201
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Goldblatt C, Lenton TM, Watson AJ. Bistability of atmospheric oxygen and the Great Oxidation. Nature 2006; 443:683-6. [PMID: 17036001 DOI: 10.1038/nature05169] [Citation(s) in RCA: 204] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2006] [Accepted: 08/14/2006] [Indexed: 11/09/2022]
Abstract
The history of the Earth has been characterized by a series of major transitions separated by long periods of relative stability. The largest chemical transition was the 'Great Oxidation', approximately 2.4 billion years ago, when atmospheric oxygen concentrations rose from less than 10(-5) of the present atmospheric level (PAL) to more than 0.01 PAL, and possibly to more than 0.1 PAL. This transition took place long after oxygenic photosynthesis is thought to have evolved, but the causes of this delay and of the Great Oxidation itself remain uncertain. Here we show that the origin of oxygenic photosynthesis gave rise to two simultaneously stable steady states for atmospheric oxygen. The existence of a low-oxygen (less than 10(-5) PAL) steady state explains how a reducing atmosphere persisted for at least 300 million years after the onset of oxygenic photosynthesis. The Great Oxidation can be understood as a switch to the high-oxygen (more than 5 x 10(-3) PAL) steady state. The bistability arises because ultraviolet shielding of the troposphere by ozone becomes effective once oxygen levels exceed 10(-5) PAL, causing a nonlinear increase in the lifetime of atmospheric oxygen. Our results indicate that the existence of oxygenic photosynthesis is not a sufficient condition for either an oxygen-rich atmosphere or the presence of an ozone layer, which has implications for detecting life on other planets using atmospheric analysis and for the evolution of multicellular life.
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Affiliation(s)
- Colin Goldblatt
- School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.
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202
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Lankenau DH. Germline Double-Strand Break Repair and Gene Targeting in Drosophila: A Trajectory System throughout Evolution. Genome Integr 2006. [DOI: 10.1007/7050_019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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203
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Mulkidjanian AY, Koonin EV, Makarova KS, Mekhedov SL, Sorokin A, Wolf YI, Dufresne A, Partensky F, Burd H, Kaznadzey D, Haselkorn R, Galperin MY. The cyanobacterial genome core and the origin of photosynthesis. Proc Natl Acad Sci U S A 2006; 103:13126-31. [PMID: 16924101 PMCID: PMC1551899 DOI: 10.1073/pnas.0605709103] [Citation(s) in RCA: 187] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Comparative analysis of 15 complete cyanobacterial genome sequences, including "near minimal" genomes of five strains of Prochlorococcus spp., revealed 1,054 protein families [core cyanobacterial clusters of orthologous groups of proteins (core CyOGs)] encoded in at least 14 of them. The majority of the core CyOGs are involved in central cellular functions that are shared with other bacteria; 50 core CyOGs are specific for cyanobacteria, whereas 84 are exclusively shared by cyanobacteria and plants and/or other plastid-carrying eukaryotes, such as diatoms or apicomplexans. The latter group includes 35 families of uncharacterized proteins, which could also be involved in photosynthesis. Only a few components of cyanobacterial photosynthetic machinery are represented in the genomes of the anoxygenic phototrophic bacteria Chlorobium tepidum, Rhodopseudomonas palustris, Chloroflexus aurantiacus, or Heliobacillus mobilis. These observations, coupled with recent geological data on the properties of the ancient phototrophs, suggest that photosynthesis originated in the cyanobacterial lineage under the selective pressures of UV light and depletion of electron donors. We propose that the first phototrophs were anaerobic ancestors of cyanobacteria ("procyanobacteria") that conducted anoxygenic photosynthesis using a photosystem I-like reaction center, somewhat similar to the heterocysts of modern filamentous cyanobacteria. From procyanobacteria, photosynthesis spread to other phyla by way of lateral gene transfer.
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Affiliation(s)
- Armen Y. Mulkidjanian
- *School of Physics, University of Osnabrück, D-49069 Osnabrück, Germany
- A. N. Belozersky Institute of Physico–Chemical Biology, Moscow State University, Moscow 119899, Russia
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894
| | - Kira S. Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894
| | - Sergey L. Mekhedov
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894
| | - Alexander Sorokin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894
| | - Yuri I. Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894
| | - Alexis Dufresne
- Station Biologique, Unité Mixte de Recherche 7144, Centre National de la Recherche Scientifique et Université Paris 6, BP74, F-29682 Roscoff Cedex, France
| | - Frédéric Partensky
- Station Biologique, Unité Mixte de Recherche 7144, Centre National de la Recherche Scientifique et Université Paris 6, BP74, F-29682 Roscoff Cedex, France
| | - Henry Burd
- Integrated Genomics, Inc., Chicago, IL 60612; and
| | | | - Robert Haselkorn
- **Department of Molecular Genetics and Cell Biology, University of Chicago, 920 East 58th Street, Chicago, IL 60637
| | - Michael Y. Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894
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204
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Affiliation(s)
- Lars E P Dietrich
- Division of Geological and Planetary Science, California Institute of Technology, Pasadena, California 91125, USA
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205
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Summons RE, Bradley AS, Jahnke LL, Waldbauer JR. Steroids, triterpenoids and molecular oxygen. Philos Trans R Soc Lond B Biol Sci 2006; 361:951-68. [PMID: 16754609 PMCID: PMC1578733 DOI: 10.1098/rstb.2006.1837] [Citation(s) in RCA: 165] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
There is a close connection between modern-day biosynthesis of particular triterpenoid biomarkers and presence of molecular oxygen in the environment. Thus, the detection of steroid and triterpenoid hydrocarbons far back in Earth history has been used to infer the antiquity of oxygenic photosynthesis. This prompts the question: were these compounds produced similarly in the past? In this paper, we address this question with a review of the current state of knowledge surrounding the oxygen requirement for steroid biosynthesis and phylogenetic patterns in the distribution of steroid and triterpenoid biosynthetic pathways. The hopanoid and steroid biosynthetic pathways are very highly conserved within the bacterial and eukaryotic domains, respectively. Bacteriohopanepolyols are produced by a wide range of bacteria, and are methylated in significant abundance at the C2 position by oxygen-producing cyanobacteria. On the other hand, sterol biosynthesis is sparsely distributed in distantly related bacterial taxa and the pathways do not produce the wide range of products that characterize eukaryotes. In particular, evidence for sterol biosynthesis by cyanobacteria appears flawed. Our experiments show that cyanobacterial cultures are easily contaminated by sterol-producing rust fungi, which can be eliminated by treatment with cycloheximide affording sterol-free samples. Sterols are ubiquitous features of eukaryotic membranes, and it appears likely that the initial steps in sterol biosynthesis were present in their modern form in the last common ancestor of eukaryotes. Eleven molecules of O2 are required by four enzymes to produce one molecule of cholesterol. Thermodynamic arguments, optimization of function and parsimony all indicate that an ancestral anaerobic pathway is highly unlikely. The known geological record of molecular fossils, especially steranes and triterpanes, is notable for the limited number of structural motifs that have been observed. With a few exceptions, the carbon skeletons are the same as those found in the lipids of extant organisms and no demonstrably extinct structures have been reported. Furthermore, their patterns of occurrence over billion year time-scales correlate strongly with environments of deposition. Accordingly, biomarkers are excellent indicators of environmental conditions even though the taxonomic affinities of all biomarkers cannot be precisely specified. Biomarkers are ultimately tied to biochemicals with very specific functional properties, and interpretations of the biomarker record will benefit from increased understanding of the biological roles of geologically durable molecules.
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Affiliation(s)
- Roger E Summons
- Massachusetts Institute of Technology, Department of Earth, Atmospheric and Planetary Sciences, 77 Massachusetts Avenue E34-246, Cambridge, MA 02139-4307, USA.
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206
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Abstract
Earth's climate during the Archaean remains highly uncertain, as the relevant geologic evidence is sparse and occasionally contradictory. Oxygen isotopes in cherts suggest that between 3.5 and 3.2 Gyr ago (Ga) the Archaean climate was hot (55-85 degrees C); however, the fact that these cherts have experienced only a modest amount of weathering suggests that the climate was temperate, as today. The presence of diamictites in the Pongola Supergroup and the Witwatersrand Basin of South Africa suggests that by 2.9 Ga the climate was glacial. The Late Archaean was relatively warm; then glaciation (possibly of global extent) reappeared in the Early Palaeoproterozoic, around 2.3-2.4 Ga. Fitting these climatic constraints with a model requires high concentrations of atmospheric CO2 or CH4, or both. Solar luminosity was 20-25% lower than today, so elevated greenhouse gas concentrations were needed just to keep the mean surface temperature above freezing. A rise in O2 at approximately 2.4 Ga, and a concomitant decrease in CH4, provides a natural explanation for the Palaeoproterozoic glaciations. The Mid-Archaean glaciations may have been caused by a drawdown in H2 and CH4 caused by the origin of bacterial sulphate reduction. More work is needed to test this latter hypothesis.
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Affiliation(s)
- James F Kasting
- Penn State University, Department of Geosciences, University Park, PA 16802, USA.
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207
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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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208
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Hayes JM, Waldbauer JR. The carbon cycle and associated redox processes through time. Philos Trans R Soc Lond B Biol Sci 2006; 361:931-50. [PMID: 16754608 PMCID: PMC1578725 DOI: 10.1098/rstb.2006.1840] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Earth's biogeochemical cycle of carbon delivers both limestones and organic materials to the crust. In numerous, biologically catalysed redox reactions, hydrogen, sulphur, iron, and oxygen serve prominently as electron donors and acceptors. The progress of these reactions can be reconstructed from records of variations in the abundance of 13C in sedimentary carbonate minerals and organic materials. Because the crust is always receiving new CO2 from the mantle and a portion of it is being reduced by photoautotrophs, the carbon cycle has continuously released oxidizing power. Most of it is represented by Fe3+ that has accumulated in the crust or been returned to the mantle via subduction. Less than 3% of the estimated, integrated production of oxidizing power since 3.8 Gyr ago is represented by O2 in the atmosphere and dissolved in seawater. The balance is represented by sulphate. The accumulation of oxidizing power can be estimated from budgets summarizing inputs of mantle carbon and rates of organic-carbon burial, but levels of O2 are only weakly and indirectly coupled to those phenomena and thus to carbon-isotopic records. Elevated abundances of 13C in carbonate minerals ca 2.3 Gyr old, in particular, are here interpreted as indicating the importance of methanogenic bacteria in sediments rather than increased burial of organic carbon.
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Affiliation(s)
- John M Hayes
- Woods Hole Oceanographic Institution, Department of Geology and Geophysics, Woods Hole, MA 02543, USA.
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209
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Fedo CM, Whitehouse MJ, Kamber BS. Geological constraints on detecting the earliest life on Earth: a perspective from the Early Archaean (older than 3.7 Gyr) of southwest Greenland. Philos Trans R Soc Lond B Biol Sci 2006; 361:851-67. [PMID: 16754603 PMCID: PMC1578730 DOI: 10.1098/rstb.2006.1836] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
At greater than 3.7 Gyr, Earth's oldest known supracrustal rocks, comprised dominantly of mafic igneous with less common sedimentary units including banded iron formation (BIF), are exposed in southwest Greenland. Regionally, they were intruded by younger tonalites, and then both were intensely dynamothermally metamorphosed to granulite facies (the highest pressures and temperatures generally encountered in the Earth's crust during metamorphism) in the Archaean and subsequently at lower grades until about 1500 Myr ago. Claims for the first preserved life on Earth have been based on the occurrence of greater than 3.8 Gyr isotopically light C occurring as graphite inclusions within apatite crystals from a 5 m thick purported BIF on the island of Akilia. Detailed geologic mapping and observations there indicate that the banding, first claimed to be depositional, is clearly deformational in origin. Furthermore, the mineralogy of the supposed BIF, being dominated by pyroxene, amphibole and quartz, is unlike well-known BIF from the Isua Greenstone Belt (IGB), but resembles enclosing mafic and ultramafic igneous rocks modified by metasomatism and repeated metamorphic recrystallization. This scenario parsimoniously links the geology, whole-rock geochemistry, 2.7 Gyr single crystal zircon ages in the unit, an approximately 1500 Myr age for apatites that lack any graphite, non-MIF sulphur isotopes in the unit and an inconclusive Fe isotope signature. Although both putative body fossils and carbon-12 enriched isotopes in graphite described at Isua are better explained by abiotic processes, more fruitful targets for examining the earliest stages in the emergence of life remain within greater than 3.7 Gyr IGB, which preserves BIF and other rocks that unambiguously formed at Earth's surface.
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210
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Brasier M, McLoughlin N, Green O, Wacey D. A fresh look at the fossil evidence for early Archaean cellular life. Philos Trans R Soc Lond B Biol Sci 2006; 361:887-902. [PMID: 16754605 PMCID: PMC1578727 DOI: 10.1098/rstb.2006.1835] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The rock record provides us with unique evidence for testing models as to when and where cellular life first appeared on Earth. Its study, however, requires caution. The biogenicity of stromatolites and 'microfossils' older than 3.0 Gyr should not be accepted without critical analysis of morphospace and context, using multiple modern techniques, plus rejection of alternative non-biological (null) hypotheses. The previous view that the co-occurrence of biology-like morphology and carbonaceous chemistry in ancient, microfossil-like objects is a presumptive indicator of biogenicity is not enough. As with the famous Martian microfossils, we need to ask not 'what do these structures remind us of?', but 'what are these structures?' Earth's oldest putative 'microfossil' assemblages within 3.4-3.5 Gyr carbonaceous cherts, such as the Apex Chert, are likewise self-organizing structures that do not pass tests for biogenicity. There is a preservational paradox in the fossil record prior to ca 2.7 Gyr: suitable rocks (e.g. isotopically light carbonaceous cherts) are widely present, but signals of life are enigmatic and hard to decipher. One new approach includes detailed mapping of well-preserved sandstone grains in the ca 3.4 Gyr Strelley Pool Chert. These can contain endolithic microtubes showing syngenicity, grain selectivity and several levels of geochemical processing. Preliminary studies invite comparison with a class of ambient inclusion trails of putative microbial origin and with the activities of modern anaerobic proteobacteria and volcanic glass euendoliths.
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Affiliation(s)
- Martin Brasier
- Oxford University, Department of Earth Sciences, Parks Road, Oxford OX1 3PR, UK.
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211
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Sadekar S, Raymond J, Blankenship RE. Conservation of distantly related membrane proteins: photosynthetic reaction centers share a common structural core. Mol Biol Evol 2006; 23:2001-7. [PMID: 16887904 DOI: 10.1093/molbev/msl079] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Photosynthesis was established on Earth more than 3 billion years ago. All available evidences suggest that the earliest photosynthetic organisms were anoxygenic and that oxygen-evolving photosynthesis is a more recent development. The reaction center complexes that form the heart of the energy storage process are integral membrane pigment proteins that span the membrane in vectorial fashion to carry out electron transfer. The origin and extent of distribution of these proteins has been perplexing from a phylogenetic point of view mostly because of extreme sequence divergence. A series of integral membrane proteins of known structure and varying degrees of sequence identity have been compared using combinatorial extension-Monte Carlo methods. The proteins include photosynthetic reaction centers from proteobacteria and cyanobacterial photosystems I and II, as well as cytochrome oxidase, bacteriorhodopsin, and cytochrome b. The reaction center complexes show a remarkable conservation of the core structure of 5 transmembrane helices, strongly implying common ancestry, even though the residual sequence identity is less than 10%, whereas the other proteins have structures that are unrelated. A relationship of sequence with structure was derived from the reaction center structures; with characteristic decay length of 1.6 A. Phylogenetic trees derived from the structural alignments give insights into the earliest photosynthetic reaction center, strongly suggesting that it was a homodimeric complex that did not evolve oxygen.
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Affiliation(s)
- Sumedha Sadekar
- Computational Biosciences Program, Arizona State University, USA
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212
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Ley RE, Harris JK, Wilcox J, Spear JR, Miller SR, Bebout BM, Maresca JA, Bryant DA, Sogin ML, Pace NR. Unexpected diversity and complexity of the Guerrero Negro hypersaline microbial mat. Appl Environ Microbiol 2006; 72:3685-95. [PMID: 16672518 PMCID: PMC1472358 DOI: 10.1128/aem.72.5.3685-3695.2006] [Citation(s) in RCA: 295] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
We applied nucleic acid-based molecular methods, combined with estimates of biomass (ATP), pigments, and microelectrode measurements of chemical gradients, to map microbial diversity vertically on a millimeter scale in a hypersaline microbial mat from Guerrero Negro, Baja California Sur, Mexico. To identify the constituents of the mat, small-subunit rRNA genes were amplified by PCR from community genomic DNA extracted from layers, cloned, and sequenced. Bacteria dominated the mat and displayed unexpected and unprecedented diversity. The majority (1,336) of the 1,586 bacterial 16S rRNA sequences generated were unique, representing 752 species (> or =97% rRNA sequence identity) in 42 of the main bacterial phyla, including 15 novel candidate phyla. The diversity of the mat samples differentiated according to the chemical milieu defined by concentrations of O(2) and H(2)S. Bacteria of the phylum Chloroflexi formed the majority of the biomass by percentage of bulk rRNA and of clones in rRNA gene libraries. This result contradicts the general belief that cyanobacteria dominate these communities. Although cyanobacteria constituted a large fraction of the biomass in the upper few millimeters (>80% of the total rRNA and photosynthetic pigments), Chloroflexi sequences were conspicuous throughout the mat. Filamentous Chloroflexi bacteria were identified by fluorescence in situ hybridization within the polysaccharide sheaths of the prominent cyanobacterium Microcoleus chthonoplastes, in addition to free living in the mat. The biological complexity of the mat far exceeds that observed in other polysaccharide-rich microbial ecosystems, such as the human and mouse distal guts, and suggests that positive feedbacks exist between chemical complexity and biological diversity. The sequences determined in this study have been submitted to the GenBank database and assigned accession numbers DQ 329539 to DQ 331020, and DQ 397339 to DQ 397511.
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Affiliation(s)
- Ruth E Ley
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309-0347, USA
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213
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214
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Nield J, Barber J. Refinement of the structural model for the Photosystem II supercomplex of higher plants. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2006; 1757:353-61. [PMID: 16729961 DOI: 10.1016/j.bbabio.2006.03.019] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2006] [Revised: 03/20/2006] [Accepted: 03/21/2006] [Indexed: 11/30/2022]
Abstract
Recent X-ray structures determined for the Photosystem II (PSII) core complex isolated from cyanobacteria have provided important information for understanding the functionality of this photosynthetic enzyme including its water splitting activity. As yet, no high-resolution structure is available for PSII of plants or eukaryotes in general. However, crystal structures have been determined for some components of plant PSII which together with the cyanobacterial structure can be used to interpret lower resolution structures of plant PSII derived from electron cryomicroscopy (cryo-EM). Here, we utilise the published X-ray structures of a cyanobacterial PSII core, Light Harvesting Complex II (LHCII), PsbP and PsbQ proteins to construct a model of the plant LHCII-PSII supercomplex using a 17 A resolution 3D electron density map of the spinach supercomplex determined by cryo-EM and single particle analysis. In so doing, we tentatively identify the relative positioning of the chlorophylls within the supercomplex and consider energy transfer pathways between the different subunits. The modelling has also allowed density to be assigned to the three extrinsic proteins of plant PSII, PsbO, PsbP and PsbQ associated with the water splitting centre and concluded that although the position of PsbO is the same as in cyanobacteria, PsbP and PsbQ are located in different positions to the cyanobacterial extrinsic PsbU and PsbV proteins.
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Affiliation(s)
- Jon Nield
- Wolfson Laboratories, Division of Molecular Biosciences, Faculty of Natural Sciences, South Kensington Campus, Imperial College London, SW7 2AZ, UK
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215
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Olson JM. Photosynthesis in the Archean era. PHOTOSYNTHESIS RESEARCH 2006; 88:109-17. [PMID: 16453059 DOI: 10.1007/s11120-006-9040-5] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2005] [Accepted: 01/08/2006] [Indexed: 05/06/2023]
Abstract
The earliest reductant for photosynthesis may have been H2. The carbon isotope composition measured in graphite from the 3.8-Ga Isua Supercrustal Belt in Greenland is attributed to H2-driven photosynthesis, rather than to oxygenic photosynthesis as there would have been no evolutionary pressure for oxygenic photosynthesis in the presence of H2. Anoxygenic photosynthesis may also be responsible for the filamentous mats found in the 3.4-Ga Buck Reef Chert in South Africa. Another early reductant was probably H2S. Eventually the supply of H2 in the atmosphere was likely to have been attenuated by the production of CH4 by methanogens, and the supply of H2S was likely to have been restricted to special environments near volcanos. Evaporites, possible stromatolites, and possible microfossils found in the 3.5-Ga Warrawoona Megasequence in Australia are attributed to sulfur-driven photosynthesis. Proteobacteria and protocyanobacteria are assumed to have evolved to use ferrous iron as reductant sometime around 3.0 Ga or earlier. This type of photosynthesis could have produced banded iron formations similar to those produced by oxygenic photosynthesis. Microfossils, stromatolites, and chemical biomarkers in Australia and South Africa show that cyanobacteria containing chlorophyll a and carrying out oxygenic photosynthesis appeared by 2.8 Ga, but the oxygen level in the atmosphere did not begin to increase until about 2.3 Ga.
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Affiliation(s)
- John M Olson
- Department of Biochemistry and Molecular Biology, 913 Lederle GRT Tower-B, University of Massachusetts Amherst, Amherst, MA 01003-9305, USA.
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216
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Abstract
The evolution of oxygenic photosynthesis and ensuing oxygenation of Earth's atmosphere represent a major transition in the history of life. Although many organisms retreated to anoxic environments, others evolved to use oxygen as a high-potential redox couple while concomitantly mitigating its toxicity. To understand the changes in biochemistry and enzymology that accompanied adaptation to O2, we integrated network analysis with information on enzyme evolution to infer how oxygen availability changed the architecture of metabolic networks. Our analysis revealed the existence of four discrete groups of networks of increasing complexity, with transitions between groups being contingent on the presence of key metabolites, including molecular oxygen, which was required for transition into the largest networks.
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Affiliation(s)
- Jason Raymond
- Microbial Systems Division, Biosciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
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217
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The early record of life. ACTA ACUST UNITED AC 2006. [DOI: 10.1029/164gm18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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218
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Abstract
Recent studies using geological and molecular phylogenetic evidence suggest several alternative evolutionary scenarios for the origin of photosynthesis. The earliest photosynthetic group is variously thought to be heliobacteria, proteobacteria or a precursor of cyanobacteria, organisms whose photosynthetic pigments make them different colors.
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Affiliation(s)
- Jin Xiong
- Department of Biology, Texas A&M University, College Station, TX 77843, USA.
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219
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Westall F. The Geological Context for the Origin of Life and the Mineral Signatures of Fossil Life. ACTA ACUST UNITED AC 2005. [DOI: 10.1007/10913406_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
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220
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Brocks JJ, Love GD, Summons RE, Knoll AH, Logan GA, Bowden SA. Biomarker evidence for green and purple sulphur bacteria in a stratified Palaeoproterozoic sea. Nature 2005; 437:866-70. [PMID: 16208367 DOI: 10.1038/nature04068] [Citation(s) in RCA: 178] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2005] [Accepted: 07/22/2005] [Indexed: 11/08/2022]
Abstract
The disappearance of iron formations from the geological record approximately 1.8 billion years (Gyr) ago was the consequence of rising oxygen levels in the atmosphere starting 2.45-2.32 Gyr ago. It marks the end of a 2.5-Gyr period dominated by anoxic and iron-rich deep oceans. However, despite rising oxygen levels and a concomitant increase in marine sulphate concentration, related to enhanced sulphide oxidation during continental weathering, the chemistry of the oceans in the following mid-Proterozoic interval (approximately 1.8-0.8 Gyr ago) probably did not yet resemble our oxygen-rich modern oceans. Recent data indicate that marine oxygen and sulphate concentrations may have remained well below current levels during this period, with one model indicating that anoxic and sulphidic marine basins were widespread, and perhaps even globally distributed. Here we present hydrocarbon biomarkers (molecular fossils) from a 1.64-Gyr-old basin in northern Australia, revealing the ecological structure of mid-Proterozoic marine communities. The biomarkers signify a marine basin with anoxic, sulphidic, sulphate-poor and permanently stratified deep waters, hostile to eukaryotic algae. Phototrophic purple sulphur bacteria (Chromatiaceae) were detected in the geological record based on the new carotenoid biomarker okenane, and they seem to have co-existed with communities of green sulphur bacteria (Chlorobiaceae). Collectively, the biomarkers support mounting evidence for a long-lasting Proterozoic world in which oxygen levels remained well below modern levels.
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Affiliation(s)
- Jochen J Brocks
- Research School of Earth Sciences, The Australian National University, Canberra, ACT 0200, Australia
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221
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Olcott AN, Sessions AL, Corsetti FA, Kaufman AJ, de Oliviera TF. Biomarker evidence for photosynthesis during neoproterozoic glaciation. Science 2005; 310:471-4. [PMID: 16195425 DOI: 10.1126/science.1115769] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Laterally extensive black shales were deposited on the São Francisco craton in southeastern Brazil during low-latitude Neoproterozoic glaciation approximately 740 to 700 million years ago. These rocks contain up to 3.0 weight % organic carbon, which we interpret as representing the preserved record of abundant marine primary productivity from glacial times. Extractable biomarkers reflect a complex and productive microbial ecosystem, including both phototrophic bacteria and eukaryotes, living in a stratified ocean with thin or absent sea ice, oxic surface waters, and euxinic conditions within the photic zone. Such an environment provides important constraints for parts of the "Snowball Earth" hypothesis.
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Affiliation(s)
- Alison N Olcott
- Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089, USA.
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222
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Simoneit BRT. A review of current applications of mass spectrometry for biomarker/molecular tracer elucidation. MASS SPECTROMETRY REVIEWS 2005; 24:719-765. [PMID: 15534872 DOI: 10.1002/mas.20036] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Mass spectrometry, especially coupled with gas chromatography or tandem, is the analytical method of choice in elucidation of biomarker compounds present in organic mixtures extracted from geological, environmental, or biological samples. This review describes the biomarker concept; i.e., the precursor natural products to the geological/environmental derivatives, and their application as tracers in the geosphere and ambient environment. The mass spectrometric methods currently utilized for such analyses are reviewed, and typical examples of applications are described with a general key to the literature.
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Affiliation(s)
- Bernd R T Simoneit
- Environmental and Petroleum Research Group, College of Oceanic and Atmospheric Sciences and Department of Chemistry, Oregon State University, Corvallis, Oregon 97331-5503, USA.
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223
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Kopp RE, Kirschvink JL, Hilburn IA, Nash CZ. The Paleoproterozoic snowball Earth: a climate disaster triggered by the evolution of oxygenic photosynthesis. Proc Natl Acad Sci U S A 2005; 102:11131-6. [PMID: 16061801 PMCID: PMC1183582 DOI: 10.1073/pnas.0504878102] [Citation(s) in RCA: 159] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2004] [Indexed: 11/18/2022] Open
Abstract
Although biomarker, trace element, and isotopic evidence have been used to claim that oxygenic photosynthesis evolved by 2.8 giga-annum before present (Ga) and perhaps as early as 3.7 Ga, a skeptical examination raises considerable doubt about the presence of oxygen producers at these times. Geological features suggestive of oxygen, such as red beds, lateritic paleosols, and the return of sedimentary sulfate deposits after a approximately 900-million year hiatus, occur shortly before the approximately 2.3-2.2 Ga Makganyene "snowball Earth" (global glaciation). The massive deposition of Mn, which has a high redox potential, practically requires the presence of environmental oxygen after the snowball. New age constraints from the Transvaal Supergroup of South Africa suggest that all three glaciations in the Huronian Supergroup of Canada predate the Snowball event. A simple cyanobacterial growth model incorporating the range of C, Fe, and P fluxes expected during a partial glaciation in an anoxic world with high-Fe oceans indicates that oxygenic photosynthesis could have destroyed a methane greenhouse and triggered a snowball event on time-scales as short as 1 million years. As the geological evidence requiring oxygen does not appear during the Pongola glaciation at 2.9 Ga or during the Huronian glaciations, we argue that oxygenic cyanobacteria evolved and radiated shortly before the Makganyene snowball.
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Affiliation(s)
- Robert E Kopp
- Division of Geological and Planetary Sciences, California Institute of Technology 170-25, Pasadena, CA 91125, USA.
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224
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Catling DC, Glein CR, Zahnle KJ, McKay CP. Why O2 is required by complex life on habitable planets and the concept of planetary "oxygenation time". ASTROBIOLOGY 2005; 5:415-38. [PMID: 15941384 DOI: 10.1089/ast.2005.5.415] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Life is constructed from a limited toolkit: the Periodic Table. The reduction of oxygen provides the largest free energy release per electron transfer, except for the reduction of fluorine and chlorine. However, the bonding of O2 ensures that it is sufficiently stable to accumulate in a planetary atmosphere, whereas the more weakly bonded halogen gases are far too reactive ever to achieve significant abundance. Consequently, an atmosphere rich in O2 provides the largest feasible energy source. This universal uniqueness suggests that abundant O2 is necessary for the high-energy demands of complex life anywhere, i.e., for actively mobile organisms of approximately 10(-1)-10(0) m size scale with specialized, differentiated anatomy comparable to advanced metazoans. On Earth, aerobic metabolism provides about an order of magnitude more energy for a given intake of food than anaerobic metabolism. As a result, anaerobes do not grow beyond the complexity of uniseriate filaments of cells because of prohibitively low growth efficiencies in a food chain. The biomass cumulative number density, n, at a particular mass, m, scales as n (> m) proportional to m(-1) for aquatic aerobes, and we show that for anaerobes the predicted scaling is n proportional to m (-1.5), close to a growth-limited threshold. Even with aerobic metabolism, the partial pressure of atmospheric O2 (P(O2)) must exceed approximately 10(3) Pa to allow organisms that rely on O2 diffusion to evolve to a size approximately 10(3) m x P(O2) in the range approximately 10(3)-10(4) Pa is needed to exceed the threshold of approximately 10(2) m size for complex life with circulatory physiology. In terrestrial life, O(2) also facilitates hundreds of metabolic pathways, including those that make specialized structural molecules found only in animals. The time scale to reach P(O(2)) approximately 10(4) Pa, or "oxygenation time," was long on the Earth (approximately 3.9 billion years), within almost a factor of 2 of the Sun's main sequence lifetime. Consequently, we argue that the oxygenation time is likely to be a key rate-limiting step in the evolution of complex life on other habitable planets. The oxygenation time could preclude complex life on Earth-like planets orbiting short-lived stars that end their main sequence lives before planetary oxygenation takes place. Conversely, Earth-like planets orbiting long-lived stars are potentially favorable habitats for complex life.
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Affiliation(s)
- David C Catling
- Department of Atmospheric Sciences and Astrobiology Program, University of Washington, Seattle, Washington, USA.
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225
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Härtner T, Straub KL, Kannenberg E. Occurrence of hopanoid lipids in anaerobic Geobacter species. FEMS Microbiol Lett 2005; 243:59-64. [PMID: 15668001 DOI: 10.1016/j.femsle.2004.11.039] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2004] [Revised: 11/12/2004] [Accepted: 11/22/2004] [Indexed: 11/23/2022] Open
Abstract
Geobacter metallireducens and G. sulfurreducens have been classified as strictly anaerobic bacteria which grow and thrive in subsurface and sediment environments. Hopanoids are pentacyclic triterpenoid lipids and are important for bacterial membrane stability and functioning. Hopanoids predominantly occur in aerobically growing bacteria of oxic environments. They rarely have been found in facultatively anaerobic bacteria and, to date, not at all in strict anaerobes. Our research shows that anaerobically grown G. metallireducens and G. sulfurreducens bacteria contain a range of hopanoid lipids, such as diploptene (i.e. hop-22(29)-ene) and hop-21-ene, and more complex, elongated hopanoids. In geological formations, diagenetic derivatives of hopanoids are widely used as biomarkers and are recognized as molecular fossils of bacterial origin. To date, these biomarkers have largely been interpreted as those derived from ancient oxic environments. Our findings presented here suggest that this interpretation needs to be re-evaluated. In addition to the origin in oxic environments, 'geohopanoids' may originate from ancient anaerobic environments as well.
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Affiliation(s)
- Thomas Härtner
- Institut für Mikrobiologie, Mikrobiologie/Biotechnologie, Universität Tübingen, Auf der Morgenstelle 28, D-72076 Tübingen, Germany
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226
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Rouxel OJ, Bekker A, Edwards KJ. Iron isotope constraints on the Archean and Paleoproterozoic ocean redox state. Science 2005; 307:1088-91. [PMID: 15718467 DOI: 10.1126/science.1105692] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The response of the ocean redox state to the rise of atmospheric oxygen about 2.3 billion years ago (Ga) is a matter of controversy. Here we provide iron isotope evidence that the change in the ocean iron cycle occurred at the same time as the change in the atmospheric redox state. Variable and negative iron isotope values in pyrites older than about 2.3 Ga suggest that an iron-rich global ocean was strongly affected by the deposition of iron oxides. Between 2.3 and 1.8 Ga, positive iron isotope values of pyrite likely reflect an increase in the precipitation of iron sulfides relative to iron oxides in a redox stratified ocean.
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Affiliation(s)
- Olivier J Rouxel
- Marine Chemistry and Geochemistry Department, Geomicrobiology Group, Woods Hole Oceanographic Institution, Mail Stop 8, Woods Hole, MA 02543, USA.
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227
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Xie S, Pancost RD, Yin H, Wang H, Evershed RP. Two episodes of microbial change coupled with Permo/Triassic faunal mass extinction. Nature 2005; 434:494-7. [PMID: 15791253 DOI: 10.1038/nature03396] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2004] [Accepted: 01/18/2005] [Indexed: 11/09/2022]
Abstract
Microbial expansion following faunal mass extinctions in Earth history can be studied by petrographic examination of microbialites (microbial crusts) or well-preserved organic-walled microbes. However, where preservation is poor, quantification of microbial communities can be problematic. We have circumvented this problem by adopting a lipid biomarker-based approach to evaluate microbial community changes across the Permo/Triassic (P/Tr) boundary at Meishan in South China. We present here a biomarker stratigraphic record showing episodic microbial changes coupled with a high-resolution record of invertebrate mass extinction. Variation in the microbial community structure is characterized by the 2-methylhopane (2-MHP) index (a ratio of the abundance of cyanobacterial biomarkers to more general bacterial biomarkers). Two episodes of faunal mass extinction were each preceded by minima in the 2-MHP index, followed by strong maxima, likely reflecting microbial responses to the catastrophic events that caused the extinction and initiated ecosystem changes. Hence, both cyanobacterial biomarker and invertebrate fossil records provide evidence for two episodes of biotic crisis across the P/Tr boundary.
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Affiliation(s)
- Shucheng Xie
- Organic Geochemistry Unit, Bristol Biogeochemistry Center, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
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228
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Ellery A, Ball AJ, Cockell C, Dickensheets D, Edwards H, Kolb C, Lammer H, Patel M, Richter L. Vanguard--a European robotic astrobiology-focussed Mars sub-surface mission proposal. ACTA ASTRONAUTICA 2005; 56:397-407. [PMID: 15754476 DOI: 10.1016/j.actaastro.2004.05.069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We present a new European Mars mission proposal to build on the UK-led Beagle2 Mars mission and continue its astrobiology-focussed investigation of Mars. The small surface element to be delivered to the Martian surface--Vanguard--is designed to be carried by a Mars Express-type spacecraft bus to Mars and adopts a similar entry, descent and landing system as Beagle2. The surface element comprises a triad of robotic devices--a lander, a micro-rover of the Sojourner class for surface mobility, and three ground-penetrating moles mounted onto the rover for sub-surface penetration to 5 m depth. The major onboard instruments on the rover include a Raman spectrometer/imager, a laser plasma spectrometer, an infrared spectrometer--these laser instruments provide the basis for in situ "remote" sensing of the sub-surface Martian environment within a powerful scientific package. The moles carry the instruments' sensor head array to the sub-surface. The moles are thus required to undergo a one-way trip down the boreholes without the need for recovery of moles or samples, eliminating much of the robotic complexity invoked by such operations.
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Affiliation(s)
- Alex Ellery
- Astronautics and Space Systems Group, School of Engineering, Kingston University, Friars Avenue, Roehampton Vale, London, UK.
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229
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Lau E, Nash CZ, Vogler DR, Cullings KW. Molecular diversity of cyanobacteria inhabiting coniform structures and surrounding mat in a Yellowstone hot spring. ASTROBIOLOGY 2005; 5:83-92. [PMID: 15711172 DOI: 10.1089/ast.2005.5.83] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Lithified coniform structures are common within cyanobacterial mats in Yellowstone National Park hot springs. It is unknown whether these structures and the mats from which they develop are inhabited by the same cyanobacterial populations. Denaturing gradient gel electrophoresis and sequencing and phylogenetic analysis of 16S rDNA was used to determine whether (1) three different morphological types of lithified coniform structures are inhabited by different cyanobacterial species, (2) these species are partitioned along a vertical gradient of these structures, and (3) lithified and non-lithified sections of mat are inhabited by different cyanobacterial species. Our results, based on multiple samplings, indicate that the cyanobacterial community compositions in the three lithified morphological types were identical and lacked any vertical differentiation. However, lithified and non-lithified portions of the same mat were inhabited by distinct and different populations of cyanobacteria. Cyanobacteria inhabiting lithified structures included at least one undefined Oscillatorialean taxon, which may represent the dominant cyanobacteria genus in lithified coniform stromatolites, Phormidium, three Synechococcus-like species, and two unknown cyanobacterial taxa. In contrast, the surrounding mats contained four closely related Synechococcus-like species. Our results indicate that the distribution of lithified coniform stromatolites may be dependent on the presence of one or more microorganisms, which are phylogenetically different from those inhabiting surrounding non-lithified mats.
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Affiliation(s)
- Evan Lau
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
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230
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Miller SR, Augustine S, Olson TL, Blankenship RE, Selker J, Wood AM. Discovery of a free-living chlorophyll d-producing cyanobacterium with a hybrid proteobacterial/cyanobacterial small-subunit rRNA gene. Proc Natl Acad Sci U S A 2005; 102:850-5. [PMID: 15637160 PMCID: PMC545527 DOI: 10.1073/pnas.0405667102] [Citation(s) in RCA: 149] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chlorophyll d-producing cyanobacteria are a recently described group of phototrophic bacteria that is a major focus of photosynthesis research, previously known only from marine environments in symbiosis with eukaryotes. We have discovered a free-living member of this group from a eutrophic hypersaline lake. Phylogenetic analyses indicated these strains are closely related to each other but not to prochlorophyte cyanobacteria that also use an alternative form of chlorophyll as the major light-harvesting pigment. We have also demonstrated that these bacteria acquired a fragment of the small-subunit rRNA gene encoding a conserved hairpin in the bacterial ribosome from a proteobacterial donor at least 10 million years before the present. Thus, our most widely used phylogenetic marker can be a mosaic of sequence fragments with widely divergent evolutionary histories.
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Affiliation(s)
- Scott R Miller
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA.
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231
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Melezhik VA, Fallick AE, Hanski EJ, Kump LR, Lepland A, Prave AR, Strauss H. Emergence of an aerobic biosphere during the Archean-Proterozoic transition: Challenges of future research. ACTA ACUST UNITED AC 2005. [DOI: 10.1130/1052-5173(2005)015[4:eoaabd]2.0.co;2] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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232
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Giordano M, Beardall J, Raven JA. CO2 concentrating mechanisms in algae: mechanisms, environmental modulation, and evolution. ANNUAL REVIEW OF PLANT BIOLOGY 2005; 56:99-131. [PMID: 15862091 DOI: 10.1146/annurev.arplant.56.032604.144052] [Citation(s) in RCA: 631] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The evolution of organisms capable of oxygenic photosynthesis paralleled a long-term reduction in atmospheric CO2 and the increase in O2. Consequently, the competition between O2 and CO2 for the active sites of RUBISCO became more and more restrictive to the rate of photosynthesis. In coping with this situation, many algae and some higher plants acquired mechanisms that use energy to increase the CO2 concentrations (CO2 concentrating mechanisms, CCMs) in the proximity of RUBISCO. A number of CCM variants are now found among the different groups of algae. Modulating the CCMs may be crucial in the energetic and nutritional budgets of a cell, and a multitude of environmental factors can exert regulatory effects on the expression of the CCM components. We discuss the diversity of CCMs, their evolutionary origins, and the role of the environment in CCM modulation.
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Affiliation(s)
- Mario Giordano
- Department of Marine Sciences, Università Politecnica delle Marche, 60121 Ancona, Italy.
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233
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Schulze-Makuch D, Irwin LN, Lipps JH, LeMone D, Dohm JM, Fairén AG. Scenarios for the evolution of life on Mars. ACTA ACUST UNITED AC 2005. [DOI: 10.1029/2005je002430] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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234
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Katz ME, Finkel ZV, Grzebyk D, Knoll AH, Falkowski PG. Evolutionary Trajectories and Biogeochemical Impacts of Marine Eukaryotic Phytoplankton. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2004. [DOI: 10.1146/annurev.ecolsys.35.112202.130137] [Citation(s) in RCA: 162] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Miriam E. Katz
- Department of Geological Sciences, Rutgers University, Piscataway, New Jersey 08854;
| | - Zoe V. Finkel
- Institute of Marine and Coastal Sciences, Rutgers University, New Brunswick, New Jersey 08901; , ,
| | - Daniel Grzebyk
- Institute of Marine and Coastal Sciences, Rutgers University, New Brunswick, New Jersey 08901; , ,
| | - Andrew H. Knoll
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138;
| | - Paul G. Falkowski
- Department of Geological Sciences, Rutgers University, Piscataway, New Jersey 08854;
- Institute of Marine and Coastal Sciences, Rutgers University, New Brunswick, New Jersey 08901; , ,
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235
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A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land. BMC Evol Biol 2004; 4:44. [PMID: 15535883 PMCID: PMC533871 DOI: 10.1186/1471-2148-4-44] [Citation(s) in RCA: 322] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2004] [Accepted: 11/09/2004] [Indexed: 11/10/2022] Open
Abstract
Background The timescale of prokaryote evolution has been difficult to reconstruct because of a limited fossil record and complexities associated with molecular clocks and deep divergences. However, the relatively large number of genome sequences currently available has provided a better opportunity to control for potential biases such as horizontal gene transfer and rate differences among lineages. We assembled a data set of sequences from 32 proteins (~7600 amino acids) common to 72 species and estimated phylogenetic relationships and divergence times with a local clock method. Results Our phylogenetic results support most of the currently recognized higher-level groupings of prokaryotes. Of particular interest is a well-supported group of three major lineages of eubacteria (Actinobacteria, Deinococcus, and Cyanobacteria) that we call Terrabacteria and associate with an early colonization of land. Divergence time estimates for the major groups of eubacteria are between 2.5–3.2 billion years ago (Ga) while those for archaebacteria are mostly between 3.1–4.1 Ga. The time estimates suggest a Hadean origin of life (prior to 4.1 Ga), an early origin of methanogenesis (3.8–4.1 Ga), an origin of anaerobic methanotrophy after 3.1 Ga, an origin of phototrophy prior to 3.2 Ga, an early colonization of land 2.8–3.1 Ga, and an origin of aerobic methanotrophy 2.5–2.8 Ga. Conclusions Our early time estimates for methanogenesis support the consideration of methane, in addition to carbon dioxide, as a greenhouse gas responsible for the early warming of the Earths' surface. Our divergence times for the origin of anaerobic methanotrophy are compatible with highly depleted carbon isotopic values found in rocks dated 2.8–2.6 Ga. An early origin of phototrophy is consistent with the earliest bacterial mats and structures identified as stromatolites, but a 2.6 Ga origin of cyanobacteria suggests that those Archean structures, if biologically produced, were made by anoxygenic photosynthesizers. The resistance to desiccation of Terrabacteria and their elaboration of photoprotective compounds suggests that the common ancestor of this group inhabited land. If true, then oxygenic photosynthesis may owe its origin to terrestrial adaptations.
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236
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Affiliation(s)
- Kay D Bidle
- Environmental Biophysics and Molecular Ecology Program, Institute of Marine and Coastal Sciences, Rutgers University, 71 Dudley Road, New Brunswick, New Jersey 08901, USA.
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237
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Falkowski PG, Katz ME, Knoll AH, Quigg A, Raven JA, Schofield O, Taylor FJR. The Evolution of Modern Eukaryotic Phytoplankton. Science 2004; 305:354-60. [PMID: 15256663 DOI: 10.1126/science.1095964] [Citation(s) in RCA: 640] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The community structure and ecological function of contemporary marine ecosystems are critically dependent on eukaryotic phytoplankton. Although numerically inferior to cyanobacteria, these organisms are responsible for the majority of the flux of organic matter to higher trophic levels and the ocean interior. Photosynthetic eukaryotes evolved more than 1.5 billion years ago in the Proterozoic oceans. However, it was not until the Mesozoic Era (251 to 65 million years ago) that the three principal phytoplankton clades that would come to dominate the modern seas rose to ecological prominence. In contrast to their pioneering predecessors, the dinoflagellates, coccolithophores, and diatoms all contain plastids derived from an ancestral red alga by secondary symbiosis. Here we examine the geological, geochemical, and biological processes that contributed to the rise of these three, distantly related, phytoplankton groups.
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Affiliation(s)
- Paul G Falkowski
- Institute of Marine and Coastal Sciences, Rutgers University, 71 Dudley Road, New Brunswick, NJ 08540, USA.
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238
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Hunsucker SW, Klage K, Slaughter SM, Potts M, Helm RF. A preliminary investigation of the Nostoc punctiforme proteome. Biochem Biophys Res Commun 2004; 317:1121-7. [PMID: 15094385 DOI: 10.1016/j.bbrc.2004.03.173] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2004] [Indexed: 10/26/2022]
Abstract
Nostoc punctiforme ATCC 29133 is a filamentous terrestrial cyanobacterium (prokaryote) that expresses several different phenotypes in response to environmental cues. When grown in nitrogen-deficient media the most abundant proteins in addition to phycobiliproteins were superoxide dismutase, ATP synthase, and peptidyl-prolyl cis-trans isomerases. A methylated peptide from an akinete marker protein was also identified, suggesting that methylation could potentially play a regulatory role through signaling. C-phycocyanin alpha-chain was methylated at the C-terminal end of the protein and tandem mass spectrometric data also identified peptides that were deamidated. Since a significant number of putative polyketide/non-ribosomal peptide synthase genes are present in the annotated genome, an analysis of a methanolic extract of whole cells was also performed, and a series of nostopeptolides were identified.
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239
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Abstract
The isoprenoid biosynthetic pathway is the source of a wide array of products. The pathway has been highly conserved throughout evolution, and isoprenoids are some of the most ancient biomolecules ever identified, playing key roles in many life forms. In this review we focus on C-10 mono-, C-15 sesqui-, and C-20 diterpenes. Evidence for interconversion between the pathway intermediates farnesyl pyrophosphate and geranylgeranyl pyrophosphate and their respective metabolites is examined. The diverse functions of these molecules are discussed in detail, including their ability to regulate expression of the beta-HMG-CoA reductase and Ras-related proteins. Additional topics include the mechanisms underlying the apoptotic effects of select isoprenoids, antiulcer activities, and the disposition and degradation of isoprenoids in the environment. Finally, the significance of pharmacological manipulation of the isoprenoid pathway and clinical correlations are discussed.
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Affiliation(s)
- Sarah A Holstein
- Departments of Internal Medicine and Pharmacology, University of Iowa, Iowa City, Iowa 52242, USA
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240
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De Las Rivas J, Balsera M, Barber J. Evolution of oxygenic photosynthesis: genome-wide analysis of the OEC extrinsic proteins. TRENDS IN PLANT SCIENCE 2004; 9:18-25. [PMID: 14729215 DOI: 10.1016/j.tplants.2003.11.007] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The appearance of oxygenic photosynthesis was a key event in the evolution of our green biosphere. Oxygen in the atmosphere is generally believed to come from the biomolecular water-splitting reaction that occurs in oxyphotosynthetic organisms catalysed by the oxygen evolving centre (OEC) of Photosystem II. Using knowledge from complete genomes and current databases, we have investigated the nature and composition of the extrinsic proteins forming the OECs of different organisms, with particular focus on the manganese stabilizing protein that is present in all known oxyphototrophs. This analysis traces the evolution of the extrinsic proteins from ancient cyanobacteria to higher plants and gives hints about the ancestral form of the OEC.
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Affiliation(s)
- Javier De Las Rivas
- Instituto de Recursos Naturales y Agrobiologia, Consejo Superior de Investigaciones Cientificas (CSIC), Salamanca, Spain
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241
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Sumner DY. Poor preservation potential of organics in Meridiani Planum hematite-bearing sedimentary rocks. ACTA ACUST UNITED AC 2004. [DOI: 10.1029/2004je002321] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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242
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Kenig F, Simons DJH, Crich D, Cowen JP, Ventura GT, Rehbein-Khalily T, Brown TC, Anderson KB. Branched aliphatic alkanes with quaternary substituted carbon atoms in modern and ancient geologic samples. Proc Natl Acad Sci U S A 2003; 100:12554-8. [PMID: 14551322 PMCID: PMC240654 DOI: 10.1073/pnas.1735581100] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2003] [Indexed: 11/18/2022] Open
Abstract
A pseudohomologous series of branched aliphatic alkanes with a quaternary substituted carbon atom (BAQCs, specifically 2,2-dimethylalkanes and 3,3- and 5,5-diethylalkanes) were identified in warm (65 degrees C) deep-sea hydrothermal waters and Late Cretaceous black shales. 5,5-Diethylalkanes were also observed in modern and Holocene marine shelf sediments and in shales spanning the last 800 million years of the geological record. The carbon number distribution of BAQCs indicates a biological origin. These compounds were observed but not identified in previous studies of 2.0 billion- to 2.2 billion-year-old metasediments and were commonly misidentified in other sediment samples, indicating that BAQCs are widespread in the geological record. The source organisms of BAQCs are unknown, but their paleobiogeographic distribution suggests that they have an affinity for sulfides and might be nonphotosynthetic sulfide oxidizers.
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Affiliation(s)
- Fabien Kenig
- Departments of Earth and Environmental Sciences and Chemistry, University of Illinois, Chicago, IL 60607, USA.
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243
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Rezanka T, Dembitsky VM, Go JV, Dor I, Prell A, Hanus L. Sterol compositions of the filamentous nitrogen-fixing terrestrial cyanobacterium Scytonema sp. Folia Microbiol (Praha) 2003; 48:357-60. [PMID: 12879746 DOI: 10.1007/bf02931366] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Thirteen unsaturated sterols were identified by gas chromatography--mass spectrometry using serially-coupled capillary columns from the filamentous nitrogen-fixing terrestrial cyanobacterium Scytonema sp. isolated from the microbial community of cyanobacterial on 'Black Cover' biofilms limestone walls in Jerusalem. The dominant sterols were cholest-5-en-3 beta-ol (18.9%), 3 beta-methoxycholest-5-ene (16.2%) and 3 beta-acetoxycholest-5-ene (11.2%).
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Affiliation(s)
- T Rezanka
- Institute of Microbiology, Academy of Sciences of the Czech Republic, 142 20 Prague, Czechia.
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244
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Berman-Frank I, Lundgren P, Falkowski P. Nitrogen fixation and photosynthetic oxygen evolution in cyanobacteria. Res Microbiol 2003; 154:157-64. [PMID: 12706503 DOI: 10.1016/s0923-2508(03)00029-9] [Citation(s) in RCA: 230] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The biological reduction of N(2) is catalyzed by nitrogenase, which is irreversibly inhibited by molecular oxygen. Cyanobacteria are the only diazotrophs (nitrogen-fixing organisms) that produce oxygen as a by-product of the photosynthetic process, and which must negotiate the inevitable presence of molecular oxygen with an essentially anaerobic enzyme. In this review, we present an analysis of the geochemical conditions under which nitrogenase evolved and examine how the evolutionary history of the enzyme complex corresponds to the physiological, morphological, and developmental strategies for reducing damage by molecular oxygen. Our review highlights biogeochemical constraints on diazotrophic cyanobacteria in the contemporary world.
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Affiliation(s)
- Ilana Berman-Frank
- Environmental Biophysics and Molecular Ecology Program, Institute of Marine and Coastal Sciences, Rutgers University, 71 Dudley Rd., New Brunswick, NJ 08901, USA.
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245
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Javaux EJ, Knoll AH, Walter M. Recognizing and interpreting the fossils of early eukaryotes. ORIGINS LIFE EVOL B 2003; 33:75-94. [PMID: 12967274 DOI: 10.1023/a:1023992712071] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Using molecular sequence data, biologists can generate hypotheses of protistan phylogeny and divergence times. Fossils, however, provide our only direct constraints on the timing and environmental context of early eukaryotic diversification. For this reason, recognition of eukaryotic fossils in Proterozoic rocks is key to the integration of geological and comparative biological perspectives on protistan evolution. Microfossils preserved in shales of the ca. 1500 Ma Roper Group, northern Australia, display characters that ally them to the Eucarya, but, at present, attribution to any particular protistan clade is uncertain. Continuing research on wall ultrastructure and microchemistry promises new insights into the nature and systematic relationships of early eukaryotic fossils.
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Affiliation(s)
- Emmanuelle J Javaux
- Organismic and Evolutionary Biology Department, Botanical Museum, Harvard University, Cambridge, MA, USA
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246
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Green BR. The Evolution of Light-harvesting Antennas. LIGHT-HARVESTING ANTENNAS IN PHOTOSYNTHESIS 2003. [DOI: 10.1007/978-94-017-2087-8_4] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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247
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248
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Talbot HM, Squier AH, Keely BJ, Farrimond P. Atmospheric pressure chemical ionisation reversed-phase liquid chromatography/ion trap mass spectrometry of intact bacteriohopanepolyols. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2003; 17:728-737. [PMID: 12661028 DOI: 10.1002/rcm.974] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Atmospheric pressure chemical ionisation liquid chromatography/multi-stage ion trap mass spectrometry (APCI-LC/MS(n)) has been applied to the study of intact bacteriohopanepolyols. Spectral characterisation of bacteriohopanepolyols of known structure present in bacterial extracts (Zymomonas mobilis and a fermenter containing methanotrophs including Methylococcus capsulatus) has revealed greater structural detail than previous liquid chromatography/mass spectrometry (LC/MS) methods and identified characteristic fragmentations indicative of numerous biohopanoid structures. Analysis of a Recent sedimentary extract from Lake Druzhby (Antarctica) has demonstrated the power of this technique to detect biohopanoids in complex samples including at least partial characterisation of previously unknown composite structures.
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Affiliation(s)
- Helen M Talbot
- NRG, School of Civil Engineering and Geosciences, Drummond Building, University of Newcastle, Newcastle upon Tyne NE1 7RU, UK.
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249
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Talbot HM, Summons R, Jahnke L, Farrimond P. Characteristic fragmentation of bacteriohopanepolyols during atmospheric pressure chemical ionisation liquid chromatography/ion trap mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2003; 17:2788-2796. [PMID: 14673828 DOI: 10.1002/rcm.1265] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Bacteriohopanepolyols (BHPs) fragment via characteristic pathways during atmospheric pressure chemical ionisation liquid chromatography/ion trap mass spectrometry (APCI-LC/MS(n)). Comparison of the MS(2) spectra of bacteriohopane-32,33,34,35-tetrol (BHT) and 2 beta-methylbacteriohopane-32,33,34,35-tetrol has confirmed the previously proposed ring-C cleavage occurring between C-9 and 11 and C-8 and 14. This fragmentation, diagnostic of all hopanoids, also occurs in BHPs containing an amino group (-NH(2)) at C-35 although the higher relative stability of the ion limits this fragmentation to a minor process after protonation of the basic nitrogen function. Studies of a number of cell cultures including a prochlorophyte (Prochlorothrix hollandica) and a cyanobacterium (Chlorogloeopsis LA) demonstrate the power of this technique to detect composite BHPs with a complex biological functionality at C-35. We also report the first observation of intact pentafunctionalised bacteriohopanepolyols using this method.
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Affiliation(s)
- Helen M Talbot
- NRG, School of Civil Engineering and Geosciences, Drummond Building, University of Newcastle, Newcastle upon Tyne NE1 7RU, UK.
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250
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