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Review |
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Xiong J, Fischer WM, Inoue K, Nakahara M, Bauer CE. Molecular evidence for the early evolution of photosynthesis. Science 2000; 289:1724-30. [PMID: 10976061 DOI: 10.1126/science.289.5485.1724] [Citation(s) in RCA: 246] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The origin and evolution of photosynthesis have long remained enigmatic due to a lack of sequence information of photosynthesis genes across the entire photosynthetic domain. To probe early evolutionary history of photosynthesis, we obtained new sequence information of a number of photosynthesis genes from the green sulfur bacterium Chlorobium tepidum and the green nonsulfur bacterium Chloroflexus aurantiacus. A total of 31 open reading frames that encode enzymes involved in bacteriochlorophyll/porphyrin biosynthesis, carotenoid biosynthesis, and photosynthetic electron transfer were identified in about 100 kilobase pairs of genomic sequence. Phylogenetic analyses of multiple magnesium-tetrapyrrole biosynthesis genes using a combination of distance, maximum parsimony, and maximum likelihood methods indicate that heliobacteria are closest to the last common ancestor of all oxygenic photosynthetic lineages and that green sulfur bacteria and green nonsulfur bacteria are each other's closest relatives. Parsimony and distance analyses further identify purple bacteria as the earliest emerging photosynthetic lineage. These results challenge previous conclusions based on 16S ribosomal RNA and Hsp60/Hsp70 analyses that green nonsulfur bacteria or heliobacteria are the earliest phototrophs. The overall consensus of our phylogenetic analysis, that bacteriochlorophyll biosynthesis evolved before chlorophyll biosynthesis, also argues against the long-held Granick hypothesis.
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25 |
246 |
3
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Bryant DA, Costas AMG, Maresca JA, Chew AGM, Klatt CG, Bateson MM, Tallon LJ, Hostetler J, Nelson WC, Heidelberg JF, Ward DM. Candidatus Chloracidobacterium thermophilum: an aerobic phototrophic Acidobacterium. Science 2007; 317:523-6. [PMID: 17656724 DOI: 10.1126/science.1143236] [Citation(s) in RCA: 239] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Only five bacterial phyla with members capable of chlorophyll (Chl)-based phototrophy are presently known. Metagenomic data from the phototrophic microbial mats of alkaline siliceous hot springs in Yellowstone National Park revealed the existence of a distinctive bacteriochlorophyll (BChl)-synthesizing, phototrophic bacterium. A highly enriched culture of this bacterium grew photoheterotrophically, synthesized BChls a and c under oxic conditions, and had chlorosomes and type 1 reaction centers. "Candidatus Chloracidobacterium thermophilum" is a BChl-producing member of the poorly characterized phylum Acidobacteria.
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Research Support, U.S. Gov't, Non-P.H.S. |
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239 |
4
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Yen HC, Marrs B. Map of genes for carotenoid and bacteriochlorophyll biosynthesis in Rhodopseudomonas capsulata. J Bacteriol 1976; 126:619-29. [PMID: 1262313 PMCID: PMC233194 DOI: 10.1128/jb.126.2.619-629.1976] [Citation(s) in RCA: 209] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The recently discovered gene transfer system of Rhodopseudomonas capsulata was used to construct a genetic map of a region concerned with bacteriochlorophyll and carotenoid production. Mutants blocked in the biosynthesis of these compounds were isolated, and each was characterized on the basis of pigments accumulated during growth under low pO2. One-point, two-point, three-point, and ratio test crosses were performed between various mutant strains, and the results were amenable to conventional genetic analyses. A mapping function was found that related cotransfer frequency to map distance. Seven clusters of mutations, five affecting carotenoid and two affecting bacteriochlorophyll biosynthesis, were arranged in one linkage group. Each cluster of mutations is thought to represent a gene. The length of the mapped region is estimated to be less than 1% of the genome. Cotransfer is observed between markers separated by about 5 to 10 genes.
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research-article |
49 |
209 |
5
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Chew AGM, Bryant DA. Chlorophyll Biosynthesis in Bacteria: The Origins of Structural and Functional Diversity. Annu Rev Microbiol 2007; 61:113-29. [PMID: 17506685 DOI: 10.1146/annurev.micro.61.080706.093242] [Citation(s) in RCA: 191] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The use of photochemical reaction centers to convert light energy into chemical energy, chlorophototrophy, occurs in organisms belonging to only five eubacterial phyla: Cyanobacteria, Proteobacteria, Chlorobi, Chloroflexi, and Firmicutes. All chlorophototrophs synthesize two types of pigments: (a) chlorophylls and bacteriochlorophylls, which function in both light harvesting and uniquely in photochemistry; and (b) carotenoids, which function primarily as photoprotective pigments but can also participate in light harvesting. Although hundreds of carotenoids have been identified, only 12 types of chlorophylls (Chl a, b, d; divinyl-Chl a and b; and 8(1)-hydroxy-Chl a) and bacteriochlorophylls (BChl a, b, c, d, e, and g) are currently known to occur in bacteria. This review summarizes recent progress in the identification of genes and enzymes in the biosynthetic pathways leading to Chls and BChls, the essential tetrapyrrole cofactors of photosynthesis, and addresses the mechanisms for generating functional diversity for solar energy capture and conversion in chlorophototrophs.
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191 |
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Labrenz M, Collins MD, Lawson PA, Tindall BJ, Schumann P, Hirsch P. Roseovarius tolerans gen. nov., sp. nov., a budding bacterium with variable bacteriochlorophyll a production from hypersaline Ekho Lake. INTERNATIONAL JOURNAL OF SYSTEMATIC BACTERIOLOGY 1999; 49 Pt 1:137-47. [PMID: 10028255 DOI: 10.1099/00207713-49-1-137] [Citation(s) in RCA: 179] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Eight Gram-negative, aerobic, pointed and budding bacteria were isolated from various depths of the hypersaline, heliothermal and meromictic Ekho Lake (Vestfold Hills, East Antarctica). The cells contained storage granules and daughter cells could be motile. Bacteriochlorophyll a was sometimes produced, but production was repressed by constant dim light. The strains tolerated a wide range of temperature, pH, concentrations of artificial seawater and NaCl, but had an absolute requirement for sodium ions. Glutamate was metabolized with and without an additional source of combined nitrogen. The dominant fatty acid was C18:1; other characteristic fatty acids were C18:2, C12:0 2-OH, C12:1 3-OH, C16:1, C16:0 and C18:0. The main polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine. The DNA G+C base composition was 62-64 mol%. 16S rRNA gene sequence comparisons showed that the isolates were phylogenetically close to the genera Antarctobacter, 'Marinosulfonomonas', Octadecabacter, Sagittula, Sulfitobacter and Roseobacter. Morphological, physiological and genotypic differences to these previously described and distinct genera support the description of a new genus and a new species, Roseovarius tolerans gen. nov., sp. nov. The type strain is EL-172T (= DSM 11457T).
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26 |
179 |
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Uffen RL. Anaerobic growth of a Rhodopseudomonas species in the dark with carbon monoxide as sole carbon and energy substrate. Proc Natl Acad Sci U S A 1976; 73:3298-302. [PMID: 1067620 PMCID: PMC431016 DOI: 10.1073/pnas.73.9.3298] [Citation(s) in RCA: 142] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
A species of Rhodopseudomonas that grows under strict anaerobic conditions in the dark and requires CO was isolated from lake and pond sediments. Although anaerobic growth in the dark occurs in a chemically defined mineral medium with CO as the only carbon and energy source, growth is stimulated by adding trypticase. Under these conditions, cells exhibit a generation time of 6.7 hr and reach a final concentration of 1 to 3 X 10(9) cells per ml of liquid medium. Resting suspensions of CO-grown cells metabolize about 6.7 mumol of CO per mg of protein in 1 hr and produce equimolar amounts of CO2 and H2 according to the equation CO + H2O leads to CO2 + H2. As predicted by this equation, when cells were suspended in tritium-labeled water containing potassium phosphate buffer at pH 7.0 and incubated with pure CO, 3H2 gas was produced at linear rate with a constant specific activity.
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research-article |
49 |
142 |
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Fujita Y, Bauer CE. Reconstitution of light-independent protochlorophyllide reductase from purified bchl and BchN-BchB subunits. In vitro confirmation of nitrogenase-like features of a bacteriochlorophyll biosynthesis enzyme. J Biol Chem 2000; 275:23583-8. [PMID: 10811655 DOI: 10.1074/jbc.m002904200] [Citation(s) in RCA: 110] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Protochlorophyllide reductase catalyzes the reductive formation of chlorophyllide from protochlorophyllide during biosynthesis of chlorophylls and bacteriochlorophylls. The light-independent (dark) form of protochlorophyllide reductase plays a key role in the ability of gymnosperms, algae, and photosynthetic bacteria to green (form chlorophyll) in the dark. Genetic and sequence analyses have indicated that dark protochlorophyllide reductase consists of three protein subunits that exhibit significant sequence similarity to the three subunits of nitrogenase, which catalyzes the reductive formation of ammonia from dinitrogen. However, unlike the well characterized features of nitrogenase, there has been no previous biochemical characterization of dark protochlorophyllide reductase. In this study, we report the first reproducible demonstration of dark protochlorophyllide reductase activity from purified protein subunits that were isolated from the purple nonsulfur photosynthetic bacterium Rhodobacter capsulatus. Two of the three subunits (Bchl and BchN) were expressed in R. capsulatus as S tag fusion proteins that facilitated affinity purification. The third subunit (BchB) was co-purified with the BchN protein indicating that BchN and BchB proteins form a tight complex. Dark protochlorophyllide reductase activity was shown to be dependent on the presence of all three subunits, ATP, and the reductant dithionite. The similarity of dark protochlorophyllide reductase to nitrogenase is discussed.
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Comparative Study |
25 |
110 |
9
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Gomelsky M, Kaplan S. appA, a novel gene encoding a trans-acting factor involved in the regulation of photosynthesis gene expression in Rhodobacter sphaeroides 2.4.1. J Bacteriol 1995; 177:4609-18. [PMID: 7642486 PMCID: PMC177224 DOI: 10.1128/jb.177.16.4609-4618.1995] [Citation(s) in RCA: 94] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
A new gene, the product of which is involved in the regulation of photosynthesis gene expression in the anoxygenic photosynthetic bacterium Rhodobacter sphaeroides 2.4.1, has been identified. The isolation of this gene, designated appA (activation of photopigment and puc expression), was based on its ability, when provided in extra copies, to partially suppress mutations in the two-component PrrB-PrrA regulatory system. The presence of extra copies of the appA gene in either prrB, prrA, or wild-type strains resulted in an activation of puc::lacZ expression under aerobic conditions. Constructed AppA null mutants did not grow photosynthetically and were impaired in the synthesis of both bacteriochlorophyll and carotenoids, as well as the structural proteins of the photosynthetic spectral complexes. When grown anaerobically in the dark, these mutants accumulated bacteriochlorophyll precursors. The expression of lacZ fusions to several photosynthesis genes and operons, including puc, puf, and bchF, was decreased in the AppA mutant strains in comparison with the wild type. To examine the role of AppA involvement in bacteriochlorophyll biosynthesis, we inactivated an early gene, bchE, of the bacteriochlorophyll pathway in both wild-type and AppA- mutant backgrounds. The double mutant, AppA- BchE-, was found to be severely impaired in photosynthesis gene expression, similar to the AppA- BchE+ mutant and in contrast to the AppA+ BchE- mutant. This result indicated that AppA is more likely involved in the regulation of expression of the bch genes than in the biosynthetic pathway per se. The appA gene was sequenced and appears to encode a protein of 450 amino acids with no obvious homology to known proteins.
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research-article |
30 |
94 |
10
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Penfold RJ, Pemberton JM. Sequencing, chromosomal inactivation, and functional expression in Escherichia coli of ppsR, a gene which represses carotenoid and bacteriochlorophyll synthesis in Rhodobacter sphaeroides. J Bacteriol 1994; 176:2869-76. [PMID: 8188588 PMCID: PMC205441 DOI: 10.1128/jb.176.10.2869-2876.1994] [Citation(s) in RCA: 89] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Sequencing of a DNA fragment that causes trans suppression of bacteriochlorophyll and carotenoid levels in Rhodobacter sphaeroides revealed two genes: orf-192 and ppsR. The ppsR gene alone is sufficient for photopigment suppression. Inactivation of the R. sphaeroides chromosomal copy of ppsR results in overproduction of both bacteriochlorophyll and carotenoid pigments. The deduced 464-amino-acid protein product of ppsR is homologous to the CrtJ protein of Rhodobacter capsulatus and contains a helix-turn-helix domain that is found in various DNA-binding proteins. Removal of the helix-turn-helix domain renders PpsR nonfunctional. The promoter of ppsR is located within the coding region of the upstream orf-192 gene. When this promoter is replaced by a lacZ promoter, ppsR is expressed in Escherichia coli. An R. sphaeroides DNA fragment carrying crtD', -E, and -F and bchC, -X, -Y, and -Z' exhibited putative promoter activity in E. coli. This putative promoter activity could be suppressed by PpsR in both E. coli and R. sphaeroides. These results suggest that PpsR is a transcriptional repressor. It could potentially act by binding to a putative regulatory palindrome found in the 5' flanking regions of a number of R. sphaeroides and R. capsulatus photosynthesis genes.
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research-article |
31 |
89 |
11
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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: 85] [Impact Index Per Article: 4.5] [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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Research Support, Non-U.S. Gov't |
19 |
85 |
12
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Reinbothe S, Reinbothe C, Apel K, Lebedev N. Evolution of chlorophyll biosynthesis--the challenge to survive photooxidation. Cell 1996; 86:703-5. [PMID: 8797817 DOI: 10.1016/s0092-8674(00)80144-0] [Citation(s) in RCA: 83] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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Review |
29 |
83 |
13
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Abstract
A review of the biosynthesis of chlorophylls and bacteriochlorophylls from protoporphyrin IX with 235 references. The literature on the enzymes magnesium chelatase, S-adenosyl-L-methionine:magnesium protoporphyrin IX O-methyltransferase, magnesium-protoporphyrin IX monomethyl ester oxidative cyclase, protochlorophyllide oxidoreductase, chlorophyll synthase, bacteriochlorophyll synthase, protochlorophyllide 8-vinyl reductase and chlorophyll a oxidase from 1989 is discussed.
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Review |
22 |
83 |
14
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Wagner-Döbler I, Rheims H, Felske A, El-Ghezal A, Flade-Schröder D, Laatsch H, Lang S, Pukall R, Tindall BJ. Oceanibulbus indolifex gen. nov., sp. nov., a North Sea alphaproteobacterium that produces bioactive metabolites. Int J Syst Evol Microbiol 2004; 54:1177-1184. [PMID: 15280288 DOI: 10.1099/ijs.0.02850-0] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A water sample from the North Sea was used to isolate the abundant heterotrophic bacteria that are able to grow on complex marine media. Isolation was by serial dilution and spread plating. Phylogenetic analysis of nearly complete 16S rRNA gene sequences revealed that one of the strains, HEL-45T, had 97·4 % sequence similarity to Sulfitobacter mediterraneus and 96·5 % sequence similarity to Staleya guttiformis. Strain HEL-45T is a Gram-negative, non-motile rod and obligate aerobe and requires sodium and 1–7 % sea salts for growth. It contains storage granules and does not produce bacteriochlorophyll. Optimal growth temperatures are 25–30 °C. The DNA base composition (G+C content) is 60·1 mol%. Strain HEL-45T has Q10 as the dominant respiratory quinone. The major polar lipids are phosphatidyl glycerol, diphosphatidyl glycerol, phosphatidyl choline, phosphatidyl ethanolamine and an aminolipid. The fatty acids comprise 18 : 1ω7c, 18 : 0, 16 : 1ω7c, 16 : 0, 3-OH 10 : 0, 3-OH 12 : 1 (or 3-oxo 12 : 0) and traces of an 18 : 2 fatty acid. Among the hydroxylated fatty acids only 3-OH 12 : 1 (or 3-oxo 12 : 0) appears to be amide linked, whereas 3-OH 10 : 0 appears to be ester linked. The minor fatty acid components (between 1 and 7 %) allow three subgroups to be distinguished in the Sulfitobacter/Staleya clade, placing HEL-45T into a separate lineage characterized by the presence of 3-OH 12 : 1 (or 3-oxo 12 : 0) and both ester- and amide-linked 16 : 1ω7c phospholipids. HEL-45T produces indole and derivatives thereof, several cyclic dipeptides and thryptanthrin. Phylogenetic analysis of 16S rRNA gene sequences and chemotaxonomic data support the description of a new genus and species, to include Oceanibulbus indolifex gen. nov., sp. nov., with the type strain HEL-45T (=DSM 14862T=NCIMB 13983T).
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MESH Headings
- Adaptation, Biological
- Aerobiosis
- Bacteriochlorophylls/biosynthesis
- Base Composition
- Cytoplasmic Granules
- DNA, Bacterial/chemistry
- DNA, Bacterial/isolation & purification
- DNA, Ribosomal/chemistry
- Fatty Acids/analysis
- Fatty Acids/isolation & purification
- Genes, rRNA
- Gentian Violet
- Indoles/metabolism
- Lipids/analysis
- Lipids/isolation & purification
- Molecular Sequence Data
- Movement
- North Sea
- Osmotic Pressure
- Peptides, Cyclic/biosynthesis
- Phenazines
- Phylogeny
- Quinones/analysis
- Quinones/isolation & purification
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Rhodobacteraceae/classification
- Rhodobacteraceae/cytology
- Rhodobacteraceae/genetics
- Rhodobacteraceae/isolation & purification
- Rhodobacteraceae/physiology
- Seawater/microbiology
- Sequence Analysis, DNA
- Sequence Homology
- Sodium Chloride
- Temperature
- Water Microbiology
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82 |
15
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Yang ZM, Bauer CE. Rhodobacter capsulatus genes involved in early steps of the bacteriochlorophyll biosynthetic pathway. J Bacteriol 1990; 172:5001-10. [PMID: 2203738 PMCID: PMC213156 DOI: 10.1128/jb.172.9.5001-5010.1990] [Citation(s) in RCA: 78] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Three open reading frames in the Rhodobacter capsulatus photosynthesis gene cluster, designated F0, F108, and F1025, were disrupted by site-directed mutagenesis. Mutants bearing insertions in these reading frames were defective in converting protoporphyrin IX to magnesium-protoporphyrin monomethyl ester, protochlorophyllide to chlorophyllide a, and magnesium-protoporphyrin monomethyl ester to protochlorophyllide, respectively. These results demonstrate that the genes examined most likely encode enzyme subunits that catalyze steps common to plant and bacterial tetrapyrrole photopigment biosynthetic pathways. The open reading frames were found to be part of a large 11-kilobase operon that encodes numerous genes involved in early steps of the bacteriochlorophyll a biosynthetic pathway.
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research-article |
35 |
78 |
16
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Frigaard NU, Bryant DA. Seeing green bacteria in a new light: genomics-enabled studies of the photosynthetic apparatus in green sulfur bacteria and filamentous anoxygenic phototrophic bacteria. Arch Microbiol 2004; 182:265-76. [PMID: 15340781 DOI: 10.1007/s00203-004-0718-9] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2004] [Revised: 07/21/2004] [Accepted: 07/22/2004] [Indexed: 10/26/2022]
Abstract
Based upon their photosynthetic nature and the presence of a unique light-harvesting antenna structure, the chlorosome, the photosynthetic green bacteria are defined as a distinctive group in the Bacteria. However, members of the two taxa that comprise this group, the green sulfur bacteria (Chlorobi) and the filamentous anoxygenic phototrophic bacteria ("Chloroflexales"), are otherwise quite different, both physiologically and phylogenetically. This review summarizes how genome sequence information facilitated studies of the biosynthesis and function of the photosynthetic apparatus and the oxidation of inorganic sulfur compounds in two model organisms that represent these taxa, Chlorobium tepidum and Chloroflexus aurantiacus. The genes involved in bacteriochlorophyll (BChl) c and carotenoid biosynthesis in these two organisms were identified by sequence homology with known BChl a and carotenoid biosynthesis enzymes, gene cluster analysis in Cfx. aurantiacus, and gene inactivation studies in Chl. tepidum. Based on these results, BChl a and BChl c biosynthesis is similar in the two organisms, whereas carotenoid biosynthesis differs significantly. In agreement with its facultative anaerobic nature, Cfx. aurantiacus in some cases apparently produces structurally different enzymes for heme and BChl biosynthesis, in which one enzyme functions under anoxic conditions and the other performs the same reaction under oxic conditions. The Chl. tepidum mutants produced with modified BChl c and carotenoid species also allow the functions of these pigments to be studied in vivo.
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21 |
77 |
17
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Clark WG, Davidson E, Marrs BL. Variation of levels of mRNA coding for antenna and reaction center polypeptides in Rhodopseudomonas capsulata in response to changes in oxygen concentration. J Bacteriol 1984; 157:945-8. [PMID: 6199343 PMCID: PMC215353 DOI: 10.1128/jb.157.3.945-948.1984] [Citation(s) in RCA: 76] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The effect of oxygen tension on the transcription of genes coding for the photosynthetic apparatus of Rhodopseudomonas capsulata was determined by the Southern hybridization technique. Restriction endonuclease digests of the R-prime plasmid pRPS404 and a subcloned fragment thereof served as DNA probes for genetically defined regions. The results showed that transcripts corresponding to the genes for certain pigment-binding polypeptides increase in amount by about 40-fold after a drop in oxygen tension. Transcripts hybridizing to genes involved in bacteriochlorophyll biosynthesis increase to a much lesser extent, and several genes involved in carotenoid biosynthesis are not affected by pO2.
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research-article |
41 |
76 |
18
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Sprague SG, Staehelin LA, DiBartolomeis MJ, Fuller RC. Isolation and development of chlorosomes in the green bacterium Chloroflexus aurantiacus. J Bacteriol 1981; 147:1021-31. [PMID: 7275928 PMCID: PMC216142 DOI: 10.1128/jb.147.3.1021-1031.1981] [Citation(s) in RCA: 76] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Freeze-fracture electron microscopy was used to study further the changes in chlorosome structure during the development of the photosynthetic apparatus in Chloroflexus aurantiacus J-10-fl. During development, in response to decreased light intensity or lower oxygen tension, the number of chlorosomes per cell increased. The same conditions also led to a general thickening of chlorosomes but did not affect their length or width. The thickening of the chlorosomes paralleled increases in the bacteriochlorophyll c/bacteriochlorophyll a ratio. Semiaerobic induction of the photosynthetic apparatus did not produce a synchronous assembly of chlorosomes in all cells of a given culture. Even adjacent cells of a single filament showed great variations in the rate and extent of response. Parallel appearance of (i) approximately 5-nm particles (in a lattice configuration) in the membrane attachment site, (ii) the crystalline baseplate material (with a periodicity of approximately 6 nm) adjacent to the membrane attachment site, and (iii) the chlorosome envelope layer preceded addition of longitudinally oriented, rodlike elements (diameter, congruent to 6 m) to the chlorosome core. It is estimated that each chlorosome can funnel energy into approximately 100 reaction centers. Chlorosomes could be isolated by a simple density gradient procedure only from cells grown at low light intensity. A bacteriochlorophyll a species absorbing at 790 nm was associated with isolated chlorosomes. Lithium dodecyl sulfate-polyacrylamide gel electrophoresis of chlorosomes showed only a few low-molecular-weight polypeptides (less than 15,000).
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research-article |
44 |
76 |
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Yokoyama K, Lilla EA. C-C bond forming radical SAM enzymes involved in the construction of carbon skeletons of cofactors and natural products. Nat Prod Rep 2018; 35:660-694. [PMID: 29633774 PMCID: PMC6051890 DOI: 10.1039/c8np00006a] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: up to the end of 2017 C-C bond formations are frequently the key steps in cofactor and natural product biosynthesis. Historically, C-C bond formations were thought to proceed by two electron mechanisms, represented by Claisen condensation in fatty acids and polyketide biosynthesis. These types of mechanisms require activated substrates to create a nucleophile and an electrophile. More recently, increasing number of C-C bond formations catalyzed by radical SAM enzymes are being identified. These free radical mediated reactions can proceed between almost any sp3 and sp2 carbon centers, allowing introduction of C-C bonds at unconventional positions in metabolites. Therefore, free radical mediated C-C bond formations are frequently found in the construction of structurally unique and complex metabolites. This review discusses our current understanding of the functions and mechanisms of C-C bond forming radical SAM enzymes and highlights their important roles in the biosynthesis of structurally complex, naturally occurring organic molecules. Mechanistic consideration of C-C bond formation by radical SAM enzymes identifies the significance of three key mechanistic factors: radical initiation, acceptor substrate activation and radical quenching. Understanding the functions and mechanisms of these characteristic enzymes will be important not only in promoting our understanding of radical SAM enzymes, but also for understanding natural product and cofactor biosynthesis.
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Review |
7 |
75 |
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Zhu YS, Hearst JE. Regulation of expression of genes for light-harvesting antenna proteins LH-I and LH-II; reaction center polypeptides RC-L, RC-M, and RC-H; and enzymes of bacteriochlorophyll and carotenoid biosynthesis in Rhodobacter capsulatus by light and oxygen. Proc Natl Acad Sci U S A 1986; 83:7613-7. [PMID: 3532117 PMCID: PMC386771 DOI: 10.1073/pnas.83.20.7613] [Citation(s) in RCA: 75] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
RNA levels were measured by blot hybridization to study the coordinate and differential expression of Rhodobacter capsulatus genes for light-harvesting I antenna proteins LH-I and LH-II; reaction center (RC) polypeptides L, M, and H; and bacteriochlorophyll and carotenoid biosynthesis in response to light and O2. The genes for LH-II alpha and beta subunits only have one transcript, 0.5 kilobase (kb) long, whereas the genes for LH-I have two transcripts (0.5 and 2.6 kb). The small transcript (0.5 kb) is the mRNA only for LH-I beta and alpha polypeptides, whereas the large transcript (2.6 kb) codes for RC-L, RC-M, and the beta and alpha polypeptides of LH-I, as well as the product of an unknown open reading frame designated ORF C2397. These five genes thus comprise a single operon (designated the puf operon). The mRNA specifying the LH-II polypeptides is more abundant, more sensitive to changes in O2 concentration, and shows a variation over a wider range than that of the mRNA for LH-I, indicating that the genes for LH-II and LH-I/RC are regulated independently. The gene for RC-H (puhA) has at least two transcripts (1.2 and 1.4 kb) that initiate within ORF F1696 and respond differentially to light intensity. The expression of the genes coding for RC-L, RC-M, and RC-H is coordinately regulated by light intensity and O2 concentration. An increase in light intensity causes a decrease in the expression of the genes for LH-I, LH-II, and RC proteins. The genes coding for the enzymes in the bacteriochlorophyll biosynthetic pathways are regulated by light intensity and O2 in a manner similar to that of the genes for LH and RC proteins. The crt genes coding for the enzymes in carotenoid biosynthetic pathways, however, are regulated in an opposite fashion: high light intensity results in increased expression of crt genes. These results are interpreted based on the protective function of carotenoids under high light intensity in the presence of O2.
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Bauer CE, Marrs BL. Rhodobacter capsulatus puf operon encodes a regulatory protein (PufQ) for bacteriochlorophyll biosynthesis. Proc Natl Acad Sci U S A 1988; 85:7074-8. [PMID: 3174621 PMCID: PMC282126 DOI: 10.1073/pnas.85.19.7074] [Citation(s) in RCA: 72] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Biosynthesis of the photochemical apparatus by purple nonsulfur photosynthetic bacteria is known to be inhibited by molecular oxygen and high light intensity. Polypeptides that bind bacteriochlorophyll (BChl) to form the light-harvesting I (LH-I) and reaction-center (RC) complexes are encoded by a single transcriptional unit termed the puf operon. In this investigation we demonstrate that the first structural gene in the puf operon (pufQ) of Rhodobacter capsulatus encodes a protein that is required for BChl biosynthesis and that there exists a linear relationship between the amount of pufQ expression and the level of BChl synthesis. Protein sequence similarity exists between PufQ and the region of RC polypeptides that are known to bind BChl and quinone. These observations suggest that pufQ may regulate BChl biosynthesis by a "carrier polypeptide" mechanism as originally proposed by Lascelles.
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Meyer J, Kelley BC, Vignais PM. Effect of light nitrogenase function and synthesis in Rhodopseudomonas capsulata. J Bacteriol 1978; 136:201-8. [PMID: 711666 PMCID: PMC218650 DOI: 10.1128/jb.136.1.201-208.1978] [Citation(s) in RCA: 71] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The metabolic versatility of the purple nonsulfur photosynethetic bacterial permits the expression of either a phototrophic or a dark aerobic mode of growth. These organism also possess nitrogenase activity which may function under semiaerboic conditions. On the basis of these important properties, the light dependence of nitrogenase function and synthesis in Rhodopseudomonas capsulata was investigated. Nitrogenase activity was strictly dependent on light; no activity was observed in the dark, even when energy (ATP) was supplied by oxidative phosphorylation. It was concluded that the low-potential reducing agent required by the nitrogenase-catalyzed reaction could only be generated by a photochemical reaction. Nitrogenase biosynthesis was also largely dependent on light; however, a small amount of synthesis was observed in resting cells incubated in the dark. Resting cells prepared from dark-grown cultures synthesized nitrogenase at high rates upon illumination. The highest stability of nitrogenase in these resting cells was observed when suspensions were exposed to a diurnal pattern of illumination rather than continuous light. Although nitrogenase function and synthesis are closely coupled to photosynthetic activity, the biosyntheses of bacteriochorophyll and nitrogenase are independent of each other and are most probably subject to different regulatory mechanisms by light.
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Bauer CE, Bollivar DW, Suzuki JY. Genetic analyses of photopigment biosynthesis in eubacteria: a guiding light for algae and plants. J Bacteriol 1993; 175:3919-25. [PMID: 8320208 PMCID: PMC204818 DOI: 10.1128/jb.175.13.3919-3925.1993] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
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Oster U, Bauer CE, Rüdiger W. Characterization of chlorophyll a and bacteriochlorophyll a synthases by heterologous expression in Escherichia coli. J Biol Chem 1997; 272:9671-6. [PMID: 9092496 DOI: 10.1074/jbc.272.15.9671] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Genes coding for putative chlorophyll a synthase (chlG) from Synechocystis sp. PCC 6803 and bacteriochlorophyll a synthase (bchG) from Rhodobacter capsulatus were amplified by the polymerase chain reaction and cloned into T7 RNA polymerase-based expression plasmids. In vitro enzymatic assays indicated that heterologous expression of the chlG and bchG gene products in Escherichia coli conferred chlorophyll a and bacteriochlorophyll a synthase activity, respectively. Chlorophyll a synthase utilized chlorophyllide a, but not bacteriochlorophyllide a, as a substrate, whereas bacteriochlorophyll a synthase utilized bacteriochlorophyllide a, but not chlorophyllide a. Both enzymes were also observed to exhibit a marked preference for phytyl diphosphate over geranylgeranyl diphosphate.
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Maresca JA, Gomez Maqueo Chew A, Ponsatí MR, Frigaard NU, Ormerod JG, Bryant DA. The bchU gene of Chlorobium tepidum encodes the c-20 methyltransferase in bacteriochlorophyll c biosynthesis. J Bacteriol 2004; 186:2558-66. [PMID: 15090495 PMCID: PMC387796 DOI: 10.1128/jb.186.9.2558-2566.2004] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacteriochlorophylls (BChls) c and d, two of the major light-harvesting pigments in photosynthetic green sulfur bacteria, differ only by the presence of a methyl group at the C-20 methine bridge position in BChl c. A gene potentially encoding the C-20 methyltransferase, bchU, was identified by comparative analysis of the Chlorobium tepidum and Chloroflexus aurantiacus genome sequences. Homologs of this gene were amplified and sequenced from Chlorobium phaeobacteroides strain 1549, Chlorobium vibrioforme strain 8327d, and C. vibrioforme strain 8327c, which produce BChls e, d, and c, respectively. A single nucleotide insertion in the bchU gene of C. vibrioforme strain 8327d was found to cause a premature, in-frame stop codon and thus the formation of a truncated, nonfunctional gene product. The spontaneous mutant of this strain that produces BChl c (strain 8327c) has a second frameshift mutation that restores the correct reading frame in bchU. The bchU gene was inactivated in C. tepidum, a BChl c-producing species, and the resulting mutant produced only BChl d. Growth rate measurements showed that BChl c- and d-producing strains of the same organism (C. tepidum or C. vibrioforme) have similar growth rates at high and intermediate light intensities but that strains producing BChl c grow faster than those with BChl d at low light intensities. Thus, the bchU gene encodes the C-20 methyltransferase for BChl c biosynthesis in Chlorobium species, and methylation at the C-20 position to produce BChl c rather than BChl d confers a significant competitive advantage to green sulfur bacteria living at limiting red and near-infrared light intensities.
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Research Support, U.S. Gov't, Non-P.H.S. |
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