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Abstract
Organismal phylogeny depends on cell division, stasis, mutational divergence, cell mergers (by sex or symbiogenesis), lateral gene transfer and death. The tree of life is a useful metaphor for organismal genealogical history provided we recognize that branches sometimes fuse. Hennigian cladistics emphasizes only lineage splitting, ignoring most other major phylogenetic processes. Though methodologically useful it has been conceptually confusing and harmed taxonomy, especially in mistakenly opposing ancestral (paraphyletic) taxa. The history of life involved about 10 really major innovations in cell structure. In membrane topology, there were five successive kinds of cell: (i) negibacteria, with two bounding membranes, (ii) unibacteria, with one bounding and no internal membranes, (iii) eukaryotes with endomembranes and mitochondria, (iv) plants with chloroplasts and (v) finally, chromists with plastids inside the rough endoplasmic reticulum. Membrane chemistry divides negibacteria into the more advanced Glycobacteria (e.g. Cyanobacteria and Proteobacteria) with outer membrane lipolysaccharide and primitive Eobacteria without lipopolysaccharide (deserving intenser study). It also divides unibacteria into posibacteria, ancestors of eukaryotes, and archaebacteria-the sisters (not ancestors) of eukaryotes and the youngest bacterial phylum. Anaerobic eobacteria, oxygenic cyanobacteria, desiccation-resistant posibacteria and finally neomura (eukaryotes plus archaebacteria) successively transformed Earth. Accidents and organizational constraints are as important as adaptiveness in body plan evolution.
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53
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Blank CE, Sánchez-Baracaldo P. Timing of morphological and ecological innovations in the cyanobacteria--a key to understanding the rise in atmospheric oxygen. GEOBIOLOGY 2010; 8:1-23. [PMID: 19863595 DOI: 10.1111/j.1472-4669.2009.00220.x] [Citation(s) in RCA: 126] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
When cyanobacteria originated and diversified, and what their ancient traits were, remain critical unresolved problems. Here, we used a phylogenomic approach to construct a well-resolved 'core' cyanobacterial tree. The branching positions of four lineages (Thermosynechococcus elongatus, Synechococcus elongatus, Synechococcus PCC 7335 and Acaryochloris marina) were problematic, probably due to long branch attraction artifacts. A consensus genomic tree was used to study trait evolution using ancestral state reconstruction (ASR). The early cyanobacteria were probably unicellular, freshwater, had small cell diameters, and lacked the traits to form thick microbial mats. Relaxed molecular clock analyses suggested that early cyanobacterial lineages were restricted to freshwater ecosystems until at least 2.4 Ga, before diversifying into coastal brackish and marine environments. The resultant increases in niche space and nutrient availability, and consequent sedimentation of organic carbon into the deep oceans, would have generated large pulses of oxygen into the biosphere, possibly explaining why oxygen rose so rapidly. Rapid atmospheric oxidation could have destroyed the methane-driven greenhouse with simultaneous drawdown in pCO(2), precipitating 'Snowball Earth' conditions. The traits associated with the formation of thick, laminated microbial mats (large cell diameters, filamentous growth, sheaths, motility and nitrogen fixation) were not seen until after diversification of the LPP, SPM and PNT clades, after 2.32 Ga. The appearance of these traits overlaps with a global carbon isotopic excursion between 2.2 and 2.1 Ga. Thus, a massive re-ordering of biogeochemical cycles caused by the appearance of complex laminated microbial communities in marine environments may have caused this excursion. Finally, we show that ASR may provide an explanation for why cyanobacterial microfossils have not been observed until after 2.0 Ga, and make suggestions for how future paleobiological searches for early cyanobacteria might proceed. In summary, key evolutionary events in the microbial world may have triggered some of the key geologic upheavals on the Paleoproterozoic Earth.
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Affiliation(s)
- C E Blank
- Department of Geosciences, University of Montana, Missoula, MT, USA.
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Jungblut AD, Lovejoy C, Vincent WF. Global distribution of cyanobacterial ecotypes in the cold biosphere. ISME JOURNAL 2009; 4:191-202. [PMID: 19890368 DOI: 10.1038/ismej.2009.113] [Citation(s) in RCA: 159] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Perennially cold habitats are diminishing as a result of climate change; however, little is known of the diversity or biogeography of microbes that thrive in such environments. Here we use targeted 16S rRNA gene surveys to evaluate the global affinities of cold-dwelling cyanobacteria from lake, stream and ice communities living at the northern limit of High Arctic Canada. Pigment signature analysis by HPLC confirmed the dominance of cyanobacteria in the phototrophic communities of these High Arctic microbial mats, with associated populations of chlorophytes and chromophytes. Microscopic analysis of the cyanobacteria revealed a diverse assemblage of morphospecies grouping into orders Oscillatoriales, Nostocales and Chroococcales. The 16S rRNA gene sequences from six clone libraries grouped into a total of 24 ribotypes, with a diversity in each mat ranging from five ribotypes in ice-based communities to 14 in land-based pond communities. However, no significant differences in composition were observed between these two microbial mat systems. Based on clone-library and phylogenetic analysis, several of the High Arctic ribotypes were found to be >99% similar to Antarctic and alpine sequences, including to taxa previously considered endemic to Antarctica. Among the latter, one High Arctic sequence was found 99.8% similar to Leptolyngbya antarctica sequenced from the Larsemann Hills, Antarctica. More than 68% of all identified ribotypes at each site matched only cyanobacterial sequences from perennially cold terrestrial ecosystems, and were <97.5% similar to sequences from warmer environments. These results imply the global distribution of low-temperature cyanobacterial ecotypes throughout the cold terrestrial biosphere.
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Affiliation(s)
- Anne D Jungblut
- Département de Biologie and Centre d'Etudes Nordiques, Université Laval, Quebec City, Quebec, Canada.
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55
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Reddy SM, Evans DAD. Palaeoproterozoic supercontinents and global evolution: correlations from core to atmosphere. ACTA ACUST UNITED AC 2009. [DOI: 10.1144/sp323.1] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
AbstractThe Palaeoproterozoic era was a time of profound change in Earth evolution and represented perhaps the first supercontinent cycle, from the amalgamation and dispersal of a possible Neoarchaean supercontinent to the formation of the 1.9–1.8 Ga supercontinent Nuna. This supercontinent cycle, although currently lacking in palaeogeographic detail, can in principle provide a contextual framework to investigate the relationships between deep-Earth and surface processes. In this article, we graphically summarize secular evolution from the Earth's core to its atmosphere, from the Neoarchaean to the Mesoproterozoic eras (specifically 3.0–1.2 Ga), to reveal intriguing temporal relationships across the various ‘spheres’ of the Earth system. At the broadest level our compilation confirms an important deep-Earth event at c. 2.7 Ga that is manifested in an abrupt increase in geodynamo palaeointensity, a peak in the global record of large igneous provinces, and a broad maximum in several mantle-depletion proxies. Temporal coincidence with juvenile continental crust production and orogenic gold, massive-sulphide and porphyry copper deposits, indicate enhanced mantle convection linked to a series of mantle plumes and/or slab avalanches. The subsequent stabilization of cratonic lithosphere, the possible development of Earth's first supercontinent and the emergence of the continents led to a changing surface environment in which voluminous banded iron-formations could accumulate on the continental margins and photosynthetic life could flourish. This in turn led to irreversible atmospheric oxidation at 2.4–2.3 Ga, extreme events in global carbon cycling, and the possible dissipation of a former methane greenhouse atmosphere that resulted in extensive Palaeoproterozoic ice ages. Following the great oxidation event, shallow marine sulphate levels rose, sediment-hosted and iron-oxide-rich metal deposits became abundant, and the transition to sulphide-stratified oceans provided the environment for early eukaryotic evolution. Recent advances in the geochronology of the global stratigraphic record have made these inferences possible. Frontiers for future research include more refined modelling of Earth's thermal and geodynamic evolution, palaeomagnetic studies of geodynamo intensity and continental motions, further geochronology and tectonic syntheses at regional levels, development of new isotopic systems to constrain geochemical cycles, and continued innovation in the search for records of early life in relation to changing palaeoenvironments.
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Affiliation(s)
- S. M. Reddy
- The Institute for Geoscience Research, Department of Applied Geology, Curtin University of Technology, GPO Box U 1987, Perth, WA 6845, Australia
| | - D. A. D. Evans
- Department of Geology and Geophysics, Yale University, New Haven, CT 06520-8109, USA
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56
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Storrie-Lombardi MC, Sattler B. Laser-induced fluorescence emission (L.I.F.E.): in situ nondestructive detection of microbial life in the ice covers of Antarctic lakes. ASTROBIOLOGY 2009; 9:659-672. [PMID: 19778277 DOI: 10.1089/ast.2009.0351] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Laser-induced fluorescence emission (L.I.F.E.) images were obtained in situ following 532 nm excitation of cryoconite assemblages in the ice covers of annual and perennially frozen Antarctic lakes during the 2008 Tawani International Expedition to Schirmacher Oasis and Lake Untersee in Dronning Maud Land, Antarctica. Laser targeting of a single millimeter-scale cryoconite results in multiple neighboring excitation events secondary to ice/air interface reflection and refraction in the bubbles surrounding the primary target. Laser excitation at 532 nm of cyanobacteria-dominated assemblages produced red and infrared autofluorescence activity attributed to the presence of phycoerythrin photosynthetic pigments. The method avoids destruction of individual target organisms and does not require the disruption of either the structure of the microbial community or the surrounding ice matrix. L.I.F.E. survey strategies described may be of interest for orbital monitoring of photosynthetic primary productivity in polar and alpine glaciers, ice sheets, snow, and lake ice of Earth's cryosphere. The findings open up the possibility of searching from either a rover or from orbit for signs of life in the polar regions of Mars and the frozen regions of exoplanets in neighboring star systems.
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57
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Cirković MM, Vukotić B, Dragićević I. Galactic punctuated equilibrium: how to undermine Carter's anthropic argument in astrobiology. ASTROBIOLOGY 2009; 9:491-501. [PMID: 19566428 DOI: 10.1089/ast.2007.0200] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A new strategy by which to defeat Carter's "anthropic" argument against extraterrestrial life and intelligence is presented. Our approach is based on relaxing hidden uniformitarian assumptions and considering instead a dynamical succession of evolutionary regimes governed by both global (Galaxy-wide) and local (planet- or planetary system-limited) regulation mechanisms. Notably, our increased understanding of the nature of supernovae, gamma-ray bursts, and strong coupling between the Solar System and the Galaxy, and the theories of "punctuated equilibria" and "macroevolutionary regimes" are in full accordance with the regulation-mechanism picture. The application of this particular strategy highlights the limits of application of Carter's argument and indicates that, in the real universe, its applicability conditions are not satisfied. We conclude that drawing far-reaching conclusions about the scarcity of extraterrestrial intelligence and the prospects of our efforts to detect it on the basis of this argument is unwarranted.
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Glass JB, Wolfe-Simon F, Anbar AD. Coevolution of metal availability and nitrogen assimilation in cyanobacteria and algae. GEOBIOLOGY 2009; 7:100-23. [PMID: 19320747 DOI: 10.1111/j.1472-4669.2009.00190.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Marine primary producers adapted over eons to the changing chemistry of the oceans. Because a number of metalloenzymes are necessary for N assimilation, changes in the availability of transition metals posed a particular challenge to the supply of this critical nutrient that regulates marine biomass and productivity. Integrating recently developed geochemical, biochemical, and genetic evidence, we infer that the use of metals in N assimilation - particularly Fe and Mo - can be understood in terms of the history of metal availability through time. Anoxic, Fe-rich Archean oceans were conducive to the evolution of Fe-using enzymes that assimilate abiogenic NH(4)(+) and NO(2)(-). The N demands of an expanding biosphere were satisfied by the evolution of biological N(2) fixation, possibly utilizing only Fe. Trace O(2) in late Archean environments, and the eventual 'Great Oxidation Event' c. 2.3 Ga, mobilized metals such as Mo, enabling the evolution of Mo (or V)-based N(2) fixation and the Mo-dependent enzymes for NO(3)(-) assimilation and denitrification by prokaryotes. However, the subsequent onset of deep-sea euxinia, an increasingly-accepted idea, may have kept ocean Mo inventories low and depressed Fe, limiting the rate of N(2) fixation and the supply of fixed N. Eukaryotic ecosystems may have been particularly disadvantaged by N scarcity and the high Mo requirement of eukaryotic NO(3)(-) assimilation. Thorough ocean oxygenation in the Neoproterozoic led to Mo-rich oceans, possibly contributing to the proliferation of eukaryotes and thus the Cambrian explosion of metazoan life. These ideas can be tested by more intensive study of the metal requirements in N assimilation and the biological strategies for metal uptake, regulation, and storage.
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Affiliation(s)
- J B Glass
- School of Earth and Space Exploration, Arizona State University, Tempe, AZ 85287, USA.
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60
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Raymond J. The role of horizontal gene transfer in photosynthesis, oxygen production, and oxygen tolerance. Methods Mol Biol 2009; 532:323-38. [PMID: 19271194 DOI: 10.1007/978-1-60327-853-9_19] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
One of the pivotal events during the early evolution of life was the advent of oxygenic photosynthesis, responsible for producing essentially all of the free oxygen in Earth's atmosphere. This molecular innovation required the development of two tandemly linked photosystems that generate a redox potential strong enough to oxidize water and then funnel those electrons ultimately to cellular processes like carbon and nitrogen fixation. The by-product of this reaction, molecular oxygen, spawned an entirely new realm of enzymatic reactions that served to mitigate its potential toxicity, as well as to take advantage of the free energy available from using O(2) as an electron acceptor. These ensuing events ultimately gave rise to aerobic, multicelled eukaryotes and new levels of biological complexity. Remarkably, instances of horizontal gene transfer have been identified at nearly every step in this transformation of the biosphere, from the evolution and radiation of photosynthesis to the development of biological pathways dependent on oxygen. This chapter discusses the evidence and examples of some of these occurrences that have been elucidated in recent years.
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Affiliation(s)
- Jason Raymond
- School of Natural Sciences, University of California, Merced, CA, USA
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61
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Ohmoto H, Runnegar B, Kump LR, Fogel ML, Kamber B, Anbar AD, Knauth PL, Lowe DR, Sumner DY, Watanabe Y. Biosignatures in ancient rocks: a summary of discussions at a field workshop on biosignatures in ancient rocks. ASTROBIOLOGY 2008; 8:883-895. [PMID: 19025466 DOI: 10.1089/ast.2008.0257] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
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Palaeoproterozoic ice houses and the evolution of oxygen-mediating enzymes: the case for a late origin of photosystem II. Philos Trans R Soc Lond B Biol Sci 2008; 363:2755-65. [PMID: 18487128 PMCID: PMC2606766 DOI: 10.1098/rstb.2008.0024] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Two major geological problems regarding the origin of oxygenic photosynthesis are (i) identifying a source of oxygen pre-dating the biological oxygen production and capable of driving the evolution of oxygen tolerance, and (ii) determining when oxygenic photosynthesis evolved. One solution to the first problem is the accumulation of photochemically produced H(2)O(2) at the surface of the glaciers and its subsequent incorporation into ice. Melting at the glacier base would release H(2)O(2), which interacts with seawater to produce O(2) in an environment shielded from the lethal levels of ultraviolet radiation needed to produce H(2)O(2). Answers to the second problem are controversial and range from 3.8 to 2.2 Gyr ago. A sceptical view, based on the metals that have the redox potentials close to oxygen, argues for the late end of the range. The preponderance of geological evidence suggests little or no oxygen in the Late Archaean atmosphere (less than 1 ppm). The main piece of evidence for an earlier evolution of oxygenic photosynthesis comes from lipid biomarkers. Recent work, however, has shown that 2-methylhopanes, once thought to be unique biomarkers for cyanobacteria, are also produced anaerobically in significant quantities by at least two strains of anoxygenic phototrophs. Sterane biomarkers provide the strongest evidence for a date 2.7 Gyr ago or above, and could also be explained by the common evolutionary pattern of replacing anaerobic enzymes with oxygen-dependent ones. Although no anaerobic sterol synthesis pathway has been identified in the modern biosphere, enzymes that perform the necessary chemistry do exist. This analysis suggests that oxygenic photosynthesis could have evolved close in geological time to the Makganyene Snowball Earth Event and argues for a causal link between the two.
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63
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Dupont CL, Neupane K, Shearer J, Palenik B. Diversity, function and evolution of genes coding for putative Ni-containing superoxide dismutases. Environ Microbiol 2008; 10:1831-43. [PMID: 18412551 DOI: 10.1111/j.1462-2920.2008.01604.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
We examined the phylogenetic distribution, functionality and evolution of the sodN gene family, which has been shown to code for a unique Ni-containing isoform of superoxide dismutase (Ni-SOD) in Streptomyces. Many of the putative sodN sequences retrieved from public domain genomic and metagenomic databases are quite divergent from structurally and functionally characterized Ni-SOD. Structural bioinformatics studies verified that the divergent members of the sodN protein family code for similar three-dimensional structures and identified evolutionarily conserved amino acid residues. Structural and biochemical studies of the N-terminus 'Ni-hook' motif coded for by the putative sodN sequences confirmed both Ni (II) ligating and superoxide dismutase activity. Both environmental and organismal genomes expanded the previously noted phylogenetic distribution of sodN, and the sequences form four well-separated clusters, with multiple subclusters. The phylogenetic distribution of sodN suggests that the gene has been acquired via horizontal gene transfer by numerous organisms of diverse phylogenetic background, including both Eukaryotes and Prokaryotes. The presence of sodN correlates with the genomic absence of the gene coding for Fe-SOD, a structurally and evolutionarily distinct isoform of SOD. Given the low levels of Fe found in the marine environment from where many sequences were attained, we suggest that the replacement of Fe-SOD with Ni-SOD may be an evolutionary adaptation to reduce iron requirements.
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Affiliation(s)
- C L Dupont
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92039, USA
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66
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Stoeck T, Kasper J, Bunge J, Leslin C, Ilyin V, Epstein S. Protistan diversity in the Arctic: a case of paleoclimate shaping modern biodiversity? PLoS One 2007; 2:e728. [PMID: 17710128 PMCID: PMC1940325 DOI: 10.1371/journal.pone.0000728] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2007] [Accepted: 07/05/2007] [Indexed: 11/25/2022] Open
Abstract
Background The impact of climate on biodiversity is indisputable. Climate changes over geological time must have significantly influenced the evolution of biodiversity, ultimately leading to its present pattern. Here we consider the paleoclimate data record, inferring that present-day hot and cold environments should contain, respectively, the largest and the smallest diversity of ancestral lineages of microbial eukaryotes. Methodology/Principal Findings We investigate this hypothesis by analyzing an original dataset of 18S rRNA gene sequences from Western Greenland in the Arctic, and data from the existing literature on 18S rRNA gene diversity in hydrothermal vent, temperate sediments, and anoxic water column communities. Unexpectedly, the community from the cold environment emerged as one of the richest observed to date in protistan species, and most diverse in ancestral lineages. Conclusions/Significance This pattern is consistent with natural selection sweeps on aerobic non-psychrophilic microbial eukaryotes repeatedly caused by low temperatures and global anoxia of snowball Earth conditions. It implies that cold refuges persisted through the periods of greenhouse conditions, which agrees with some, although not all, current views on the extent of the past global cooling and warming events. We therefore identify cold environments as promising targets for microbial discovery.
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Affiliation(s)
- Thorsten Stoeck
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Jennifer Kasper
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany
| | - John Bunge
- Department of Statistical Science, Cornell University, Ithaca, New York, United States of America
| | - Chesley Leslin
- Department of Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Valya Ilyin
- Department of Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Slava Epstein
- Department of Biology, Northeastern University, Boston, Massachusetts, United States of America
- Marine Science Center, Northeastern University, Nahant, Massachusetts, United States of America
- * To whom correspondence should be addressed. E-mail:
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67
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Hansen J, Sato M, Kharecha P, Russell G, Lea DW, Siddall M. Climate change and trace gases. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2007; 365:1925-54. [PMID: 17513270 DOI: 10.1098/rsta.2007.2052] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Palaeoclimate data show that the Earth's climate is remarkably sensitive to global forcings. Positive feedbacks predominate. This allows the entire planet to be whipsawed between climate states. One feedback, the 'albedo flip' property of ice/water, provides a powerful trigger mechanism. A climate forcing that 'flips' the albedo of a sufficient portion of an ice sheet can spark a cataclysm. Inertia of ice sheet and ocean provides only moderate delay to ice sheet disintegration and a burst of added global warming. Recent greenhouse gas (GHG) emissions place the Earth perilously close to dramatic climate change that could run out of our control, with great dangers for humans and other creatures. Carbon dioxide (CO2) is the largest human-made climate forcing, but other trace constituents are also important. Only intense simultaneous efforts to slow CO2 emissions and reduce non-CO2 forcings can keep climate within or near the range of the past million years. The most important of the non-CO2 forcings is methane (CH4), as it causes the second largest human-made GHG climate forcing and is the principal cause of increased tropospheric ozone (O3), which is the third largest GHG forcing. Nitrous oxide (N2O) should also be a focus of climate mitigation efforts. Black carbon ('black soot') has a high global warming potential (approx. 2000, 500 and 200 for 20, 100 and 500 years, respectively) and deserves greater attention. Some forcings are especially effective at high latitudes, so concerted efforts to reduce their emissions could preserve Arctic ice, while also having major benefits for human health, agricultural productivity and the global environment.
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Affiliation(s)
- James Hansen
- NASA Goddard Institute for Space Studies and Columbia University Earth Institute, New York, NY 10025, USA.
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Liang MC, Hartman H, Kopp RE, Kirschvink JL, Yung YL. Production of hydrogen peroxide in the atmosphere of a Snowball Earth and the origin of oxygenic photosynthesis. Proc Natl Acad Sci U S A 2006; 103:18896-9. [PMID: 17138669 PMCID: PMC1672611 DOI: 10.1073/pnas.0608839103] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2005] [Indexed: 11/18/2022] Open
Abstract
During Proterozoic time, Earth experienced two intervals with one or more episodes of low-latitude glaciation, which are probable "Snowball Earth" events. Although the severity of the historical glaciations is debated, theoretical "hard Snowball" conditions are associated with the nearly complete shutdown of the hydrological cycle. We show here that, during such long and severe glacial intervals, a weak hydrological cycle coupled with photochemical reactions involving water vapor would give rise to the sustained production of hydrogen peroxide. The photochemical production of hydrogen peroxide has been proposed previously as the primary mechanism for oxidizing the surface of Mars. During a Snowball, hydrogen peroxide could be stored in the ice; it would then be released directly into the ocean and the atmosphere upon melting and could mediate global oxidation events in the aftermath of the Snowball, such as that recorded in the Fe and Mn oxides of the Kalahari Manganese Field, deposited after the Paleoproterozoic low-latitude Makganyene glaciation. Low levels of peroxides and molecular oxygen generated during Archean and earliest Proterozoic non-Snowball glacial intervals could have driven the evolution of oxygen-mediating and -using enzymes and thereby paved the way for the eventual appearance of oxygenic photosynthesis.
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Affiliation(s)
- Mao-Chang Liang
- Division of Geological and Planetary Sciences, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA.
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Hartman H, Favaretto P, Smith TF. The archaeal origins of the eukaryotic translational system. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2006; 2:1-9. [PMID: 16877317 PMCID: PMC2685589 DOI: 10.1155/2006/431618] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Among the 78 eukaryotic ribosomal proteins, eleven are specific to Eukarya, 33 are common only to Archaea and Eukarya and 34 are homologous (at least in part) to those of both Bacteria and Archaea. Several other translational proteins are common only to Eukarya and Archaea (e.g., IF2a, SRP19, etc.), whereas others are shared by the three phyla (e.g., EFTu/EF1A and SRP54). Although this and other analyses strongly support an archaeal origin for a substantial fraction of the eukaryotic translational machinery, especially the ribosomal proteins, there have been numerous unique and ubiquitous additions to the eukaryotic translational system besides the 11 unique eukaryotic ribosomal proteins. These include peptide additions to most of the 67 archaeal homolog proteins, rRNA insertions, the 5.8S RNA and the Alu extension to the SRP RNA. Our comparative analysis of these and other eukaryotic features among the three different cellular phylodomains supports the idea that an archaeal translational system was most likely incorporated by means of endosymbiosis into a host cell that was neither bacterial nor archaeal in any modern sense. Phylogenetic analyses provide support for the timing of this acquisition coinciding with an ancient bottleneck in prokaryotic diversity.
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Affiliation(s)
- Hyman Hartman
- Biological Engineering Division, Building 56, Room 354, Massachusetts Institute of Technology, Cambridge MA 02139, USA
- BioMolecular Engineering Research Center, Boston University, 36 Cummington St., Boston MA 02215, USA
| | - Paola Favaretto
- BioMolecular Engineering Research Center, Boston University, 36 Cummington St., Boston MA 02215, USA
| | - Temple F. Smith
- BioMolecular Engineering Research Center, Boston University, 36 Cummington St., Boston MA 02215, USA
- Corresponding author ()
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70
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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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71
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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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72
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Kaštovská K, Stibal M, Šabacká M, Černá B, Šantrůčková H, Elster J. Microbial community structure and ecology of subglacial sediments in two polythermal Svalbard glaciers characterized by epifluorescence microscopy and PLFA. Polar Biol 2006. [DOI: 10.1007/s00300-006-0181-y] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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73
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Cavalier-Smith T. Rooting the tree of life by transition analyses. Biol Direct 2006; 1:19. [PMID: 16834776 PMCID: PMC1586193 DOI: 10.1186/1745-6150-1-19] [Citation(s) in RCA: 140] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2006] [Accepted: 07/11/2006] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Despite great advances in clarifying the family tree of life, it is still not agreed where its root is or what properties the most ancient cells possessed--the most difficult problems in phylogeny. Protein paralogue trees can theoretically place the root, but are contradictory because of tree-reconstruction artefacts or poor resolution; ribosome-related and DNA-handling enzymes suggested one between neomura (eukaryotes plus archaebacteria) and eubacteria, whereas metabolic enzymes often place it within eubacteria but in contradictory places. Palaeontology shows that eubacteria are much more ancient than eukaryotes, and, together with phylogenetic evidence that archaebacteria are sisters not ancestral to eukaryotes, implies that the root is not within the neomura. Transition analysis, involving comparative/developmental and selective arguments, can polarize major transitions and thereby systematically exclude the root from major clades possessing derived characters and thus locate it; previously the 20 shared neomuran characters were thus argued to be derived, but whether the root was within eubacteria or between them and archaebacteria remained controversial. RESULTS I analyze 13 major transitions within eubacteria, showing how they can all be congruently polarized. I infer the first fully resolved prokaryote tree, with a basal stem comprising the new infrakingdom Glidobacteria (Chlorobacteria, Hadobacteria, Cyanobacteria), which is entirely non-flagellate and probably ancestrally had gliding motility, and two derived branches (Gracilicutes and Unibacteria/Eurybacteria) that diverged immediately following the origin of flagella. Proteasome evolution shows that the universal root is outside a clade comprising neomura and Actinomycetales (proteates), and thus lies within other eubacteria, contrary to a widespread assumption that it is between eubacteria and neomura. Cell wall and flagellar evolution independently locate the root outside Posibacteria (Actinobacteria and Endobacteria), and thus among negibacteria with two membranes. Posibacteria are derived from Eurybacteria and ancestral to neomura. RNA polymerase and other insertions strongly favour the monophyly of Gracilicutes (Proteobacteria, Planctobacteria, Sphingobacteria, Spirochaetes). Evolution of the negibacterial outer membrane places the root within Eobacteria (Hadobacteria and Chlorobacteria, both primitively without lipopolysaccharide): as all phyla possessing the outer membrane beta-barrel protein Omp85 are highly probably derived, the root lies between them and Chlorobacteria, the only negibacteria without Omp85, or possibly within Chlorobacteria. CONCLUSION Chlorobacteria are probably the oldest and Archaebacteria the youngest bacteria, with Posibacteria of intermediate age, requiring radical reassessment of dominant views of bacterial evolution. The last ancestor of all life was a eubacterium with acyl-ester membrane lipids, large genome, murein peptidoglycan walls, and fully developed eubacterial molecular biology and cell division. It was a non-flagellate negibacterium with two membranes, probably a photosynthetic green non-sulphur bacterium with relatively primitive secretory machinery, not a heterotrophic posibacterium with one membrane.
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74
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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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75
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Kurtz DM. Avoiding high-valent iron intermediates: superoxide reductase and rubrerythrin. J Inorg Biochem 2006; 100:679-93. [PMID: 16504301 DOI: 10.1016/j.jinorgbio.2005.12.017] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2005] [Accepted: 12/13/2005] [Indexed: 10/25/2022]
Abstract
The Fenton or Fenton-type reaction between aqueous ferrous ion and hydrogen peroxide generates a highly oxidizing species, most often formulated as hydroxyl radical or ferryl ([Fe(IV)O](2+)). Intracellular Fenton-type chemistry can be lethal if not controlled. Nature has, therefore, evolved enzymes to scavenge superoxide and hydrogen peroxide, the reduced dioxygen species that initiate intracellular Fenton-type chemistry. Two such enzymes found predominantly in air-sensitive bacteria and archaea, superoxide reductase (SOR) and rubrerythrin (Rbr), functioning as a peroxidase (hydrogen peroxide reductase), contain non-heme iron. The iron coordination spheres in these enzymes contain five or six protein ligands from His and Glu residues, and, in the case of SOR, a Cys residue. SOR contains a mononuclear active site that is designed to protonate and rapidly expel peroxide generated as a product of the enzymatic reaction. The ferrous SOR reacts adventitiously but relatively slowly (several seconds to a few minutes) with exogenous hydrogen peroxide, presumably in a Fenton-type reaction. The diferrous active site of Rbr reacts more rapidly with hydrogen peroxide but can divert Fenton-type reactions towards the two-electron reduction of hydrogen peroxide to water. Proximal aromatic residues may function as radical sinks for Fenton-generated oxidants. Fenton-initiated damage to these iron active sites may become apparent only under extremely oxidizing intracellular conditions.
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Affiliation(s)
- Donald M Kurtz
- Department of Chemistry and Center for Metalloenzyme Studies, University of Georgia, Athens, GA 30602, USA.
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76
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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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77
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Methé BA, Nelson KE, Deming JW, Momen B, Melamud E, Zhang X, Moult J, Madupu R, Nelson WC, Dodson RJ, Brinkac LM, Daugherty SC, Durkin AS, DeBoy RT, Kolonay JF, Sullivan SA, Zhou L, Davidsen TM, Wu M, Huston AL, Lewis M, Weaver B, Weidman JF, Khouri H, Utterback TR, Feldblyum TV, Fraser CM. The psychrophilic lifestyle as revealed by the genome sequence of Colwellia psychrerythraea 34H through genomic and proteomic analyses. Proc Natl Acad Sci U S A 2005; 102:10913-8. [PMID: 16043709 PMCID: PMC1180510 DOI: 10.1073/pnas.0504766102] [Citation(s) in RCA: 431] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The completion of the 5,373,180-bp genome sequence of the marine psychrophilic bacterium Colwellia psychrerythraea 34H, a model for the study of life in permanently cold environments, reveals capabilities important to carbon and nutrient cycling, bioremediation, production of secondary metabolites, and cold-adapted enzymes. From a genomic perspective, cold adaptation is suggested in several broad categories involving changes to the cell membrane fluidity, uptake and synthesis of compounds conferring cryotolerance, and strategies to overcome temperature-dependent barriers to carbon uptake. Modeling of three-dimensional protein homology from bacteria representing a range of optimal growth temperatures suggests changes to proteome composition that may enhance enzyme effectiveness at low temperatures. Comparative genome analyses suggest that the psychrophilic lifestyle is most likely conferred not by a unique set of genes but by a collection of synergistic changes in overall genome content and amino acid composition.
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Affiliation(s)
- Barbara A Methé
- The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA.
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78
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Vishwanath P, Favaretto P, Hartman H, Mohr SC, Smith TF. Ribosomal protein-sequence block structure suggests complex prokaryotic evolution with implications for the origin of eukaryotes. Mol Phylogenet Evol 2005; 33:615-25. [PMID: 15522791 DOI: 10.1016/j.ympev.2004.07.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2004] [Revised: 06/29/2004] [Indexed: 11/18/2022]
Abstract
Amino acid sequence alignments of orthologous ribosomal proteins found in Bacteria, Archaea, and Eukaryota display, relative to one another, an unusual segment or block structure, with major evolutionary implications. Within each of the prokaryotic phylodomains the sequences exhibit substantial similarity, but cross-domain alignments break up into (a) universal blocks (conserved in both phylodomains), (b) bacterial blocks (unalignable with any archaeal counterparts), and (c) archaeal blocks (unalignable with any bacterial counterparts). Sequences of those eukaryotic cytoplasmic riboproteins that have orthologs in both Bacteria and Archaea, exclusively match the archaeal block structure. The distinct blocks do not correlate consistently with any identifiable functional or structural feature including RNA and protein contacts. This phylodomain-specific block pattern also exists in a number of other proteins associated with protein synthesis, but not among enzymes of intermediary metabolism. While the universal blocks imply that modern Bacteria and Archaea (as defined by their translational machinery) clearly have had a common ancestor, the phylodomain-specific blocks imply that these two groups derive from single, phylodomain-specific types that came into existence at some point long after that common ancestor. The simplest explanation for this pattern would be a major evolutionary bottleneck, or other scenario that drastically limited the progenitors of modern prokaryotic diversity at a time considerably after the evolution of a fully functional translation apparatus. The vast range of habitats and metabolisms that prokaryotes occupy today would thus reflect divergent evolution after such a restricting event. Interestingly, phylogenetic analysis places the origin of eukaryotes at about the same time and shows a closer relationship of the eukaryotic ribosome-associated proteins to crenarchaeal rather than euryarchaeal counterparts.
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Affiliation(s)
- Prashanth Vishwanath
- BioMolecular Engineering Research Center, Boston University, 36 Cummington St., Boston, MA 02215, USA
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79
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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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80
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Peck LS, Clark MS, Clarke A, Cockell CS, Convey P, Detrich HW, Fraser KPP, Johnston IA, Methe BA, Murray AE, Römisch K, Rogers AD. Genomics: applications to Antarctic ecosystems. Polar Biol 2004. [DOI: 10.1007/s00300-004-0671-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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81
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Sienkiewicz N, Daher W, Dive D, Wrenger C, Viscogliosi E, Wintjens R, Jouin H, Capron M, Müller S, Khalife J. Identification of a mitochondrial superoxide dismutase with an unusual targeting sequence in Plasmodium falciparum. Mol Biochem Parasitol 2004; 137:121-32. [PMID: 15279958 DOI: 10.1016/j.molbiopara.2004.05.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2004] [Revised: 05/12/2004] [Accepted: 05/15/2004] [Indexed: 10/26/2022]
Abstract
The intraerythrocytic stages of Plasmodium falciparum are exposed to oxidative stress and require functional anti-oxidant systems to survive. In addition to the parasite's known iron-dependent superoxide dismutase PfSOD1, a second SOD gene (PfSOD2) interrupted by 8 introns was identified on chromosome 6. Molecular modelling shows that the structure of PfSOD2 is similar to other iron-dependent SODs and phylogenetic analysis suggests PfSOD1 and PfSOD2 are the result of an ancestral gene duplication. The deduced amino acid sequence of PfSOD2 is similar to PfSOD1 but has a long N-terminal extension. Immunofluorescence studies show that PfSOD1 is cytosolic, whereas the N-terminal extension of PfSOD2 targets a green fluorescent protein fusion into the parasite's mitochondrion. Both SOD genes are transcribed during the erythrocytic cycle with PfSOD1 mRNA levels up to 35-fold higher than those of PfSOD2. Northern blots demonstrated that the mRNA levels of both SOD genes are up-regulated upon exposure to oxidative stress.
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Affiliation(s)
- Natasha Sienkiewicz
- Division of Biological Chemistry and Molecular Microbiology, School of Life Sciences, University of Dundee, WTB/MSI Complex, DD15EH, UK
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82
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Glacial Periods on Early Earth and Implications for the Evolution of Life. ACTA ACUST UNITED AC 2004. [DOI: 10.1007/1-4020-2522-x_29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
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83
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Raymond J, Blankenship RE. Horizontal gene transfer in eukaryotic algal evolution. Proc Natl Acad Sci U S A 2003; 100:7419-20. [PMID: 12810941 PMCID: PMC164597 DOI: 10.1073/pnas.1533212100] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Jason Raymond
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287-1604, USA
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84
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Christner BC, Kvitko BH, Reeve JN. Molecular identification of bacteria and Eukarya inhabiting an Antarctic cryoconite hole. Extremophiles 2003; 7:177-83. [PMID: 12768448 DOI: 10.1007/s00792-002-0309-0] [Citation(s) in RCA: 203] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2002] [Accepted: 11/21/2002] [Indexed: 10/28/2022]
Abstract
Inhabitants of a cryoconite hole formed in the Canada Glacier in the McMurdo Dry Valley region of Antarctica have been isolated and identified by small subunit (16S/18S) rDNA amplification, cloning, and sequencing. The sequences obtained revealed the presence of members of eight bacterial lineages (Acidobacterium, Actinobacteria, Cyanobacteria, Cytophagales, Gemmimonas, Planctomycetes, Proteobacteria, and Verrucomicrobia) and metazoan (nematode, tardigrade, and rotifer), truffle (Choiromyces), ciliate (Spathidium), and green algal (Pleurastrium) Eukarya. Bacterial recovery was approximately 20-fold higher at 4 degrees C and 15 degrees C than at 22 degrees C, and obligately psychrophilic bacteria were identified and isolated. Several of the rDNA molecules amplified from isolates and directly from cryoconite DNA preparations had sequences similar to rDNA molecules of species present in adjacent lake ice and microbial mat environments. This cryoconite hole community was therefore most likely seeded by particulates from these local environments. Cryoconite holes may serve as biological refuges that, on glacial melting, can repopulate the local environments.
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Affiliation(s)
- Brent C Christner
- Department of Microbiology, Ohio State University, Columbus, OH 43210-1292, USA
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85
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Abstract
Ice that forms the bottom 18 m of a 308 m ice core drilled from the Guliya ice cap on the Qinghan-Tibetan plateau in Western China is over 750000 years old and is the oldest glacial ice known to date. Fourteen bacterial isolates have been recovered from samples of this ice from approximately 296 m below the surface (mbs). Based on 16S rDNA sequences, these are members of the alpha- and beta-proteobacterial, actinobacterial and low-G + C Gram-positive bacterial lineages. 16S rDNA molecules have also been amplified directly, cloned and sequenced from the ice-core melt water. These originated from Pseudomonas and Acinetobacter gamma-proteobacterial species. These results demonstrate that bacteria can be recovered from water ice that has frozen for time periods relevant to biological survival through terrestrial ice ages or during interplanetary transport.
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Affiliation(s)
- Brent C Christner
- Department of Microbiology, Ohio State University, Columbus, OH 43210-1292, USA
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86
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Douglas AE, Raven JA. Genomes at the interface between bacteria and organelles. Philos Trans R Soc Lond B Biol Sci 2003; 358:5-17; discussion 517-8. [PMID: 12594915 PMCID: PMC1693093 DOI: 10.1098/rstb.2002.1188] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The topic of the transition of the genome of a free-living bacterial organism to that of an organelle is addressed by considering three cases. Two of these are relatively clear-cut as involving respectively organisms (cyanobacteria) and organelles (plastids). Cyanobacteria are usually free-living but some are involved in symbioses with a range of eukaryotes in which the cyanobacterial partner contributes photosynthesis, nitrogen fixation, or both of these. In several of these symbioses the cyanobacterium is vertically transmitted, and in a few instances, sufficient unsuccessful attempts have been made to culture the cyanobiont independently for the association to be considered obligate for the cyanobacterium. Plastids clearly had a cyanobacterial ancestor but cannot grow independently of the host eukaryote. Plastid genomes have at most 15% of the number of genes encoded by the cyanobacterium with the smallest number of genes; more genes than are retained in the plastid genome have been transferred to the eukaryote nuclear genome, while the rest of the cyanobacterial genes have been lost. Even the most cyanobacteria-like plastids, for example the "cyanelles" of glaucocystophyte algae, are functionally and genetically very similar to other plastids and give little help in indicating intermediates in the evolution of plastids. The third case considered is the vertically transmitted intracellular bacterial symbionts of insects where the symbiosis is usually obligate for both partners. The number of genes encoded by the genomes of these obligate symbionts is intermediate between that of organelles and that of free-living bacteria, and the genomes of the insect symbionts also show rapid rates of sequence evolution and AT (adenine, thymine) bias. Genetically and functionally, these insect symbionts show considerable similarity to organelles.
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Affiliation(s)
- Angela E Douglas
- Department of Biology, University of York, PO Box 373, York YO10 5YW, UK
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87
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Kring DA. Environmental consequences of impact cratering events as a function of ambient conditions on Earth. ASTROBIOLOGY 2003; 3:133-152. [PMID: 12809133 DOI: 10.1089/153110703321632471] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The end of the Mesozoic Era is defined by a dramatic floral and faunal turnover that has been linked with the Chicxulub impact event, thus leading to the realization that impact cratering can affect both the geologic and biologic evolution of Earth. However, the environmental consequences of an impact event and any subsequent biological effects rely on several factors, including the ambient environmental conditions and the extant ecosystem structures at the time of impact. Some of the severest environmental perturbations of the Chicxulub impact event would not have been significant in some periods of Earth history. Consequently, the environmental and biological effects of an impact event must be evaluated in the context in which it occurs.
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Affiliation(s)
- David A Kring
- Lunar and Planetary Laboratory, Department of Planetary Sciences, The University of Arizona, Tucson 85721, USA.
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88
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Raven JA, Johnston AM, Kübler JE, Korb R, McInroy SG, Handley LL, Scrimgeour CM, Walker DI, Beardall J, Clayton MN, Vanderklift M, Fredriksen S, Dunton KH. Seaweeds in cold seas: evolution and carbon acquisition. ANNALS OF BOTANY 2002; 90:525-36. [PMID: 12324277 PMCID: PMC4240374 DOI: 10.1093/aob/mcf171] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Much evidence suggests that life originated in hydrothermal habitats, and for much of the time since the origin of cyanobacteria (at least 2.5 Ga ago) and of eukaryotic algae (at least 2.1 Ga ago) the average sea surface and land surface temperatures were higher than they are today. However, there have been at least four significant glacial episodes prior to the Pleistocene glaciations. Two of these (approx. 2.1 and 0.7 Ga ago) may have involved a 'Snowball Earth' with a very great impact on the algae (sensu lato) of the time (cyanobacteria, Chlorophyta and Rhodophyta) and especially those that were adapted to warm habitats. By contrast, it is possible that heterokont, dinophyte and haptophyte phototrophs only evolved after the Carboniferous-Permian ice age (approx. 250 Ma ago) and so did not encounter low (=5 degrees C) sea surface temperatures until the Antarctic cooled some 15 Ma ago. Despite this, many of the dominant macroalgae in cooler seas today are (heterokont) brown algae, and many laminarians cannot reproduce at temperatures above 18-25 degrees C. By contrast to plants in the aerial environment, photosynthetic structures in water are at essentially the same temperature as the fluid medium. The impact of low temperatures on photosynthesis by marine macrophytes is predicted to favour diffusive CO(2) entry rather than a CO(2)-concentrating mechanism. Some evidence favours this suggestion, but more data are needed.
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Affiliation(s)
- John A Raven
- Division of Environmental and Applied Biology, School of Life Sciences, University of Dundee, Biological Sciences Institute, Dundee DD1 4HN, UK.
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89
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Abstract
Recent data imply that for much of the Proterozoic Eon (2500 to 543 million years ago), Earth's oceans were moderately oxic at the surface and sulfidic at depth. Under these conditions, biologically important trace metals would have been scarce in most marine environments, potentially restricting the nitrogen cycle, affecting primary productivity, and limiting the ecological distribution of eukaryotic algae. Oceanic redox conditions and their bioinorganic consequences may thus help to explain observed patterns of Proterozoic evolution.
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Affiliation(s)
- A D Anbar
- Department of Earth and Environmental Sciences, University of Rochester, Rochester, NY 14627, USA.
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90
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Newman DK, Banfield JF. Geomicrobiology: how molecular-scale interactions underpin biogeochemical systems. Science 2002; 296:1071-7. [PMID: 12004119 DOI: 10.1126/science.1010716] [Citation(s) in RCA: 105] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Microorganisms populate every habitable environment on Earth and, through their metabolic activity, affect the chemistry and physical properties of their surroundings. They have done this for billions of years. Over the past decade, genetic, biochemical, and genomic approaches have allowed us to document the diversity of microbial life in geologic systems without cultivation, as well as to begin to elucidate their function. With expansion of culture-independent analyses of microbial communities, it will be possible to quantify gene activity at the species level. Genome-enabled biogeochemical modeling may provide an opportunity to determine how communities function, and how they shape and are shaped by their environments.
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Affiliation(s)
- Dianne K Newman
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA
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91
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Abstract
Mutation plays the primary role in evolution that Weismann mistakenly attributed to sex. Homologous recombination, as in sex, is important for population genetics--shuffling of minor variants, but relatively insignificant for large-scale evolution. Major evolutionary innovations depend much more on illegitimate recombination, which makes novel genes by gene duplication and by gene chimaerisation--essentially mutational forces. The machinery of recombination and sex evolved in two distinct bouts of quantum evolution separated by nearly 3 Gy of stasis; I discuss their nature and causes. The dominant selective force in the evolution of recombination and sex has been selection for replicational fidelity and viability; without the recombination machinery, accurate reproduction, stasis, resistance to radical deleterious evolutionary change and preservation of evolutionary innovations would be impossible. Recombination proteins betray in their phylogeny and domain structure a key role for gene duplication and chimaerisation in their own origin. They arose about 3.8 Gy ago to enable faithful replication and segregation of the first circular DNA genomes in precellular ancestors of Gram-negative eubacteria. Then they were recruited and modified by selfish genetic parasites (viruses; transposons) to help them spread from host to host. Bacteria differ fundamentally from eukaryotes in that gene transfer between cells, whether incidental to their absorptive feeding on DNA and virus infection or directly by plasmids, involves only genomic fragments. This was radically changed by the neomuran revolution about 850 million years ago when a posibacterium evolved into the thermophilic cenancestor of eukaryotes and archaebacteria (jointly called neomurans), radically modifying or substituting its DNA-handling enzymes (those responsible for transcription as well as for replication, repair and recombination) as a coadaptive consequence of the origin of core histones to stabilise its chromosome. Substitution of glycoprotein for peptidoglycan walls in the neomuran ancestor and the evolution of an endoskeleton and endomembrane system in eukaryotes alone required the origin of nuclei, mitosis and novel cell cycle controls and enabled them to evolve cell fusion and thereby the combination of whole genomes from different cells. Meiosis evolved because of resulting selection for periodic ploidy reduction, with incidental consequences for intrapopulation genetic exchange. Little modification was needed to recombination enzymes or to the ancient bacterial catalysts of homology search by spontaneous base pairing to mediate chromosome pairing. The key innovation was the origin of meiotic cohesins delaying centromere splitting to allow two successive divisions before reversion to vegetative growth and replication, necessarily yielding two-step meiosis. Also significant was the evolution of synaptonemal complexes to stabilise bivalents and of monopolins to orient sister centromeres to one spindle pole. The primary significance of sex was not to promote evolutionary change but to limit it by facilitating ploidy cycles to balance the conflicting selective forces acting on rapidly growing phagotrophic protozoa and starved dormant cysts subject to radiation and other damage.
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Affiliation(s)
- T Cavalier-Smith
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK.
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92
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Hedges SB, Chen H, Kumar S, Wang DYC, Thompson AS, Watanabe H. A genomic timescale for the origin of eukaryotes. BMC Evol Biol 2001; 1:4. [PMID: 11580860 PMCID: PMC56995 DOI: 10.1186/1471-2148-1-4] [Citation(s) in RCA: 145] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2001] [Accepted: 09/12/2001] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Genomic sequence analyses have shown that horizontal gene transfer occurred during the origin of eukaryotes as a consequence of symbiosis. However, details of the timing and number of symbiotic events are unclear. A timescale for the early evolution of eukaryotes would help to better understand the relationship between these biological events and changes in Earth's environment, such as the rise in oxygen. We used refined methods of sequence alignment, site selection, and time estimation to address these questions with protein sequences from complete genomes of prokaryotes and eukaryotes. RESULTS Eukaryotes were found to evolve faster than prokaryotes, with those eukaryotes derived from eubacteria evolving faster than those derived from archaebacteria. We found an early time of divergence (approximately 4 billion years ago, Ga) for archaebacteria and the archaebacterial genes in eukaryotes. Our analyses support at least two horizontal gene transfer events in the origin of eukaryotes, at 2.7 Ga and 1.8 Ga. Time estimates for the origin of cyanobacteria (2.6 Ga) and the divergence of an early-branching eukaryote that lacks mitochondria (Giardia) (2.2 Ga) fall between those two events. CONCLUSIONS We find support for two symbiotic events in the origin of eukaryotes: one premitochondrial and a later mitochondrial event. The appearance of cyanobacteria immediately prior to the earliest undisputed evidence for the presence of oxygen (2.4-2.2 Ga) suggests that the innovation of oxygenic photosynthesis had a relatively rapid impact on the environment as it set the stage for further evolution of the eukaryotic cell.
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Affiliation(s)
- S Blair Hedges
- Astrobiology Research Center and Department of Biology, 208 Mueller Laboratory, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Hsiong Chen
- Astrobiology Research Center and Department of Biology, 208 Mueller Laboratory, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Sudhir Kumar
- Department of Biology, Arizona State University, Tempe, Arizona 85287, USA
| | - Daniel YC Wang
- Astrobiology Research Center and Department of Biology, 208 Mueller Laboratory, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Amanda S Thompson
- Astrobiology Research Center and Department of Biology, 208 Mueller Laboratory, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Hidemi Watanabe
- RIKEN Genomic Sciences Center, Yokohama, Kanagawa-ken 230-0045, Japan
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93
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Khuri S, Bakker FT, Dunwell JM. Phylogeny, function, and evolution of the cupins, a structurally conserved, functionally diverse superfamily of proteins. Mol Biol Evol 2001; 18:593-605. [PMID: 11264412 DOI: 10.1093/oxfordjournals.molbev.a003840] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The cupin superfamily is a group of functionally diverse proteins that are found in all three kingdoms of life, Archaea, Eubacteria, and Eukaryota. These proteins have a characteristic signature domain comprising two histidine- containing motifs separated by an intermotif region of variable length. This domain consists of six beta strands within a conserved beta barrel structure. Most cupins, such as microbial phosphomannose isomerases (PMIs), AraC- type transcriptional regulators, and cereal oxalate oxidases (OXOs), contain only a single domain, whereas others, such as seed storage proteins and oxalate decarboxylases (OXDCs), are bi-cupins with two pairs of motifs. Although some cupins have known functions and have been characterized at the biochemical level, the majority are known only from gene cloning or sequencing projects. In this study, phylogenetic analyses were conducted on the conserved domain to investigate the evolution and structure/function relationships of cupins, with an emphasis on single- domain plant germin-like proteins (GLPs). An unrooted phylogeny of cupins from a wide spectrum of evolutionary lineages identified three main clusters, microbial PMIs, OXDCs, and plant GLPs. The sister group to the plant GLPs in the global analysis was then used to root a phylogeny of all available plant GLPs. The resulting phylogeny contained three main clades, classifying the GLPs into distinct subfamilies. It is suggested that these subfamilies correlate with functional categories, one of which contains the bifunctional barley germin that has both OXO and superoxide dismutase (SOD) activity. It is proposed that GLPs function primarily as SODs, enzymes that protect plants from the effects of oxidative stress. Closer inspection of the DNA sequence encoding the intermotif region in plant GLPs showed global conservation of thymine in the second codon position, a character associated with hydrophobic residues. Since many of these proteins are multimeric and enzymatically inactive in their monomeric state, this conservation of hydrophobicity is thought to be associated with the need to maintain the various monomer- monomer interactions. The type of structure-based predictive analysis presented in this paper is an important approach for understanding gene function and evolution in an era when genomes from a wide range of organisms are being sequenced at a rapid rate.
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Affiliation(s)
- S Khuri
- School of Plant Sciences, University of Reading, Reading, England
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94
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Lumppio HL, Shenvi NV, Summers AO, Voordouw G, Kurtz DM. Rubrerythrin and rubredoxin oxidoreductase in Desulfovibrio vulgaris: a novel oxidative stress protection system. J Bacteriol 2001; 183:101-8. [PMID: 11114906 PMCID: PMC94855 DOI: 10.1128/jb.183.1.101-108.2001] [Citation(s) in RCA: 159] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2000] [Accepted: 10/11/2000] [Indexed: 11/20/2022] Open
Abstract
Evidence is presented for an alternative to the superoxide dismutase (SOD)-catalase oxidative stress defense system in Desulfovibrio vulgaris (strain Hildenborough). This alternative system consists of the nonheme iron proteins, rubrerythrin (Rbr) and rubredoxin oxidoreductase (Rbo), the product of the rbo gene (also called desulfoferrodoxin). A Deltarbo strain of D. vulgaris was found to be more sensitive to internal superoxide exposure than was the wild type. Unlike Rbo, expression of plasmid-borne Rbr failed to restore the aerobic growth of a SOD-deficient strain of Escherichia coli. Conversely, plasmid-borne expression of two different Rbrs from D. vulgaris increased the viability of a catalase-deficient strain of E. coli that had been exposed to hydrogen peroxide whereas Rbo actually decreased the viability. A previously undescribed D. vulgaris gene was found to encode a protein having 50% sequence identity to that of E. coli Fe-SOD. This gene also encoded an extended N-terminal sequence with high homologies to export signal peptides of periplasmic redox proteins. The SOD activity of D. vulgaris is not affected by the absence of Rbo and is concentrated in the periplasmic fraction of cell extracts. These results are consistent with a superoxide reductase rather than SOD activity of Rbo and with a peroxidase activity of Rbr. A joint role for Rbo and Rbr as a novel cytoplasmic oxidative stress protection system in D. vulgaris and other anaerobic microorganisms is proposed.
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Affiliation(s)
- H L Lumppio
- Department of Microbiology, University of Georgia, Athens, Georgia 30602, USA
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95
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