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Narsing Rao MP, Luo ZH, Dong ZY, Li Q, Liu BB, Guo SX, Nie GX, Li WJ. Metagenomic analysis further extends the role of Chloroflexi in fundamental biogeochemical cycles. ENVIRONMENTAL RESEARCH 2022; 209:112888. [PMID: 35143804 DOI: 10.1016/j.envres.2022.112888] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/02/2022] [Accepted: 02/01/2022] [Indexed: 06/14/2023]
Abstract
Chloroflexi members are ubiquitous and have been extensively studied; however, the evolution and metabolic pathways of Chloroflexi members have long been debated. In the present study, the evolution and the metabolic potentials of 17 newly obtained Chloroflexi metagenome-assembled genomes (MAGs) were evaluated using genome and horizontal gene transfer (HGT) analysis. Taxonomic analysis suggests that the MAGs of the present study might be novel. One MAG encodes genes for anoxygenic phototrophy. The HGT analysis suggest that genes responsible for anoxygenic phototrophy in the MAG might have been transferred from Proteobacteria/Chlorobi. The evolution of anaerobic photosynthesis, which has long been questioned, has now been shown to be the result of HGT events. An incomplete Wood-Ljungdahl pathway (with missing genes metF, acsE, fdh, and acsA) was reported in Dehalococcoidetes members. In the present study, MAGs that were not the Dehalococcoidetes members encode genes acsA, acsB, metF and acsE. The genes responsible for sulfate reduction (sat, cysC and sir), dissimilatory sulfite reductase (dsrA and dsrB), and aerobic and anaerobic carbon monoxide oxidation (coxSML and cooSF) were detected in the present study MAGs. The present study expands our knowledge of the possible metabolic potentials of the phylum Chloroflexi and clarifies the evolution of anaerobic photosynthesis.
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Affiliation(s)
- Manik Prabhu Narsing Rao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Zhen-Hao Luo
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Zhou-Yan Dong
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China; Department of Pathogenic Biology, Binzhou Medical University, Yantai, 264003, PR China
| | - Qi Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Bing-Bing Liu
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, College of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, 473004, PR China
| | - Shu-Xian Guo
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, College of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, 473004, PR China
| | - Guo-Xin Nie
- College of Fisheries, Henan Normal University, Xinxiang, 453007, PR China.
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China.
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2
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Bahiri Elitzur S, Cohen-Kupiec R, Yacobi D, Fine L, Apt B, Diament A, Tuller T. Prokaryotic rRNA-mRNA interactions are involved in all translation steps and shape bacterial transcripts. RNA Biol 2021; 18:684-698. [PMID: 34586043 DOI: 10.1080/15476286.2021.1978767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
The well-established Shine-Dalgarno model suggests that translation initiation in bacteria is regulated via base-pairing between ribosomal RNA (rRNA) and mRNA. We used novel computational analyses and modelling of 823 bacterial genomes coupled with experiments to demonstrate that rRNA-mRNA interactions are diverse and regulate all translation steps from pre-initiation to termination. Previous research has reported the significant influence of rRNA-mRNA interactions, mainly in the initiation phase of translation. The results reported in this paper suggest that, in addition to the rRNA-mRNA interactions near the start codon that trigger initiation in bacteria, rRNA-mRNA interactions affect all sub-stages of the translation process (pre-initiation, initiation, elongation, termination). As these interactions dictate translation efficiency, they serve as an evolutionary driving force for shaping transcripts in bacteria while considering trade-offs between the effects of different interactions across different transcript regions on translation efficacy and efficiency. We observed selection for strong interactions in regions where such interactions are likely to enhance initiation, regulate early elongation, and ensure translation termination fidelity. We discovered selection against strong interactions and for intermediate interactions in coding regions and presented evidence that these patterns maximize elongation efficiency while also enhancing initiation. These finding are relevant to all biomedical disciplines due to the centrality of the translation process and the effect of rRNA-mRNA interactions on transcript evolution.
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Affiliation(s)
| | | | - Dana Yacobi
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel
| | - Larissa Fine
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel
| | - Boaz Apt
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel
| | - Alon Diament
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel.,The Sagol School of Neuroscience, Tel-Aviv University, Tel Aviv, Israel
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3
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Dewey ED, Stokes LM, Burchell BM, Shaffer KN, Huntington AM, Baker JM, Nadendla S, Giglio MG, Bender KS, Touchman JW, Blankenship RE, Madigan MT, Sattley WM. Analysis of the Complete Genome of the Alkaliphilic and Phototrophic Firmicute Heliorestis convoluta Strain HH T. Microorganisms 2020; 8:microorganisms8030313. [PMID: 32106460 PMCID: PMC7143216 DOI: 10.3390/microorganisms8030313] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 02/16/2020] [Accepted: 02/22/2020] [Indexed: 11/16/2022] Open
Abstract
Despite significant interest and past work to elucidate the phylogeny and photochemistry of species of the Heliobacteriaceae, genomic analyses of heliobacteria to date have been limited to just one published genome, that of the thermophilic species Heliobacterium (Hbt.) modesticaldum str. Ice1T. Here we present an analysis of the complete genome of a second heliobacterium, Heliorestis (Hrs.) convoluta str. HHT, an alkaliphilic, mesophilic, and morphologically distinct heliobacterium isolated from an Egyptian soda lake. The genome of Hrs. convoluta is a single circular chromosome of 3.22 Mb with a GC content of 43.1% and 3263 protein-encoding genes. In addition to culture-based observations and insights gleaned from the Hbt. modesticaldum genome, an analysis of enzyme-encoding genes from key metabolic pathways supports an obligately photoheterotrophic lifestyle for Hrs. convoluta. A complete set of genes encoding enzymes for propionate and butyrate catabolism and the absence of a gene encoding lactate dehydrogenase distinguishes the carbon metabolism of Hrs. convoluta from its close relatives. Comparative analyses of key proteins in Hrs. convoluta, including cytochrome c553 and the Fo alpha subunit of ATP synthase, with those of related species reveal variations in specific amino acid residues that likely contribute to the success of Hrs. convoluta in its highly alkaline environment.
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Affiliation(s)
- Emma D. Dewey
- Division of Natural Sciences, Indiana Wesleyan University, Marion, IN 46953, USA; (E.D.D.); (L.M.S.); (B.M.B.); (K.N.S.); (A.M.H.); (J.M.B.)
| | - Lynn M. Stokes
- Division of Natural Sciences, Indiana Wesleyan University, Marion, IN 46953, USA; (E.D.D.); (L.M.S.); (B.M.B.); (K.N.S.); (A.M.H.); (J.M.B.)
| | - Brad M. Burchell
- Division of Natural Sciences, Indiana Wesleyan University, Marion, IN 46953, USA; (E.D.D.); (L.M.S.); (B.M.B.); (K.N.S.); (A.M.H.); (J.M.B.)
| | - Kathryn N. Shaffer
- Division of Natural Sciences, Indiana Wesleyan University, Marion, IN 46953, USA; (E.D.D.); (L.M.S.); (B.M.B.); (K.N.S.); (A.M.H.); (J.M.B.)
| | - Austin M. Huntington
- Division of Natural Sciences, Indiana Wesleyan University, Marion, IN 46953, USA; (E.D.D.); (L.M.S.); (B.M.B.); (K.N.S.); (A.M.H.); (J.M.B.)
| | - Jennifer M. Baker
- Division of Natural Sciences, Indiana Wesleyan University, Marion, IN 46953, USA; (E.D.D.); (L.M.S.); (B.M.B.); (K.N.S.); (A.M.H.); (J.M.B.)
| | - Suvarna Nadendla
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA; (S.N.); (M.G.G.)
| | - Michelle G. Giglio
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA; (S.N.); (M.G.G.)
| | - Kelly S. Bender
- Department of Microbiology, Southern Illinois University, Carbondale, IL 62901, USA; (K.S.B.); (M.T.M.)
| | | | - Robert E. Blankenship
- Departments of Biology and Chemistry, Washington University in Saint Louis, St. Louis, MO 63130, USA;
| | - Michael T. Madigan
- Department of Microbiology, Southern Illinois University, Carbondale, IL 62901, USA; (K.S.B.); (M.T.M.)
| | - W. Matthew Sattley
- Division of Natural Sciences, Indiana Wesleyan University, Marion, IN 46953, USA; (E.D.D.); (L.M.S.); (B.M.B.); (K.N.S.); (A.M.H.); (J.M.B.)
- Correspondence: ; Tel.: +1-765-677-2128
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4
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Ward LM, Shih PM. The evolution and productivity of carbon fixation pathways in response to changes in oxygen concentration over geological time. Free Radic Biol Med 2019; 140:188-199. [PMID: 30790657 DOI: 10.1016/j.freeradbiomed.2019.01.049] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 01/12/2019] [Accepted: 01/31/2019] [Indexed: 12/25/2022]
Abstract
The fixation of inorganic carbon species like CO2 to more reduced organic forms is one of the most fundamental processes of life as we know it. Although several carbon fixation pathways are known to exist, on Earth today nearly all global carbon fixation is driven by the Calvin cycle in oxygenic photosynthetic plants, algae, and Cyanobacteria. At other times in Earth history, other organisms utilizing different carbon fixation pathways may have played relatively larger roles, with this balance shifting over geological time as the environmental context of life has changed and evolutionary innovations accumulated. Among the most dramatic changes that our planet and the biosphere have undergone are those surrounding the rise of O2 in our atmosphere-first during the Great Oxygenation Event at ∼2.3 Ga, and perhaps again during Neoproterozoic or Paleozoic time. These oxygenation events likely represent major step changes in the tempo and mode of biological productivity as a result of the increased productivity of oxygenic photosynthesis and the introduction of O2 into geochemical and biological systems, and likely involved shifts in the relative contribution of different carbon fixation pathways. Here, we review what is known from both the rock record and comparative biology about the evolution of carbon fixation pathways, their contributions to primary productivity through time, and their relationship to the evolving oxygenation state of the fluid Earth following the evolution and expansion of oxygenic photosynthesis.
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Affiliation(s)
- Lewis M Ward
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, United States.
| | - Patrick M Shih
- Department of Plant Biology, University of California, Davis, Davis, CA, United States; Department of Energy, Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, United States; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
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5
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Ward LM, Hemp J, Shih PM, McGlynn SE, Fischer WW. Evolution of Phototrophy in the Chloroflexi Phylum Driven by Horizontal Gene Transfer. Front Microbiol 2018. [PMID: 29515543 PMCID: PMC5826079 DOI: 10.3389/fmicb.2018.00260] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The evolutionary mechanisms behind the extant distribution of photosynthesis is a point of substantial contention. Hypotheses range from the presence of phototrophy in the last universal common ancestor and massive gene loss in most lineages, to a later origin in Cyanobacteria followed by extensive horizontal gene transfer into the extant phototrophic clades, with intermediate scenarios that incorporate aspects of both end-members. Here, we report draft genomes of 11 Chloroflexi: the phototrophic Chloroflexia isolate Kouleothrix aurantiaca as well as 10 genome bins recovered from metagenomic sequencing of microbial mats found in Japanese hot springs. Two of these metagenome bins encode photrophic reaction centers and several of these bins form a metabolically diverse, monophyletic clade sister to the Anaerolineae class that we term Candidatus Thermofonsia. Comparisons of organismal (based on conserved ribosomal) and phototrophy (reaction center and bacteriochlorophyll synthesis) protein phylogenies throughout the Chloroflexi demonstrate that two new lineages acquired phototrophy independently via horizontal gene transfer (HGT) from different ancestral donors within the classically phototrophic Chloroflexia class. These results illustrate a complex history of phototrophy within this group, with metabolic innovation tied to HGT. These observations do not support simple hypotheses for the evolution of photosynthesis that require massive character loss from many clades; rather, HGT appears to be the defining mechanic for the distribution of phototrophy in many of the extant clades in which it appears.
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Affiliation(s)
- Lewis M Ward
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, United States
| | - James Hemp
- Department of Gastroenterology, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Patrick M Shih
- Department of Energy, Joint BioEnergy Institute, Emeryville, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Shawn E McGlynn
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro, Japan
| | - Woodward W Fischer
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, United States
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6
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Kondo T, Matsuoka M, Azai C, Itoh S, Oh-oka H. Orientations of Iron–Sulfur Clusters FA and FB in the Homodimeric Type-I Photosynthetic Reaction Center of Heliobacterium modesticaldum. J Phys Chem B 2016; 120:4204-12. [DOI: 10.1021/acs.jpcb.6b01112] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Toru Kondo
- Division
of Material Science (Physics), Graduate School of Science, Nagoya University, Furocho, Chikusa, Nagoya 464-8602, Japan
| | - Masahiro Matsuoka
- Department
of Biological Sciences, Graduate School of Science, Osaka University, Osaka 560-0043, Japan
| | - Chihiro Azai
- Department
of Biological Sciences, Graduate School of Science, Osaka University, Osaka 560-0043, Japan
| | - Shigeru Itoh
- Center
for Gene Research, Nagoya University, Furocho, Chikusa, Nagoya 464-8602, Japan
| | - Hirozo Oh-oka
- Department
of Biological Sciences, Graduate School of Science, Osaka University, Osaka 560-0043, Japan
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7
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Cardona T. A fresh look at the evolution and diversification of photochemical reaction centers. PHOTOSYNTHESIS RESEARCH 2015; 126:111-34. [PMID: 25512103 PMCID: PMC4582080 DOI: 10.1007/s11120-014-0065-x] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 12/05/2014] [Indexed: 05/18/2023]
Abstract
In this review, I reexamine the origin and diversification of photochemical reaction centers based on the known phylogenetic relations of the core subunits, and with the aid of sequence and structural alignments. I show, for example, that the protein folds at the C-terminus of the D1 and D2 subunits of Photosystem II, which are essential for the coordination of the water-oxidizing complex, were already in place in the most ancestral Type II reaction center subunit. I then evaluate the evolution of reaction centers in the context of the rise and expansion of the different groups of bacteria based on recent large-scale phylogenetic analyses. I find that the Heliobacteriaceae family of Firmicutes appears to be the earliest branching of the known groups of phototrophic bacteria; however, the origin of photochemical reaction centers and chlorophyll synthesis cannot be placed in this group. Moreover, it becomes evident that the Acidobacteria and the Proteobacteria shared a more recent common phototrophic ancestor, and this is also likely for the Chloroflexi and the Cyanobacteria. Finally, I argue that the discrepancies among the phylogenies of the reaction center proteins, chlorophyll synthesis enzymes, and the species tree of bacteria are best explained if both types of photochemical reaction centers evolved before the diversification of the known phyla of phototrophic bacteria. The primordial phototrophic ancestor must have had both Type I and Type II reaction centers.
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Affiliation(s)
- Tanai Cardona
- Department of Life Sciences, Imperial College London, Exhibition Road, London, SW7 2AZ, UK.
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8
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Kondo T, Itoh S, Matsuoka M, Azai C, Oh-oka H. Menaquinone as the Secondary Electron Acceptor in the Type I Homodimeric Photosynthetic Reaction Center of Heliobacterium modesticaldum. J Phys Chem B 2015; 119:8480-9. [PMID: 26075484 DOI: 10.1021/acs.jpcb.5b03723] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The type I photosynthetic reaction center (RC) of heliobacteria (hRC) is a homodimer containing cofactors almost analogous to those in the plant photosystem I (PS I). However, its three-dimensional structure is not yet clear. PS I uses phylloquinone (PhyQ) as a secondary electron acceptor (A1), while the available evidence has suggested that menaquinone (MQ) in hRC has no function as A1. The present study identified a new transient electron spin-polarized electron paramagnetic resonance (ESP-EPR) signal, arising from the radical pair of the oxidized electron donor and the reduced electron acceptor (P800(+)MQ(-)), in the hRC core complex and membranes from Heliobacterium modesticaldum. The ESP signal could be detected at 5-20 K upon flash excitation only after prereduction of the iron-sulfur center, F(X), and was selectively lost by extraction of MQ with diethyl ether. MQ was suggested to be located closer to F(X) than PhyQ in PS I based on the simulation of the unique A/E (A, absorption; E, emission) ESP pattern, the reduction/oxidation rates of MQ, and the power saturation property of the static MQ(-) signal. The result revealed the quinone usage as the secondary electron acceptor in hRC, as in the case of PS I.
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Affiliation(s)
| | | | - Masahiro Matsuoka
- §Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka 560-0043, Japan
| | - Chihiro Azai
- §Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka 560-0043, Japan
| | - Hirozo Oh-oka
- §Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka 560-0043, Japan
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9
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Energy Conservation in Heliobacteria: Photosynthesis and Central Carbon Metabolism. THE STRUCTURAL BASIS OF BIOLOGICAL ENERGY GENERATION 2014. [DOI: 10.1007/978-94-017-8742-0_13] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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10
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Romberger SP, Golbeck JH. The FX iron-sulfur cluster serves as the terminal bound electron acceptor in heliobacterial reaction centers. PHOTOSYNTHESIS RESEARCH 2012; 111:285-290. [PMID: 22297911 DOI: 10.1007/s11120-012-9723-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Accepted: 01/13/2012] [Indexed: 05/31/2023]
Abstract
Phototrophs of the family Heliobacteriaceae contain the simplest known Type I reaction center (RC), consisting of a homodimeric (PshA)(2) core devoid of bound cytochromes and antenna proteins. Unlike plant and cyanobacterial Photosystem I in which the F(A)/F(B) protein, PsaC, is tightly bound to P(700)-F(X) cores, the RCs of Heliobacterium modesticaldum contain two F(A)/F(B) proteins, PshBI and PshBII, which are loosely bound to P(800)-F(X) cores. These two 2[4Fe-4S] ferredoxins have been proposed to function as mobile redox proteins, reducing downstream metabolic partners much in the same manner as does [2Fe-2S] ferredoxin or flavodoxin (Fld) in PS I. Using P(800)-F(X) cores devoid of PshBI and PshBII, we show that iron-sulfur cluster F(X) directly reduces Fld without the involvement of F(A) or F(B) (Fld is used as a proxy for soluble redox proteins even though a gene encoding Fld is not identified in the H. modesticaldum genome). The reduction of Fld is suppressed by the addition of PshBI or PshBII, an effect explained by competition for the electron on F(X). In contrast, P(700)-F(X) cores require the presence of the PsaC, and hence, the F(A)/F(B) clusters for Fld (or ferredoxin) reduction. Thus, in H. modesticaldum, the interpolypeptide F(X) cluster serves as the terminal bound electron acceptor. This finding implies that the homodimeric (PshA)(2) cores should be capable of donating electrons to a wide variety of yet-to-be characterized soluble redox partners.
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Affiliation(s)
- Steven P Romberger
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
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11
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de Vitry C. Cytochrome c maturation system on the negative side of bioenergetic membranes: CCB or System IV. FEBS J 2011; 278:4189-97. [DOI: 10.1111/j.1742-4658.2011.08373.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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12
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Baymann F, Nitschke W. Heliobacterial Rieske/cytb complex. PHOTOSYNTHESIS RESEARCH 2010; 104:177-187. [PMID: 20091229 DOI: 10.1007/s11120-009-9524-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2009] [Accepted: 12/21/2009] [Indexed: 05/28/2023]
Abstract
Data on structure and function of the Rieske/cytb complex from Heliobacteria are scarce. They indicate that the complex is related to the b (6) f complex in agreement with the phylogenetic position of the organism. It is composed of a diheme cytochrome c, and a Rieske iron-sulfur protein, together with transmembrane cytochrome b (6) and subunit IV. Additional small subunits may be part of the complex. The cofactor content comprises heme c (i), first discovered in the Q(i) binding pocket of b (6) f complexes. The redox midpoint potentials are more negative than in b (6) f complex in agreement with the lower redox midpoint potentials (by about 150 mV) of its reaction partners, menaquinone, and cytochrome c (553). The enzyme is implicated in cyclic electron transfer around the RCI. Functional studies are favored by the absence of antennae and the simple photosynthetic reaction chain but are hampered by the high oxygen sensitivity of the organism, its chlorophyll, and lipids.
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Affiliation(s)
- F Baymann
- BIP, Centre National de la Recherche Scientifique, UPR9036, IFR88, 31 Chemin Joseph Aiguier, Marseille, France.
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13
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Nitschke W, van Lis R, Schoepp-Cothenet B, Baymann F. The "green" phylogenetic clade of Rieske/cytb complexes. PHOTOSYNTHESIS RESEARCH 2010; 104:347-355. [PMID: 20130997 DOI: 10.1007/s11120-010-9532-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2009] [Accepted: 01/16/2010] [Indexed: 05/28/2023]
Abstract
More than a decade ago, Heliobacteria were recognised to contain a Rieske/cytb complex in which the cytochrome b subunit is split into two separate proteins, a peculiar feature characteristic of the cyanobacterial and plastidic b (6) f complex. The common presence of RCI-type reaction centres further emphasise possible evolutionary links between Heliobacteria, Chlorobiaceae and Cyanobacteria. In this contribution, we further explore the evolutionary relationships among these three phototrophic lineages by both molecular phylogeny and consideration of phylogenetic marker traits of the superfamily of Rieske/cytb complexes. The combination of these two methods suggests the existence of a "green" clade involving many non-phototrophs in addition to the mentioned RCI-type photosynthetic organisms. Structural and functional idiosyncrasies are (re-)interpreted in the framework of evolutionary biology and more specifically evolutionary bioenergetics.
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Affiliation(s)
- W Nitschke
- BIP, Centre National de la Recherche Scientifique, UPR9036, IFR88, 31 Chemin Joseph Aiguier, Marseille, France.
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14
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Romberger SP, Castro C, Sun Y, Golbeck JH. Identification and characterization of PshBII, a second FA/FB-containing polypeptide in the photosynthetic reaction center of Heliobacterium modesticaldum. PHOTOSYNTHESIS RESEARCH 2010; 104:293-303. [PMID: 20502966 DOI: 10.1007/s11120-010-9558-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2010] [Accepted: 04/29/2010] [Indexed: 05/29/2023]
Abstract
All known Type I photosynthetic reaction centers harbor three [4Fe-4S] clusters named F(X), F(A) and F(B) that function as terminal electron acceptors. We reported earlier that F(A) and F(B) in the homodimeric Type I reaction center from Heliobacterium modesticaldum reside on a loosely bound 54 amino acid protein named PshB. Time-resolved optical spectroscopy and low temperature EPR spectroscopy showed that on illumination, electrons were transferred from F(X) (-) to F(A) and F(B) at both cryogenic and room temperatures. Interestingly, the gene that codes for PshB, HM1_1462, is part of a predicted dicistronic operon that contains a second gene, named HM1_1461, which codes for a second ferredoxin-like protein with high sequence homology to PshB, including the two traditional [4Fe-4S] cluster binding motifs. RT-PCR results confirm that both genes are transcribed as a single transcript. We have cloned the HM1_1461 gene through PCR amplification of the H. modesticaldum chromosomal DNA and overexpressed the apoprotein in Escherichia coli. Reconstitution studies with inorganic reagents have shown that the holoprotein harbors ~8 iron and ~8 sulfide atoms in the form of two [4Fe-4S] clusters. Incubation of the reconstituted holoprotein with heliobacterial reaction center cores results in a charge-separated state characteristic of electron transfer past the F(X) cluster to the terminal [4Fe-4S] clusters F(A) and F(B). These results suggest that the HM1_1461 product, which we have named PshBII, is capable of functioning in lieu of PshB (renamed PshBI) as an alternative terminal electron transfer protein. Thus, unlike PS I, to which PsaC is tightly bound, two loosely bound ferredoxins, PshBI and PshBII, are capable of interacting with the heliobacterial reaction center. The presence of two, loosely bound F(A)/F(B) proteins represents a significant shift in our understanding of structure-function relationships in Type I reaction centers.
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Affiliation(s)
- Steven P Romberger
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
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15
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Asao M, Madigan MT. Taxonomy, phylogeny, and ecology of the heliobacteria. PHOTOSYNTHESIS RESEARCH 2010; 104:103-111. [PMID: 20094790 DOI: 10.1007/s11120-009-9516-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2009] [Accepted: 12/07/2009] [Indexed: 05/28/2023]
Abstract
Heliobacteria are a recently discovered group of anoxygenic phototrophic bacteria, first described in 1983. Heliobacteria contain bacteriochlorophyll g, a pigment unique to species of this group, and synthesize the simplest photosynthetic complexes of all known phototrophs. Also, unlike all other phototrophs, heliobacteria lack a mechanism for autotrophy and produce endospores. Four genera of heliobacteria containing a total of 10 species are known. Species of the genera Heliobacterium, Heliobacillus, and Heliophilum grow best at neutral pH, whereas species of Heliorestis are alkaliphilic. Heliobacterium, Heliobacillus, and Heliophilum species form one phylogenetic clade of heliobacteria, while Heliorestis species form a second within the phylum Firmicutes of the domain Bacteria. Heliobacteria have a unique ecology, being primarily terrestrial rather than aquatic phototrophs, and may have evolved a mutualistic relationship with plants, in particular, rice plants. The genome sequence of the thermophile Heliobacterium modesticaldum supports the hypothesis that heliobacteria are "minimalist phototrophs" and that they may have played a key role in the evolution of phototrophic bacteria.
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Affiliation(s)
- Marie Asao
- Department of Microbiology, Southern Illinois University, Carbondale, IL 62901, USA
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16
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Affiliation(s)
- Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
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17
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Miyamoto R, Mino H, Kondo T, Itoh S, Oh-oka H. An Electron Spin-Polarized Signal of the P800+A1(Q)− State in the Homodimeric Reaction Center Core Complex of Heliobacterium modesticaldum. Biochemistry 2008; 47:4386-93. [DOI: 10.1021/bi701612v] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ryo Miyamoto
- Division of Material Science (Physics), Graduate School of Science, Nagoya University, Furocho, Chikusa, Nagoya 464-8602, Japan, and Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka 560-0043, Japan
| | - Hiroyuki Mino
- Division of Material Science (Physics), Graduate School of Science, Nagoya University, Furocho, Chikusa, Nagoya 464-8602, Japan, and Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka 560-0043, Japan
| | - Toru Kondo
- Division of Material Science (Physics), Graduate School of Science, Nagoya University, Furocho, Chikusa, Nagoya 464-8602, Japan, and Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka 560-0043, Japan
| | - Shigeru Itoh
- Division of Material Science (Physics), Graduate School of Science, Nagoya University, Furocho, Chikusa, Nagoya 464-8602, Japan, and Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka 560-0043, Japan
| | - Hirozo Oh-oka
- Division of Material Science (Physics), Graduate School of Science, Nagoya University, Furocho, Chikusa, Nagoya 464-8602, Japan, and Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka 560-0043, Japan
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18
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Heinnickel M, Golbeck JH. Heliobacterial photosynthesis. PHOTOSYNTHESIS RESEARCH 2007; 92:35-53. [PMID: 17457690 DOI: 10.1007/s11120-007-9162-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2007] [Accepted: 03/23/2007] [Indexed: 05/15/2023]
Abstract
Heliobacteria contain Type I reaction centers (RCs) and a homodimeric core, but unlike green sulfur bacteria, they do not contain an extended antenna system. Given their simplicity, the heliobacterial RC (HbRC) should be ideal for the study of a prototypical homodimeric RC. However, there exist enormous gaps in our knowledge, particularly with regard to the nature of the secondary and tertiary electron acceptors. To paraphrase S. Neerken and J. Amesz (2001 Biochim Biophys Acta 1507:278-290): with the sole exception of primary charge separation, little progress has been made in recent years on the HbRC, either with respect to the polypeptide composition, or the nature of the electron acceptor chain, or the kinetics of forward and backward electron transfer. This situation, however, has changed. First, the low molecular mass polypeptide that contains the terminal FA and FB iron-sulfur clusters has been identified. The change in the lifetime of the flash-induced kinetics from 75 ms to 15 ms on its removal shows that the former arises from the P798+ [FA/FB]- recombination, and the latter from P798+ FX- recombination. Second, FX has been identified in HbRC cores by EPR and Mössbauer spectroscopy, and shown to be a [4Fe-4S]1+,2+ cluster with a ground spin state of S=3/2. Since all of the iron in HbRC cores is in the FX cluster, a ratio of approximately 22 Bchl g/P798 could be calculated from chemical assays of non-heme iron and Bchl g. Third, the N-terminal amino acid sequence of the FA/FB-containing polypeptide led to the identification and cloning of its gene. The expressed protein can be rebound to isolated HbRC cores, thereby regaining both the 75 ms kinetic phase resulting from P798+ [FA/FB]- recombination and the light-induced EPR resonances of FA- and FB-. The gene was named 'pshB' and the protein 'PshB' in keeping with the accepted nomenclature for Type I RCs. This article reviews the current state of knowledge on the structure and function of the HbRC.
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Affiliation(s)
- Mark Heinnickel
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
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19
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Cavalier-Smith T. Cell evolution and Earth history: stasis and revolution. Philos Trans R Soc Lond B Biol Sci 2006; 361:969-1006. [PMID: 16754610 PMCID: PMC1578732 DOI: 10.1098/rstb.2006.1842] [Citation(s) in RCA: 147] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
This synthesis has three main parts. The first discusses the overall tree of life and nature of the last common ancestor (cenancestor). I emphasize key steps in cellular evolution important for ordering and timing the major evolutionary innovations in the history of the biosphere, explaining especially the origins of the eukaryote cell and of bacterial flagella and cell envelope novelties. Second, I map the tree onto the fossil record and discuss dates of key events and their biogeochemical impact. Finally, I present a broad synthesis, discussing evidence for a three-phase history of life. The first phase began perhaps ca 3.5 Gyr ago, when the origin of cells and anoxic photosynthesis generated the arguably most primitive prokaryote phylum, Chlorobacteria (= Chloroflexi), the first negibacteria with cells bounded by two acyl ester phospholipid membranes. After this 'chlorobacterial age' of benthic anaerobic evolution protected from UV radiation by mineral grains, two momentous quantum evolutionary episodes of cellular innovation and microbial radiation dramatically transformed the Earth's surface: the glycobacterial revolution initiated an oxygenic 'age of cyanobacteria' and, as the ozone layer grew, the rise of plankton; immensely later, probably as recently as ca 0.9 Gyr ago, the neomuran revolution ushered in the 'age of eukaryotes', Archaebacteria (arguably the youngest bacterial phylum), and morphological complexity. Diversification of glycobacteria ca 2.8 Gyr ago, predominantly inhabiting stratified benthic mats, I suggest caused serial depletion of 13C by ribulose 1,5-bis-phosphate caboxylase/oxygenase (Rubisco) to yield ultralight late Archaean organic carbon formerly attributed to methanogenesis plus methanotrophy. The late origin of archaebacterial methanogenesis ca 720 Myr ago perhaps triggered snowball Earth episodes by slight global warming increasing weathering and reducing CO2 levels, to yield runaway cooling; the origin of anaerobic methane oxidation ca 570 Myr ago reduced methane flux at source, stabilizing Phanerozoic climates. I argue that the major cellular innovations exhibit a pattern of quantum evolution followed by very rapid radiation and then substantial stasis, as described by Simpson. They yielded organisms that are a mosaic of extremely conservative and radically novel features, as characterized by De Beer's phrase 'mosaic evolution'. Evolution is not evenly paced and there are no real molecular clocks.
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20
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Asao M, Jung DO, Achenbach LA, Madigan MT. Heliorestis convoluta sp. nov., a coiled, alkaliphilic heliobacterium from the Wadi El Natroun, Egypt. Extremophiles 2006; 10:403-10. [PMID: 16628377 DOI: 10.1007/s00792-006-0513-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2005] [Accepted: 01/06/2006] [Indexed: 11/27/2022]
Abstract
A morphologically distinct heliobacterium, strain HH, was isolated from Lake El Hamra, a soda lake in the Wadi El Natroun region of northwest Egypt. Strain HH consisted of ring-shaped cells that remained attached after cell division to yield coils of various lengths. Strain HH showed several of the physiological properties of known heliobacteria and grouped in the Heliorestis clade by virtue of its phylogeny and alkaliphily. The closest relative of strain HH was the filamentous alkaliphilic heliobacterium Heliorestis daurensis. However, genomic DNA:DNA hybridization results clearly indicated that strain HH was a distinct species of Heliorestis. Based on its unique phenotypic and genetic properties we describe strain HH here as a new species of the genus Heliorestis, H. convoluta sp. nov.
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Affiliation(s)
- Marie Asao
- Department of Microbiology, Southern Illinois University, Carbondale, IL 62901, USA
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21
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Pollack JD, Li Q, Pearl DK. Taxonomic utility of a phylogenetic analysis of phosphoglycerate kinase proteins of Archaea, Bacteria, and Eukaryota: Insights by Bayesian analyses. Mol Phylogenet Evol 2005; 35:420-30. [PMID: 15804412 DOI: 10.1016/j.ympev.2005.02.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2004] [Revised: 02/04/2005] [Accepted: 02/07/2005] [Indexed: 10/25/2022]
Abstract
We studied 131 protein sequences of the essentially ubiquitous glycolytic enzyme 3-phosphoglycerate kinase (3-PGK) by Bayesian analyses in three Domains: 15 Archaea, 83 Bacteria, and 33 Eukaryota. The posterior distribution of phylogenetic trees developed were based on a uniform prior, the WAG model of protein evolution, Metropolis-Hastings sampling in a Markov chain Monte Carlo analysis, and a package of diagnostics to critically evaluate the validity of the analyses. The 15 Archaea separated with high posterior probability. The archaean Phyla Euryarchaeota and the apparently Euryarchaeota derived Crenarchaeota were monophyletic. The 33 Eukaryota separated into two main groups: the non-chlorophyllous forms with coherent sub-groupings of Euglenozoa, Alveolata, Fungi, and Metazoa and all the chlorophyllous species studied: the Plantae (Viridaeplantae), chlorophyllous Stramenopiles, and the chlorophyllous Bacteria. This association supports other opinions concerning the related lineage of cyanobacteria and the Plantae. The 3-PGK sequences from 83 Bacteria in almost every instance associated by their recognized taxal group: alpha-, beta-, gamma-, epsilon-proteobacteria, Chlamydia, Actinobacteridae, and Firmicutes. Firmicutes sequences were subdivided into three apparently monophyletic groups: the anaerobic Clostridia, the spore-forming Bacillales and a group containing the Mollicutes, Lactobacillales and non-spore-forming Bacillales. The 3-PGK-gene tree assemblage was notable both for its pervasive clustering in three Domains according to recognized taxonomic groupings of Class, Order, Family, and Genus. The 3-PGK enzyme or 3-PGK-like activity may have played a central role in the metabolism of the Universal Ancestor.
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Affiliation(s)
- J Dennis Pollack
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, 333 West 10th Avenue, Columbus, OH 43210, USA.
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22
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Enkh-Amgalan J, Kawasaki H, Seki T. NifH and NifD sequences of heliobacteria: a new lineage in the nitrogenase phylogeny. FEMS Microbiol Lett 2005; 243:73-9. [PMID: 15668003 DOI: 10.1016/j.femsle.2004.11.044] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2004] [Revised: 11/24/2004] [Accepted: 11/24/2004] [Indexed: 11/26/2022] Open
Abstract
We determined almost complete nifH and nifD genes from representatives of all recognized genera of heliobacteria, the strictly anaerobic phototrophs belonging to the low GC gram-positive bacteria. The heliobacterial sequences formed a highly supported monophyletic group that is clearly distinct from any known diazotrophs, in both NifH and NifD trees. According to the classification of nitrogenase genes in four major clusters, the clade of heliobacterial sequences belonged to cluster I and did not cluster with any of the Clostridium (cluster III) or Paenibacillus (cluster I) species, the close neighbors of heliobacteria based on the 16S rRNA phylogeny. One partial anfH or alternative nitrogenase sequence was detected from Heliobacterium gestii. Although Heliophilum fasciatum is known to fix nitrogen based on the acetylene reduction test, nifH and/or nifD genes were not detected by either the PCR amplification or Southern hybridization methods.
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Affiliation(s)
- Jigjiddorj Enkh-Amgalan
- The International Center for Biotechnology, Osaka University, 2-1 Yamada-oka, Suita-city, Osaka 565-0871, Japan
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23
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Liebl U, Rutherford A, Nitschke W. Evidence for a unique Rieske iron-sulphur centre in Heliobacterium chlorum. FEBS Lett 2001. [DOI: 10.1016/0014-5793(90)80608-l] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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24
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Neerken S, Amesz J. The antenna reaction center complex of heliobacteria: composition, energy conversion and electron transfer. BIOCHIMICA ET BIOPHYSICA ACTA 2001; 1507:278-90. [PMID: 11687220 DOI: 10.1016/s0005-2728(01)00207-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
A survey is given of various aspects of the photosynthetic processes in heliobacteria. The review mainly refers to results obtained since 1995, which had not been covered earlier. It first discusses the antenna organization and pigmentation. The pigments of heliobacteria include some unusual species: bacteriochlorophyll (BChl) g, the main pigment, 8(1) hydroxy chlorophyll a, which acts as primary electron acceptor, and 4,4'-diaponeurosporene, a carotenoid with 30 carbon atoms. Energy conversion within the antenna is very fast: at room temperature thermal equilibrium among the approx. 35 BChls g of the antenna is largely completed within a few ps. This is then followed by primary charge separation, involving a dimer of BChl g (P798) as donor, but recent evidence indicates that excitation of the acceptor pigment 8(1) hydroxy chlorophyll a gives rise to an alternative primary reaction not involving excited P798. The final section of the review concerns secondary electron transfer, an area that is relatively poorly known in heliobacteria.
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Affiliation(s)
- S Neerken
- Department of Biophysics, Huygens Laboratory, Leiden University, P.O. Box 9504, 2300 RA, Leiden, The Netherlands.
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25
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Rössler D, Ludwig W, Schleifer KH, Lin C, McGill TJ, Wisotzkey JD, Jurtshuk P, Fox GE. Phylogenetic diversity in the genus Bacillus as seen by 16S rRNA sequencing studies. Syst Appl Microbiol 2001; 14:266-9. [PMID: 11538306 DOI: 10.1016/s0723-2020(11)80379-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Comparative sequence analysis of 16S ribosomal (r)RNAs or DNAs of Bacillus alvei, B. laterosporus, B. macerans, B. macquariensis, B. polymyxa and B. stearothermophilus revealed the phylogenetic diversity of the genus Bacillus. Based on the presently available data set of 16S rRNA sequences from bacilli and relatives at least four major "Bacillus clusters" can be defined: a "Bacillus subtilis cluster" including B. stearothermophilus, a "B. brevis cluster" including B. laterosporus, a "B. alvei cluster" including B. macerans, B. maquariensis and B. polymyxa and a "B. cycloheptanicus branch".
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Affiliation(s)
- D Rössler
- Lehrstuhl für Mikrobiologie, Technische Universität München, Germany
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26
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Abstract
Thermotoga maritima is one of the more unusual eubacteria: It is highly thermophilic, growing at temperatures higher than any other eubacterium; its cell wall appears to have a unique structure and its lipids a unique composition; and the organism is surrounded by a loose-fitting sheath of unknown function. Its phenotypic uniqueness is matched by its phylogenetic position; Thermotoga maritima represents the deepest known branching in the eubacterial line of descent, as measured by ribosomal RNA sequence comparisons. T. maritima also represents the most slowly evolving of eubacterial lineages. The fact that the two deepest branchings in the eubacterial line of descent (the other, the green non-sulfur bacteria and relatives, i.e. Chloroflexus, Thermomicrobium, etc.) are both basically thermophilic and slowly evolving, strongly suggests that all eubacteria have ultimately arisen from a thermophilic ancestor.
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Affiliation(s)
- L Achenbach-Richter
- Department of Genetics and Development, University of Illinois, Urbana 61801, USA
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27
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Oyaizu H, Debrunner-Vossbrinck B, Mandelco L, Studier JA, Woese CR. The green non-sulfur bacteria: a deep branching in the eubacterial line of descent. Syst Appl Microbiol 2001; 9:47-53. [PMID: 11542088 DOI: 10.1016/s0723-2020(87)80055-3] [Citation(s) in RCA: 104] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Ribosomal RNA sequence comparisons define a phylogenetic grouping, the green non-sulfur bacteria and relatives (GNS), known to contain the genera Chloroflexus, Herpetosiphon and Thermomicrobium--organisms that have little phenotypic similarity. The unit is phylogenetically deep, but entirely distinct from any other eubacterial division (phylum). It is also relatively ancient--branching from the common eubacterial stem earlier than any other group of eubacteria reported thus far. The group phenotype is predominantly thermophilic, and its thermophilic members, especially Thermomicrobium, are more slowly evolving than Herpetosiphon, a mesophile. The GNS unit appears significantly older than either the green sulfur bacteria or the cyanobacteria--making it likely that organisms such as Chloroflexus, not the cyanobacteria, generated the oldest stromatolites, which formed over three billion years ago.
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Affiliation(s)
- H Oyaizu
- Department of Genetics and Development, University of Illinois, Urbana 61801, USA
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28
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Kimble-Long LK, Madigan MT. Molecular evidence that the capacity for endosporulation is universal among phototrophic heliobacteria. FEMS Microbiol Lett 2001; 199:191-5. [PMID: 11377866 DOI: 10.1111/j.1574-6968.2001.tb10673.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Although enrichment cultures for anoxygenic phototrophic heliobacteria commonly contain sporulating cells, once strains of heliobacteria are obtained in pure culture, they all but cease to sporulate. In fact, some species of heliobacteria have never been observed to sporulate. Thus, despite their phylogenetic connection to endospore-forming bacteria, the question of sporulation capacity in heliobacteria remains open. We have investigated this problem using PCR and Southern hybridization as tools and show here that all recognized species of heliobacteria tested, as well as several unclassified strains, contain homologs to the ssp genes of Clostridium and Bacillus species, genes that encode key sporulation-specific proteins. It can therefore be concluded that as a group, heliobacteria are likely all to be endospore-forming bacteria in agreement with their phylogenetic placement within the 'low GC' Gram-positive bacteria.
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Affiliation(s)
- L K Kimble-Long
- Department of Microbiology and Center for Systematic Biology, Southern Illinois University, Carbondale, IL 62901-6508, USA
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29
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Bryantseva IA, Gorlenko VM, Tourova TP, Kuznetsov BB, Lysenko AM, Bykova SA, Gal’chenko VF, Mityushina LL, Osipov GA. Heliobacterium sulfidophilum sp. nov. andHeliobacterium undosum sp. nov.: Sulfideoxidizing heliobacteria from thermal sulfidic springs. Microbiology (Reading) 2000. [DOI: 10.1007/bf02756742] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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30
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Gupta RS, Mukhtar T, Singh B. Evolutionary relationships among photosynthetic prokaryotes (Heliobacterium chlorum, Chloroflexus aurantiacus, cyanobacteria, Chlorobium tepidum and proteobacteria): implications regarding the origin of photosynthesis. Mol Microbiol 1999; 32:893-906. [PMID: 10361294 DOI: 10.1046/j.1365-2958.1999.01417.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The presence of shared conserved insertions or deletions in proteins (referred to as signature sequences) provides a powerful means to deduce the evolutionary relationships among prokaryotic organisms. This approach was used in the present work to deduce the branching orders of various eubacterial taxa consisting of photosynthetic organisms. For this purpose, portions of the Hsp60 and Hsp70 genes, covering known signature sequence regions, were PCR-amplified and sequenced from Heliobacterium chlorum, Chloroflexus aurantiacus and Chlorobium tepidum. This information was integrated with sequence data for several other proteins from numerous species to deduce the branching orders of different photosynthetic taxa. Based on signature sequences that are present in different proteins, it is possible to infer that the various eubacterial phyla evolved from a common ancestor in the following order: low G+C Gram-positive (H. chlorum) --> high G+C Gram-positive --> Deinococcus-Thermus --> green non-sulphur bacteria (Cf. aurantiacus ) --> cyanobacteria --> spirochaetes --> Chlamydia-Cytophaga-Aquifex-flavobacteria-green sulphur bacteria (Cb. tepidum) --> proteobacteria (alpha, delta and epsilon) and --> proteobacteria (beta and gamma). The members of the Heliobacteriaceae family that contain a Fe-S type of reaction centre (RC-1) and represent the sole photosynthetic phylum from the Gram-positive or monoderm group of prokaryotes are indicated to be the most ancestral of the photosynthetic lineages. Among the Gram-negative bacteria or diderm prokaryotes, green non-sulphur bacteria such as Cf. aurantiacus, which contains a pheophytin-quinone type of reaction centre (RC-2), are indicated to have evolved very early. Thus, the organisms containing either RC-1 or RC-2 existed before the evolution of cyanobacteria, which contain both these reaction centres to carry out oxygenic photosynthesis. The eubacterial divisions consisting of green sulphur bacteria and proteobacteria are indicated to have diverged after cyanobacteria. Some implications of these results concerning the origin of photosynthesis and the earliest prokaryotic fossils are discussed.
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Affiliation(s)
- R S Gupta
- Department of Biochemistry, McMaster University, Hamilton, Ontario, Canada L8N 3Z5.
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31
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Hiraishi A, Kishimoto N, Kosako Y, Wakao N, Tano T. Phylogenetic position of the menaquinone-containing acidophilic chemo-organotroph Acidobacterium capsulatum. FEMS Microbiol Lett 1995; 132:91-4. [PMID: 7590170 DOI: 10.1111/j.1574-6968.1995.tb07816.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The phylogenetic position of an acidophilic chemo-organotrophic menaquinone-containing bacterium, Acidobacterium capsulatum, was studied on the basis of 16S rRNA gene sequence information. A. capsulatum showed the highest level of sequence similarity to Heliobacterium chlorum, a member of the Gram-positive group, yet this level was only 81%. Distance matrix tree analysis suggested that A. capsulatum belongs to a unique lineage deeply branching from the Chlamydia-Planctomyces group or from the Gram-positive line.
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Affiliation(s)
- A Hiraishi
- Laboratory of Environmental Biotechnology, Konishi Co., Tokyo, Japan
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32
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Amesz J. The heliobacteria, a new group of photosynthetic bacteria. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 1995. [DOI: 10.1016/1011-1344(95)07207-i] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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33
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Kimble LK, Mandelco L, Woese CR, Madigan MT. Heliobacterium modesticaldum, sp. nov., a thermophilic heliobacterium of hot springs and volcanic soils. Arch Microbiol 1995. [DOI: 10.1007/bf00393378] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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34
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Sutcliffe IC. The Lipoteichoic Acids and Lipoglycans of Gram-positive Bacteria: A Chemotaxonomic Perspective. Syst Appl Microbiol 1995. [DOI: 10.1016/s0723-2020(11)80064-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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35
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Tourova TP, Boulygina ES, Zhilina TN, Hanson RS, Zavarzin GA. Phylogenetic Study of Haloanaerobic Bacteria by 16S Ribosomal RNA Sequences Analysis. Syst Appl Microbiol 1995. [DOI: 10.1016/s0723-2020(11)80389-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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36
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Pickett MW, Weiss N, Kelly DJ. Gram-positive cell wall structure of the A3 gamma type in heliobacteria. FEMS Microbiol Lett 1994; 122:7-12. [PMID: 7958780 DOI: 10.1111/j.1574-6968.1994.tb07135.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The amino acid composition and structure of the peptidoglycan from Heliobacillus mobilis was determined by one- and two-dimensional thin-layer chromatography of completely and partially hydrolysed cell wall preparations. The structure was found to be of the A3 gamma type, with L,L-diaminopimelate in position 3, D-alanine in position 4 and a glycine interpeptide bridge, as found in certain groups of Gram-positive bacteria including Clostridium perfringens and Nocardioides simplex. The presence of a Gram-positive type of cell wall in heliobacteria is consistent with their phylogenetic relationship to the 'low G + C' Gram-positive bacteria, as previously demonstrated by 16S rRNA sequencing.
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Affiliation(s)
- M W Pickett
- Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, UK
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Vermaas WF. Evolution of heliobacteria: Implications for photosynthetic reaction center complexes. PHOTOSYNTHESIS RESEARCH 1994; 41:285-294. [PMID: 24310035 DOI: 10.1007/bf02184169] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/1994] [Accepted: 03/10/1994] [Indexed: 06/02/2023]
Abstract
The evolutionary position of the heliobacteria, a group of green photosynthetic bacteria with a photosynthetic apparatus functionally resembling Photosystem I of plants and cyanobacteria, has been investigated with respect to the evolutionary relationship to Gram-positive bacteria and cyanobacteria. On the basis of 16S rRNA sequence analysis, the heliobacteria appear to be most closely related to Gram-positive bacteria, but also an evolutionary link to cyanobacteria is evident. Interestingly, a 46-residue domain including the putative sixth membrane-spanning region of the heliobacterial reaction center protein shows rather strong similarity (33% identity and 72% similarity) to a region including the sixth membrane-spanning region of the CP47 protein, a chlorophyll-binding core antenna polypeptide of Photosystem II. The N-terminal half of the heliobacterial reaction center polypeptide shows a moderate sequence similarity (22% identity over 232 residues) with the CP47 protein, which is significantly more than the similarity with the Photosystem I core polypeptides in this region. An evolutionary model for photosynthetic reaction center complexes is discussed, in which an ancestral homodimeric reaction center protein (possibly resembling the heliobacterial reaction center protein) with 11 membrane-spanning regions per polypeptide has diverged to give rise to core of Photosystem I, Photosystem II, and of the photosynthetic apparatus in green, purple, and heliobacteria.
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Affiliation(s)
- W F Vermaas
- Department of Botany, Arizona State University, 85287-1601, Tempe, AZ, USA
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38
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Pickett MW, Williamson MP, Kelly DJ. An enzyme and(13)C-NMR study of carbon metabolism in heliobacteria. PHOTOSYNTHESIS RESEARCH 1994; 41:75-88. [PMID: 24310015 DOI: 10.1007/bf02184147] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/1993] [Accepted: 02/07/1994] [Indexed: 06/02/2023]
Abstract
Heliobacteria are a group of anoxygenic phototrophs that can grow photoheterotrophically in defined minimal media on only a limited range of organic substrates as carbon sources. In this study the mechanisms which operate to assimilate carbon and the routes employed for the biosynthesis of cellular intermediates were investigated in a newHeliobacterium strain, HY-3. This was achieved using two approaches (1) by measuring the activities of key enzymes in cell-free extracts and (2) by the use of(13)C nuclear magnetic resonance (NMR) spectroscopy to analyze in detail the labelling pattern of amino-acids of cells grown on [(13)C] pyruvate and [(13)C] acetate.Heliobacterium strain HY-3 was unable to grow autotrophically on CO2/H2 and neither (ATP)-citrate lyase nor ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBPcase) were detectable in cell-free extracts. The enzyme profile of pyruvate grown cells indicated the presence of a pyruvate:acceptor oxidoreductase at high specific activity which could convert pyruvate to acetyl-Coenzyme A. No pyridine nucleotide dependent pyruvate dehydrogenase complex activity was detected. Of the citric-acid cycle enzymes, malate dehydrogenase, fumarase, fumarate reductase and an NADP-specific isocitrate dehydrogenase were readily detectable but no aconitase or citrate synthase activity was found. However, the labelling pattern of glutamate in long-term 2-[(13)C] acetate incorporation experiments indicated that a mechanism exists for the conversion of carbon from acetyl-CoA into 2-oxoglutarate. A 2-oxoglutarate:acceptor oxidoreductase activity was present which was also assayable by isotope exchange, but no 2-oxoglutarate dehydrogenase complex activity could be detected. Heliobacteria appear to use a type of incomplete reductive carboxylic acid pathway for the conversion of pyruvate to 2-oxoglutarate but are unable to grow autotrophically using this metabolic route due to the absence of ATP-citrate lyase.
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Affiliation(s)
- M W Pickett
- Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, P.O. Box 594, S10 2UH, Sheffield, UK
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Aase B, Jantzen E, Bryn K, Ormerod J. Lipids of heliobacteria are characterised by a high proportion of monoenoic fatty acids with variable double bond positions. PHOTOSYNTHESIS RESEARCH 1994; 41:67-74. [PMID: 24310014 DOI: 10.1007/bf02184146] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/1993] [Accepted: 02/03/1994] [Indexed: 06/02/2023]
Abstract
The fatty acid composition and lipid pattern of six strains of heliobacteria have been analysed. The results were fairly uniform for all strains. Phosphatidyl ethanolamine and phosphatidyl glycerol were the dominating lipids found, with the former as the major one. No glycolipids were detected. The general fatty acid pattern was dominated by acids of chain length C16 to C18. An unusually large proportion of monoenoic acids was seen, with up to four positional isomers for each chain length. Methyl branched (iso) fatty acids were present, but not cyclopropyl or hydroxy fatty acids nor fatty alcohols.
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Affiliation(s)
- B Aase
- Department of Vaccine, National Institute of Public Health, Oslo, Norway
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40
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Gest H. A microbiologist's odyssey: Bacterial viruses to photosynthetic bacteria. PHOTOSYNTHESIS RESEARCH 1994; 40:129-146. [PMID: 24311283 DOI: 10.1007/bf00019331] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/1994] [Accepted: 01/13/1994] [Indexed: 06/02/2023]
Abstract
Perspective can be defined as the relationships or relative importance of facts or matters from any special point of view. Thus, my Personal perspective reflects the threads I followed in a 50-year journey of research in the complex tapestry of bioenergetics and various aspects of microbial metabolism. An early interest in biochemical and microbial evolution led to the fertile hunting grounds of anoxygenic photosynthetic bacteria. Viewed as a physiological class, these organisms show remarkable metabolic versatility in that certain individual species are capable of using all the known major types of energy conversion (photosynthetic, respiratory, and fermentative) to support growth. Since such anoxyphototrophs are readily amenable to molecular genetic/biological manipulation, it can be expected that they will eventually provide important clues for unraveling the evolutionary relationships of the several kinds of energy conversion. I gradually came to believe that understanding the evolution of phototrophs would require detailed knowledge not only of how light is converted to chemical energy, but also of a) pathways of monomer production from extracellular sources of carbon and nitrogen and b) mechanisms cells use for integrating ATP regeneration with the energy-requiring biosyntheses of biological macromolecules. Serendipic observation of photoproduction of H2 from organic compounds by Rhodospirillum rubrum in 1949 led to discovery of N2 fixation by anoxyphototrophs, and this capacity was later exploited for the isolation of hitherto unknown species of photosynthetic prokaryotes, including the heliobacteria. Recent studies on the reaction centers of the heliobacteria suggest the possibility that these bacteria are descendents of early phototrophs that gave rise to oxygenic photosynthetic organisms.
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Affiliation(s)
- H Gest
- Photosynthetic Bacteria Group, Department of Biology, Indiana University, 47405, Bloomington, IN, USA
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41
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Nakagawa T, Shimada M, Mukai H, Asada K, Kato I, Fujino K, Sato T. Detection of alcohol-tolerant hiochi bacteria by PCR. Appl Environ Microbiol 1994; 60:637-40. [PMID: 7510942 PMCID: PMC201360 DOI: 10.1128/aem.60.2.637-640.1994] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
We report a sensitive and rapid method for detection of hiochi bacteria by PCR. This method involves the electrophoresis of amplified DNA. Nucleotide sequences of the spacer region between 16S and 23S rRNA genes of 11 Lactobacillus strains were identified by analysis of PCR products. Five primers were designed by analysis of similarities among these sequences. A single cell of Lactobacillus casei subsp. casei could be detected when purified genomic DNA was used as the template. When various cell concentrations of L. casei subsp. casei were added to 50 ml of pasteurized sake and the cells were recovered, the detection limit was about one cell. No discrete band was observed in electrophoresis after PCR when human, Escherichia coli, mycoplasma, Acholeplasma, yeast, or mold DNA was used as the template.
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Affiliation(s)
- T Nakagawa
- Biotechnology Research Laboratories, Takara Shuzo Co., Ltd., Shiga, Japan
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42
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Blankenship RE. Protein structure, electron transfer and evolution of prokaryotic photosynthetic reaction centers. Antonie Van Leeuwenhoek 1994; 65:311-29. [PMID: 7832589 DOI: 10.1007/bf00872216] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Photosynthetic reaction centers from a variety of organisms have been isolated and characterized. The groups of prokaryotic photosynthetic organisms include the purple bacteria, the filamentous green bacteria, the green sulfur bacteria and the heliobacteria as anoxygenic representatives as well as the cyanobacteria and prochlorophytes as oxygenic representatives. This review focuses on structural and functional comparisons of the various groups of photosynthetic reaction centers and considers possible evolutionary scenarios to explain the diversity of existing photosynthetic organisms.
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Affiliation(s)
- R E Blankenship
- Department of Chemistry and Biochemistry, Arizona State University, Tempe 85287-1604
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Rainey FA, Ward NL, Morgan HW, Toalster R, Stackebrandt E. Phylogenetic analysis of anaerobic thermophilic bacteria: aid for their reclassification. J Bacteriol 1993; 175:4772-9. [PMID: 7687600 PMCID: PMC204929 DOI: 10.1128/jb.175.15.4772-4779.1993] [Citation(s) in RCA: 102] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Small subunit rDNA sequences were determined for 20 species of the genera Acetogenium, Clostridium, Thermoanaerobacter, Thermoanaerobacterium, Thermoanaerobium, and Thermobacteroides, 3 non-validly described species, and 5 isolates of anaerobic thermophilic bacteria, providing a basis for a phylogenetic analysis of these organisms. Several species contain a version of the molecule significantly longer than that of Escherichia coli because of the presence of inserts. On the basis of normal evolutionary distances, the phylogenetic tree indicates that all bacteria investigated in this study with a maximum growth temperature above 65 degrees C form a supercluster within the subphylum of gram-positive bacteria that also contains Clostridium thermosaccharolyticum and Clostridium thermoaceticum, which have been previously sequenced. This supercluster appears to be equivalent in its phylogenetic depth to the supercluster of mesophilic clostridia and their nonspore-forming relatives. Several phylogenetically and phenotypically coherent clusters that are defined by sets of signature nucleotides emerge within the supercluster of thermophiles. Clostridium thermobutyricum and Clostridium thermopalmarium are members of Clostridium group I. A phylogenetic tree derived from transversion distances demonstrated the artificial clustering of some organisms with high rDNA G+C moles percent, i.e., Clostridium fervidus and the thermophilic, cellulolytic members of the genus Clostridium. The results of this study can be used as an aid for future taxonomic restructuring of anaerobic sporogenous and asporogenous thermophillic, gram-positive bacteria.
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Affiliation(s)
- F A Rainey
- Department of Microbiology, University of Queensland, St. Lucia, Australia
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44
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Ludwig W, Kirchhof G, Klugbauer N, Weizenegger M, Betzl D, Ehrmann M, Hertel C, Jilg S, Tatzel R, Zitzelsberger H, Liebl S, Hochberger M, Shah J, Lane D, Wallnöfer PR, Scheifer KH. Complete 23S Ribosomal RNA Sequences of Gram-positive Bacteria with a Low DNA G+C Content. Syst Appl Microbiol 1992. [DOI: 10.1016/s0723-2020(11)80107-4] [Citation(s) in RCA: 92] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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45
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Weller R, Bateson MM, Heimbuch BK, Kopczynski ED, Ward DM. Uncultivated cyanobacteria, Chloroflexus-like inhabitants, and spirochete-like inhabitants of a hot spring microbial mat. Appl Environ Microbiol 1992; 58:3964-9. [PMID: 1282313 PMCID: PMC183212 DOI: 10.1128/aem.58.12.3964-3969.1992] [Citation(s) in RCA: 83] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Analysis of 16S rRNA sequences retrieved as cDNA (16S rcDNA) from the Octopus Spring cyanobacterial mat has permitted phylogenetic characterization of some uncultivated community members, expanding our knowledge or diversity within this microbial community. Two new cyanobacterial 16S rRNA sequences were discovered, raising to four the number of cyanobacterial sequence types known to occur in the mat. None of the sequences found is that of the cultivated thermophilic cyanobacterium Synechococcus lividus. A new 16S rRNA sequence characteristic of green nonsulfur bacteria and their relatives was discovered, raising to two the number of such sequences known to exist in the mat. Both are unique among the 16S rRNA sequences of cultivated members of this group, including an Octopus Spring isolate of Chloroflexus aurantiacus and Heliothrix oregonensis, whose sequences we report herein. Two spirochete-like 16S rRNA sequences were discovered. One can be placed in the leptospira subdivision of the spirochete group, but the other has such a loose affiliation with the spirochete group that it might actually belong to an as yet unrecognized subdivision or even to a new eubacterial line of descent.
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Affiliation(s)
- R Weller
- Department of Microbiology, Montana State University, Bozeman 59717
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47
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Kimble LK, Madigan MT. Evidence for an alternative nitrogenase in Heliobacterium gestii. FEMS Microbiol Lett 1992. [DOI: 10.1111/j.1574-6968.1992.tb05712.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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48
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Both B, Buckel W, Kroppenstedt R, Stackebrandt E. Phylogenetic and chemotaxonomic characterization ofAcidaminococcus fermentans. FEMS Microbiol Lett 1992. [DOI: 10.1111/j.1574-6968.1992.tb05431.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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49
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50
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Trost JT, Brune DC, Blankenship RE. Protein sequences and redox titrations indicate that the electron acceptors in reaction centers from heliobacteria are similar to Photosystem I. PHOTOSYNTHESIS RESEARCH 1992; 32:11-22. [PMID: 24408151 DOI: 10.1007/bf00028794] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/1991] [Accepted: 12/02/1991] [Indexed: 06/03/2023]
Abstract
Photosynthetic reaction centers isolated from Heliobacillus mobilis exhibit a single major protein on SDS-PAGE of 47 000 Mr. Attempts to sequence the reaction center polypeptide indicated that the N-terminus is blocked. After enzymatic and chemical cleavage, four peptide fragments were sequenced from the Heliobacillus mobilis apoprotein. Only one of these sequences showed significant specific similarity to any of the protein and deduced protein sequences in the GenBank data base. This fragment is identical with 56% of the residues, including both cysteines, found in the highly conserved region that is proposed to bind iron-sulfur center FX in the Photosystem I reaction center peptide that is the psaB gene product. The similarity to the psaA gene product in this region is 48%.Redox titrations of laser-flash-induced photobleaching with millisecond decay kinetics on isolated reaction centers from Heliobacterium gestii indicate a midpoint potential of -414 mV with n=2 titration behavior. In membranes, the behavior is intermediate between n=1 and n=2, and the apparent midpoint potential is -444 mV. This is compared to the behavior in Photosystem I, where the intermediate electron acceptor A1, thought to be a phylloquinone molecule, has been proposed to undergo a double reduction at low redox potentials in the presence of viologen redox mediators.These results strongly suggest that the acceptor side electron transfer system in reaction centers from heliobacteria is indeed analogous to that found in Photosystem I. The sequence similarities indicate that the divergence of the heliobacteria from the Photosystem I line occurred before the gene duplication and subsequent divergence that lead to the heterodimeric protein core of the Photosystem I reaction center.
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Affiliation(s)
- J T Trost
- Department of Chemistry and Biochemistry, Center for the Study of Early Events in Photosynthesis, Arizona State Univeristy, 85287-1604, Tempe, AZ, USA
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