of puhA. A nonpolar mutation of orf162b was generated by replacing most of the coding region with an antibiotic resistance cartridge. Although the mutant strain initiated rapid photosynthetic growth, growth slowed progressively and cultures often entered a pseudostationary phase. The amounts of the RC and light harvesting complex I (LHI) in cells obtained from such photosynthetic cultures were abnormally low, but these deficiencies were less severe when the mutant was grown to a pseudostationary phase induced by low aeration in the absence of illumination. The orf162b mutation did not significantly affect the expression of a pufB::lacZ translationally in-frame gene fusion under the control of the puf promoter, indicating normal transcription and translation of RC and LHI genes. Spontaneous secondary mutations in the strain with the orf162b disruption resulted in a bypass of the photosynthetic growth retardation and reduced the level of light harvesting complex II. These results and the presence of sequences similar to orf162b in other species indicate that the Orf162b protein is required for normal levels of the photosynthetic apparatus in purple photosynthetic bacteria.
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Affiliation(s)
- M Aklujkar
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
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