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Coleman GA, Davín AA, Mahendrarajah TA, Szánthó LL, Spang A, Hugenholtz P, Szöllősi GJ, Williams TA. A rooted phylogeny resolves early bacterial evolution. Science 2021; 372:372/6542/eabe0511. [PMID: 33958449 DOI: 10.1126/science.abe0511] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 11/05/2020] [Accepted: 04/01/2021] [Indexed: 12/17/2022]
Abstract
A rooted bacterial tree is necessary to understand early evolution, but the position of the root is contested. Here, we model the evolution of 11,272 gene families to identify the root, extent of horizontal gene transfer (HGT), and the nature of the last bacterial common ancestor (LBCA). Our analyses root the tree between the major clades Terrabacteria and Gracilicutes and suggest that LBCA was a free-living flagellated, rod-shaped double-membraned organism. Contrary to recent proposals, our analyses reject a basal placement of the Candidate Phyla Radiation, which instead branches sister to Chloroflexota within Terrabacteria. While most gene families (92%) have evidence of HGT, overall, two-thirds of gene transmissions have been vertical, suggesting that a rooted tree provides a meaningful frame of reference for interpreting bacterial evolution.
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Affiliation(s)
- Gareth A Coleman
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
| | - Adrián A Davín
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Tara A Mahendrarajah
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, 1790 AB Den Burg, Netherlands
| | - Lénárd L Szánthó
- Department of Biological Physics, Eötvös Loránd University, 1117 Budapest, Hungary.,MTA-ELTE "Lendület" Evolutionary Genomics Research Group, 1117 Budapest, Hungary
| | - Anja Spang
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, 1790 AB Den Burg, Netherlands.,Department of Cell- and Molecular Biology, Uppsala University, SE-75123 Uppsala, Sweden
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia.
| | - Gergely J Szöllősi
- Department of Biological Physics, Eötvös Loránd University, 1117 Budapest, Hungary. .,MTA-ELTE "Lendület" Evolutionary Genomics Research Group, 1117 Budapest, Hungary.,Institute of Evolution, Centre for Ecological Research, 1121 Budapest, Hungary
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK.
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Cherlin S, Heaps SE, Nye TMW, Boys RJ, Williams TA, Embley TM. The Effect of Nonreversibility on Inferring Rooted Phylogenies. Mol Biol Evol 2018; 35:984-1002. [PMID: 29149300 PMCID: PMC5889004 DOI: 10.1093/molbev/msx294] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Most phylogenetic models assume that the evolutionary process is stationary and reversible. In addition to being biologically improbable, these assumptions also impair inference by generating models under which the likelihood does not depend on the position of the root. Consequently, the root of the tree cannot be inferred as part of the analysis. Yet identifying the root position is a key component of phylogenetic inference because it provides a point of reference for polarizing ancestor-descendant relationships and therefore interpreting the tree. In this paper, we investigate the effect of relaxing the unrealistic reversibility assumption and allowing the position of the root to be another unknown. We propose two hierarchical models that are centered on a reversible model but perturbed to allow nonreversibility. The models differ in the degree of structure imposed on the perturbations. The analysis is performed in the Bayesian framework using Markov chain Monte Carlo methods for which software is provided. We illustrate the performance of the two nonreversible models in analyses of simulated data using two types of topological priors. We then apply the models to a real biological data set, the radiation of polyploid yeasts, for which there is robust biological opinion about the root position. Finally, we apply the models to a second biological alignment for which the rooted tree is controversial: the ribosomal tree of life. We compare the two nonreversible models and conclude that both are useful in inferring the position of the root from real biological data.
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Affiliation(s)
- Svetlana Cherlin
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Sarah E Heaps
- School of Mathematics, Statistics and Physics, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Tom M W Nye
- School of Mathematics, Statistics and Physics, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Richard J Boys
- School of Mathematics, Statistics and Physics, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - T Martin Embley
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
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3
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van Eijk E, Paschalis V, Green M, Friggen AH, Larson MA, Spriggs K, Briggs GS, Soultanas P, Smits WK. Primase is required for helicase activity and helicase alters the specificity of primase in the enteropathogen Clostridium difficile. Open Biol 2017; 6:rsob.160272. [PMID: 28003473 PMCID: PMC5204125 DOI: 10.1098/rsob.160272] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 11/22/2016] [Indexed: 12/16/2022] Open
Abstract
DNA replication is an essential and conserved process in all domains of life and may serve as a target for the development of new antimicrobials. However, such developments are hindered by subtle mechanistic differences and limited understanding of DNA replication in pathogenic microorganisms. Clostridium difficile is the main cause of healthcare-associated diarrhoea and its DNA replication machinery is virtually uncharacterized. We identify and characterize the mechanistic details of the putative replicative helicase (CD3657), helicase-loader ATPase (CD3654) and primase (CD1454) of C. difficile, and reconstitute helicase and primase activities in vitro. We demonstrate a direct and ATP-dependent interaction between the helicase loader and the helicase. Furthermore, we find that helicase activity is dependent on the presence of primase in vitro. The inherent trinucleotide specificity of primase is determined by a single lysine residue and is similar to the primase of the extreme thermophile Aquifex aeolicus. However, the presence of helicase allows more efficient de novo synthesis of RNA primers from non-preferred trinucleotides. Thus, loader–helicase–primase interactions, which crucially mediate helicase loading and activation during DNA replication in all organisms, differ critically in C. difficile from that of the well-studied Gram-positive Bacillus subtilis model.
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Affiliation(s)
- Erika van Eijk
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Vasileios Paschalis
- School of Chemistry, Center for Biomolecular Sciences, University of Nottingham, UK
| | - Matthew Green
- School of Chemistry, Center for Biomolecular Sciences, University of Nottingham, UK
| | - Annemieke H Friggen
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Marilynn A Larson
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198-5900, USA.,National Strategic Research Institute, Omaha, NE 68105, USA
| | | | - Geoffrey S Briggs
- School of Chemistry, Center for Biomolecular Sciences, University of Nottingham, UK
| | - Panos Soultanas
- School of Chemistry, Center for Biomolecular Sciences, University of Nottingham, UK
| | - Wiep Klaas Smits
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
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4
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Tocheva EI, Ortega DR, Jensen GJ. Sporulation, bacterial cell envelopes and the origin of life. Nat Rev Microbiol 2016; 14:535-542. [PMID: 28232669 DOI: 10.1038/nrmicro.2016.85] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Electron cryotomography (ECT) enables the 3D reconstruction of intact cells in a near-native state. Images produced by ECT have led to the proposal that an ancient sporulation-like event gave rise to the second membrane in diderm bacteria. Tomograms of sporulating monoderm and diderm bacterial cells show how sporulation can lead to the generation of diderm cells. Tomograms of Gram-negative and Gram-positive cell walls and purified sacculi suggest that they are more closely related than previously thought and support the hypothesis that they share a common origin. Mapping the distribution of cell envelope architectures onto a recent phylogenetic tree of life indicates that the diderm cell plan, and therefore the sporulation-like event that gave rise to it, must be very ancient. One explanation for this model is that during the cataclysmic transitions of the early Earth, cellular evolution may have gone through a bottleneck in which only spores survived, which implies that the last bacterial common ancestor was a spore.
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Affiliation(s)
- Elitza I Tocheva
- Department of Stomatology and the Department of Biochemistry and Molecular Medicine, Université de Montréal, P. O. Box 6128 Station Centre-Ville, Montreal, Québec H3C 3J7, Canada
| | - Davi R Ortega
- Department of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, USA
| | - Grant J Jensen
- Howard Hughes Medical Institute, Department of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, USA
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5
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Gouy R, Baurain D, Philippe H. Rooting the tree of life: the phylogenetic jury is still out. Philos Trans R Soc Lond B Biol Sci 2016; 370:20140329. [PMID: 26323760 DOI: 10.1098/rstb.2014.0329] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
This article aims to shed light on difficulties in rooting the tree of life (ToL) and to explore the (sociological) reasons underlying the limited interest in accurately addressing this fundamental issue. First, we briefly review the difficulties plaguing phylogenetic inference and the ways to improve the modelling of the substitution process, which is highly heterogeneous, both across sites and over time. We further observe that enriched taxon samplings, better gene samplings and clever data removal strategies have led to numerous revisions of the ToL, and that these improved shallow phylogenies nearly always relocate simple organisms higher in the ToL provided that long-branch attraction artefacts are kept at bay. Then, we note that, despite the flood of genomic data available since 2000, there has been a surprisingly low interest in inferring the root of the ToL. Furthermore, the rare studies dealing with this question were almost always based on methods dating from the 1990s that have been shown to be inaccurate for much more shallow issues! This leads us to argue that the current consensus about a bacterial root for the ToL can be traced back to the prejudice of Aristotle's Great Chain of Beings, in which simple organisms are ancestors of more complex life forms. Finally, we demonstrate that even the best models cannot yet handle the complexity of the evolutionary process encountered both at shallow depth, when the outgroup is too distant, and at the level of the inter-domain relationships. Altogether, we conclude that the commonly accepted bacterial root is still unproven and that the root of the ToL should be revisited using phylogenomic supermatrices to ensure that new evidence for eukaryogenesis, such as the recently described Lokiarcheota, is interpreted in a sound phylogenetic framework.
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Affiliation(s)
- Richard Gouy
- Eukaryotic Phylogenomics, Department of Life Sciences and PhytoSYSTEMS, University of Liège, Liège 4000, Belgium Centre for Biodiversity Theory and Modelling, USR CNRS 2936, Station d'Ecologie Expérimentale du CNRS, Moulis 09200, France
| | - Denis Baurain
- Eukaryotic Phylogenomics, Department of Life Sciences and PhytoSYSTEMS, University of Liège, Liège 4000, Belgium
| | - Hervé Philippe
- Centre for Biodiversity Theory and Modelling, USR CNRS 2936, Station d'Ecologie Expérimentale du CNRS, Moulis 09200, France Département de Biochimie, Centre Robert-Cedergren, Université de Montréal, Montréal, Quebec, Canada H3C 3J7
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6
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Cavalier-Smith T. The neomuran revolution and phagotrophic origin of eukaryotes and cilia in the light of intracellular coevolution and a revised tree of life. Cold Spring Harb Perspect Biol 2014; 6:a016006. [PMID: 25183828 PMCID: PMC4142966 DOI: 10.1101/cshperspect.a016006] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Three kinds of cells exist with increasingly complex membrane-protein targeting: Unibacteria (Archaebacteria, Posibacteria) with one cytoplasmic membrane (CM); Negibacteria with a two-membrane envelope (inner CM; outer membrane [OM]); eukaryotes with a plasma membrane and topologically distinct endomembranes and peroxisomes. I combine evidence from multigene trees, palaeontology, and cell biology to show that eukaryotes and archaebacteria are sisters, forming the clade neomura that evolved ~1.2 Gy ago from a posibacterium, whose DNA segregation and cell division were destabilized by murein wall loss and rescued by the evolving novel neomuran endoskeleton, histones, cytokinesis, and glycoproteins. Phagotrophy then induced coevolving serial major changes making eukaryote cells, culminating in two dissimilar cilia via a novel gliding-fishing-swimming scenario. I transfer Chloroflexi to Posibacteria, root the universal tree between them and Heliobacteria, and argue that Negibacteria are a clade whose OM, evolving in a green posibacterium, was never lost.
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Abstract
Reconstructing early evolutionary events like the origins of informational and operational genes, membranes, and photophosphorylation is difficult because early evolutionary events can be masked by subsequent gene flows. Furthermore, as evolution progresses through both Darwinian survival of the fittest (tree-like evolution) and symbiotic/endosymbiotic cooperation (ring-like evolution), trees alone are not adequate to represent Earth's evolutionary history. Here, we reconstruct and root the New Rings of Life and use it as a framework for interpreting early events in the evolution of life. Unlike the three-domain hypothesis, the rings do not fit all life into one of three immutable categories, but rather accommodate new gene flows as novel organisms are discovered. A draft of the Rooted Rings of Life is reconstructed by analyzing the phylogenetic distributions of indels (insertions/deletions) and genes coding for fundamental molecular processes. Their phylogenetic distributions are inconsistent with all trees. Hypergeometric distribution analyses of them strongly localize the root of the rings to a segment of the deepest ring (P < 10(-21) and P < 10(-194)), and whole-genome analyses independently confirm the topology of the rooted rings (P < 7.1 × 10(-6)). The rings identify several large gene flows, including a flow of a thousand genes into the Halobacteria and the Eubacteria, the related photocyte flow, the flow of genes into the last common ancestor of the eocytes and the eukaryotes, and the informational and operational gene flows into the eukaryotes. The rooted rings also chronologically order steps in the evolution of extant taxa, that is, phototrophy evolved from Halobacteria (photophosphorylation) → Heliobacteria (photosynthesis) → Cyanobacteria (oxygenic photosynthesis).
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Affiliation(s)
- James A Lake
- Department of MCD Biology, University of California, Los Angeles
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8
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Williams TA, Foster PG, Cox CJ, Embley TM. An archaeal origin of eukaryotes supports only two primary domains of life. Nature 2014; 504:231-6. [PMID: 24336283 DOI: 10.1038/nature12779] [Citation(s) in RCA: 316] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 10/14/2013] [Indexed: 02/07/2023]
Abstract
The discovery of the Archaea and the proposal of the three-domains 'universal' tree, based on ribosomal RNA and core genes mainly involved in protein translation, catalysed new ideas for cellular evolution and eukaryotic origins. However, accumulating evidence suggests that the three-domains tree may be incorrect: evolutionary trees made using newer methods place eukaryotic core genes within the Archaea, supporting hypotheses in which an archaeon participated in eukaryotic origins by founding the host lineage for the mitochondrial endosymbiont. These results provide support for only two primary domains of life--Archaea and Bacteria--because eukaryotes arose through partnership between them.
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Affiliation(s)
- Tom A Williams
- Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne NE2 4HH, UK
| | - Peter G Foster
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
| | - Cymon J Cox
- Centro de Ciências do Mar, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - T Martin Embley
- Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne NE2 4HH, UK
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10
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Molecular Evolution of Translin Superfamily Proteins Within the Genomes of Eubacteria, Archaea and Eukaryotes. J Mol Evol 2012. [DOI: 10.1007/s00239-012-9534-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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11
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Williams TA, Foster PG, Nye TMW, Cox CJ, Embley TM. A congruent phylogenomic signal places eukaryotes within the Archaea. Proc Biol Sci 2012; 279:4870-9. [PMID: 23097517 PMCID: PMC3497233 DOI: 10.1098/rspb.2012.1795] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Determining the relationships among the major groups of cellular life is important for understanding the evolution of biological diversity, but is difficult given the enormous time spans involved. In the textbook ‘three domains’ tree based on informational genes, eukaryotes and Archaea share a common ancestor to the exclusion of Bacteria. However, some phylogenetic analyses of the same data have placed eukaryotes within the Archaea, as the nearest relatives of different archaeal lineages. We compared the support for these competing hypotheses using sophisticated phylogenetic methods and an improved sampling of archaeal biodiversity. We also employed both new and existing tests of phylogenetic congruence to explore the level of uncertainty and conflict in the data. Our analyses suggested that much of the observed incongruence is weakly supported or associated with poorly fitting evolutionary models. All of our phylogenetic analyses, whether on small subunit and large subunit ribosomal RNA or concatenated protein-coding genes, recovered a monophyletic group containing eukaryotes and the TACK archaeal superphylum comprising the Thaumarchaeota, Aigarchaeota, Crenarchaeota and Korarchaeota. Hence, while our results provide no support for the iconic three-domain tree of life, they are consistent with an extended eocyte hypothesis whereby vital components of the eukaryotic nuclear lineage originated from within the archaeal radiation.
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Affiliation(s)
- Tom A Williams
- Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne NE2 4HH, UK
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12
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Berendzen J, Bruno WJ, Cohn JD, Hengartner NW, Kuske CR, McMahon BH, Wolinsky MA, Xie G. Rapid phylogenetic and functional classification of short genomic fragments with signature peptides. BMC Res Notes 2012; 5:460. [PMID: 22925230 PMCID: PMC3772700 DOI: 10.1186/1756-0500-5-460] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 08/08/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Classification is difficult for shotgun metagenomics data from environments such as soils, where the diversity of sequences is high and where reference sequences from close relatives may not exist. Approaches based on sequence-similarity scores must deal with the confounding effects that inheritance and functional pressures exert on the relation between scores and phylogenetic distance, while approaches based on sequence alignment and tree-building are typically limited to a small fraction of gene families. We describe an approach based on finding one or more exact matches between a read and a precomputed set of peptide 10-mers. RESULTS At even the largest phylogenetic distances, thousands of 10-mer peptide exact matches can be found between pairs of bacterial genomes. Genes that share one or more peptide 10-mers typically have high reciprocal BLAST scores. Among a set of 403 representative bacterial genomes, some 20 million 10-mer peptides were found to be shared. We assign each of these peptides as a signature of a particular node in a phylogenetic reference tree based on the RNA polymerase genes. We classify the phylogeny of a genomic fragment (e.g., read) at the most specific node on the reference tree that is consistent with the phylogeny of observed signature peptides it contains. Using both synthetic data from four newly-sequenced soil-bacterium genomes and ten real soil metagenomics data sets, we demonstrate a sensitivity and specificity comparable to that of the MEGAN metagenomics analysis package using BLASTX against the NR database. Phylogenetic and functional similarity metrics applied to real metagenomics data indicates a signal-to-noise ratio of approximately 400 for distinguishing among environments. Our method assigns ~6.6 Gbp/hr on a single CPU, compared with 25 kbp/hr for methods based on BLASTX against the NR database. CONCLUSIONS Classification by exact matching against a precomputed list of signature peptides provides comparable results to existing techniques for reads longer than about 300 bp and does not degrade severely with shorter reads. Orders of magnitude faster than existing methods, the approach is suitable now for inclusion in analysis pipelines and appears to be extensible in several different directions.
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Affiliation(s)
- Joel Berendzen
- Physics Division, MS D454, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - William J Bruno
- Theoretical Division, MS K710, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Judith D Cohn
- Computer, Computational, and Statistical Sciences Division, MS B256, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Nicolas W Hengartner
- Computer, Computational, and Statistical Sciences Division, MS B256, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Cheryl R Kuske
- Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Benjamin H McMahon
- Theoretical Division, MS K710, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Murray A Wolinsky
- Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Gary Xie
- Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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13
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Braakman R, Smith E. The emergence and early evolution of biological carbon-fixation. PLoS Comput Biol 2012; 8:e1002455. [PMID: 22536150 PMCID: PMC3334880 DOI: 10.1371/journal.pcbi.1002455] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2011] [Accepted: 02/13/2012] [Indexed: 11/18/2022] Open
Abstract
The fixation of CO₂ into living matter sustains all life on Earth, and embeds the biosphere within geochemistry. The six known chemical pathways used by extant organisms for this function are recognized to have overlaps, but their evolution is incompletely understood. Here we reconstruct the complete early evolutionary history of biological carbon-fixation, relating all modern pathways to a single ancestral form. We find that innovations in carbon-fixation were the foundation for most major early divergences in the tree of life. These findings are based on a novel method that fully integrates metabolic and phylogenetic constraints. Comparing gene-profiles across the metabolic cores of deep-branching organisms and requiring that they are capable of synthesizing all their biomass components leads to the surprising conclusion that the most common form for deep-branching autotrophic carbon-fixation combines two disconnected sub-networks, each supplying carbon to distinct biomass components. One of these is a linear folate-based pathway of CO₂ reduction previously only recognized as a fixation route in the complete Wood-Ljungdahl pathway, but which more generally may exclude the final step of synthesizing acetyl-CoA. Using metabolic constraints we then reconstruct a "phylometabolic" tree with a high degree of parsimony that traces the evolution of complete carbon-fixation pathways, and has a clear structure down to the root. This tree requires few instances of lateral gene transfer or convergence, and instead suggests a simple evolutionary dynamic in which all divergences have primary environmental causes. Energy optimization and oxygen toxicity are the two strongest forces of selection. The root of this tree combines the reductive citric acid cycle and the Wood-Ljungdahl pathway into a single connected network. This linked network lacks the selective optimization of modern fixation pathways but its redundancy leads to a more robust topology, making it more plausible than any modern pathway as a primitive universal ancestral form.
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Affiliation(s)
- Rogier Braakman
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
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14
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Wall ME, Raghavan S, Cohn JD, Dunbar J. Genome majority vote improves gene predictions. PLoS Comput Biol 2011; 7:e1002284. [PMID: 22131910 PMCID: PMC3219611 DOI: 10.1371/journal.pcbi.1002284] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Accepted: 10/06/2011] [Indexed: 11/18/2022] Open
Abstract
Recent studies have noted extensive inconsistencies in gene start sites among orthologous genes in related microbial genomes. Here we provide the first documented evidence that imposing gene start consistency improves the accuracy of gene start-site prediction. We applied an algorithm using a genome majority vote (GMV) scheme to increase the consistency of gene starts among orthologs. We used a set of validated Escherichia coli genes as a standard to quantify accuracy. Results showed that the GMV algorithm can correct hundreds of gene prediction errors in sets of five or ten genomes while introducing few errors. Using a conservative calculation, we project that GMV would resolve many inconsistencies and errors in publicly available microbial gene maps. Our simple and logical solution provides a notable advance toward accurate gene maps.
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Affiliation(s)
- Michael E Wall
- Computer, Computational, and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA.
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15
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The falsifiability of the models for the origin of eukaryotes. Curr Genet 2011; 57:367-90. [DOI: 10.1007/s00294-011-0357-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Revised: 09/29/2011] [Accepted: 09/30/2011] [Indexed: 01/13/2023]
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16
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Rooting phylogenies using gene duplications: An empirical example from the bees (Apoidea). Mol Phylogenet Evol 2011; 60:295-304. [DOI: 10.1016/j.ympev.2011.05.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2010] [Revised: 04/26/2011] [Accepted: 05/03/2011] [Indexed: 12/23/2022]
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17
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The origin of a derived superkingdom: how a gram-positive bacterium crossed the desert to become an archaeon. Biol Direct 2011; 6:16. [PMID: 21356104 PMCID: PMC3056875 DOI: 10.1186/1745-6150-6-16] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Accepted: 02/28/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The tree of life is usually rooted between archaea and bacteria. We have previously presented three arguments that support placing the root of the tree of life in bacteria. The data have been dismissed because those who support the canonical rooting between the prokaryotic superkingdoms cannot imagine how the vast divide between the prokaryotic superkingdoms could be crossed. RESULTS We review the evidence that archaea are derived, as well as their biggest differences with bacteria. We argue that using novel data the gap between the superkingdoms is not insurmountable. We consider whether archaea are holophyletic or paraphyletic; essential to understanding their origin. Finally, we review several hypotheses on the origins of archaea and, where possible, evaluate each hypothesis using bioinformatics tools. As a result we argue for a firmicute ancestry for archaea over proposals for an actinobacterial ancestry. CONCLUSION We believe a synthesis of the hypotheses of Lake, Gupta, and Cavalier-Smith is possible where a combination of antibiotic warfare and viral endosymbiosis in the bacilli led to dramatic changes in a bacterium that resulted in the birth of archaea and eukaryotes. REVIEWERS This article was reviewed by Patrick Forterre, Eugene Koonin, and Gáspár Jékely.
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18
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McDonald GD, Storrie-Lombardi MC. Biochemical constraints in a protobiotic earth devoid of basic amino acids: the "BAA(-) world". ASTROBIOLOGY 2010; 10:989-1000. [PMID: 21162678 DOI: 10.1089/ast.2010.0484] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
It has been hypothesized in this journal and elsewhere, based on surveys of published data from prebiotic synthesis experiments and carbonaceous meteorite analyses, that basic amino acids such as lysine and arginine were not abundant on prebiotic Earth. If the basic amino acids were incorporated only rarely into the first peptides formed in that environment, it is important to understand what protobiotic chemistry is possible in their absence. As an initial test of the hypothesis that basic amino acid negative [BAA(-)] proteins could have performed at least a subset of protobiotic chemistry, the current work reports on a survey of 13 archaeal and 13 bacterial genomes that has identified 61 modern gene sequences coding for known or putative proteins not containing arginine or lysine. Eleven of the sequences found code for proteins whose functions are well known and important in the biochemistry of modern microbial life: lysine biosynthesis protein LysW, arginine cluster proteins, copper ion binding proteins, bacterial flagellar proteins, and PE or PPE family proteins. These data indicate that the lack of basic amino acids does not prevent peptides or proteins from serving useful structural and biochemical functions. However, as would be predicted from fundamental physicochemical principles, we see no fossil evidence of prebiotic BAA(-) peptide sequences capable of interacting directly with nucleic acids.
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Affiliation(s)
- Gene D McDonald
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, USA.
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Fournier GP, Dick AA, Williams D, Gogarten JP. Evolution of the Archaea: emerging views on origins and phylogeny. Res Microbiol 2010; 162:92-8. [PMID: 21034818 DOI: 10.1016/j.resmic.2010.09.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2010] [Accepted: 09/10/2010] [Indexed: 01/04/2023]
Abstract
Of the three domains of life, the Archaea are the most recently discovered and, from the perspective of systematics, perhaps the least understood. More than three decades after their discovery, there is still no overwhelming consensus as to their phylogenetic status, with diverse evidence supporting in varying degrees their monophyly, paraphyly, or even polyphyly. As a further complication, their evolutionary history is inextricably linked to the origin of Eukarya, one of the most challenging problems in evolutionary biology. This exclusive relationship between the eukaryal nucleocytoplasm and the Archaea is further supported by a new methodology for rooting the ribosomal Tree of Life based on amino acid composition. Novel approaches such as utilizing horizontal gene transfers as synchronizing events and branch length analysis of deep paralogs will help to clarify temporal relationships between these lineages, and may prove useful in evaluating the numerous conflicting hypotheses related to the evolution of the Archaea and Eukarya.
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Affiliation(s)
- Gregory P Fournier
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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20
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Gribaldo S, Poole AM, Daubin V, Forterre P, Brochier-Armanet C. The origin of eukaryotes and their relationship with the Archaea: are we at a phylogenomic impasse? Nat Rev Microbiol 2010; 8:743-52. [PMID: 20844558 DOI: 10.1038/nrmicro2426] [Citation(s) in RCA: 131] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The origin of eukaryotes and their evolutionary relationship with the Archaea is a major biological question and the subject of intense debate. In the context of the classical view of the universal tree of life, the Archaea and the Eukarya have a common ancestor, the nature of which remains undetermined. Alternative views propose instead that the Eukarya evolved directly from a bona fide archaeal lineage. Several recent large-scale phylogenomic studies using an array of approaches are divided in supporting either one or the other scenario, despite analysing largely overlapping data sets of universal genes. We examine the reasons for such a lack of consensus and consider how alternative approaches may enable progress in answering this fascinating and as-yet-unresolved question.
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Booker ML, Bastos CM, Kramer ML, Barker RH, Skerlj R, Sidhu AB, Deng X, Celatka C, Cortese JF, Guerrero Bravo JE, Crespo Llado KN, Serrano AE, Angulo-Barturen I, Jiménez-Díaz MB, Viera S, Garuti H, Wittlin S, Papastogiannidis P, Lin JW, Janse CJ, Khan SM, Duraisingh M, Coleman B, Goldsmith EJ, Phillips MA, Munoz B, Wirth DF, Klinger JD, Wiegand R, Sybertz E. Novel inhibitors of Plasmodium falciparum dihydroorotate dehydrogenase with anti-malarial activity in the mouse model. J Biol Chem 2010; 285:33054-33064. [PMID: 20702404 DOI: 10.1074/jbc.m110.162081] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Plasmodium falciparum, the causative agent of the most deadly form of human malaria, is unable to salvage pyrimidines and must rely on de novo biosynthesis for survival. Dihydroorotate dehydrogenase (DHODH) catalyzes the rate-limiting step in the pyrimidine biosynthetic pathway and represents a potential target for anti-malarial therapy. A high throughput screen and subsequent medicinal chemistry program identified a series of N-alkyl-5-(1H-benzimidazol-1-yl)thiophene-2-carboxamides with low nanomolar in vitro potency against DHODH from P. falciparum, P. vivax, and P. berghei. The compounds were selective for the parasite enzymes over human DHODH, and x-ray structural data on the analog Genz-667348, demonstrated that species selectivity could be attributed to amino acid differences in the inhibitor-binding site. Compounds from this series demonstrated in vitro potency against the 3D7 and Dd2 strains of P. falciparum, good tolerability and oral exposure in the mouse, and ED(50) values in the 4-day murine P. berghei efficacy model of 13-21 mg/kg/day with oral twice-daily dosing. In particular, treatment with Genz-667348 at 100 mg/kg/day resulted in sterile cure. Two recent analogs of Genz-667348 are currently undergoing pilot toxicity testing to determine suitability as clinical development candidates.
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Affiliation(s)
| | | | | | | | - Renato Skerlj
- From Genzyme Corporation, Waltham, Massachusetts 02451
| | - Amar Bir Sidhu
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02141
| | - Xiaoyi Deng
- Departments of Pharmacology, Dallas, Texas 75390-9041
| | | | - Joseph F Cortese
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02141
| | - Jose E Guerrero Bravo
- Department of Microbiology and Medical Zoology, University of Puerto Rico School of Medicine, P. O. Box 365067, San Juan, Puerto Rico 00936-5067
| | - Keila N Crespo Llado
- Department of Microbiology and Medical Zoology, University of Puerto Rico School of Medicine, P. O. Box 365067, San Juan, Puerto Rico 00936-5067
| | - Adelfa E Serrano
- Department of Microbiology and Medical Zoology, University of Puerto Rico School of Medicine, P. O. Box 365067, San Juan, Puerto Rico 00936-5067
| | - Iñigo Angulo-Barturen
- Medicines Development Campus, Diseases of the Developing World, GlaxoSmithKline, c/Severo Ochoa 2, 28760 Tres Cantos, Spain
| | - María Belén Jiménez-Díaz
- Medicines Development Campus, Diseases of the Developing World, GlaxoSmithKline, c/Severo Ochoa 2, 28760 Tres Cantos, Spain
| | - Sara Viera
- Medicines Development Campus, Diseases of the Developing World, GlaxoSmithKline, c/Severo Ochoa 2, 28760 Tres Cantos, Spain
| | - Helen Garuti
- Medicines Development Campus, Diseases of the Developing World, GlaxoSmithKline, c/Severo Ochoa 2, 28760 Tres Cantos, Spain
| | - Sergio Wittlin
- Swiss Tropical and Public Health Institute, Socinstrasse 57, CH-4002, Basel, Switzerland; University of Basel, Petersplatz 1, CH-4003, Basel, Switzerland
| | - Petros Papastogiannidis
- Swiss Tropical and Public Health Institute, Socinstrasse 57, CH-4002, Basel, Switzerland; University of Basel, Petersplatz 1, CH-4003, Basel, Switzerland
| | - Jing-Wen Lin
- Leiden Malaria Research Group, Department of Parasitology, Centre for Infectious Diseases, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Chris J Janse
- Leiden Malaria Research Group, Department of Parasitology, Centre for Infectious Diseases, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Shahid M Khan
- Leiden Malaria Research Group, Department of Parasitology, Centre for Infectious Diseases, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Manoj Duraisingh
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts 02115
| | - Bradley Coleman
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts 02115
| | - Elizabeth J Goldsmith
- Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9041
| | | | - Benito Munoz
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02141
| | - Dyann F Wirth
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts 02115
| | | | - Roger Wiegand
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02141
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23
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Cavalier-Smith T. Origin of the cell nucleus, mitosis and sex: roles of intracellular coevolution. Biol Direct 2010; 5:7. [PMID: 20132544 PMCID: PMC2837639 DOI: 10.1186/1745-6150-5-7] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2009] [Accepted: 02/04/2010] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The transition from prokaryotes to eukaryotes was the most radical change in cell organisation since life began, with the largest ever burst of gene duplication and novelty. According to the coevolutionary theory of eukaryote origins, the fundamental innovations were the concerted origins of the endomembrane system and cytoskeleton, subsequently recruited to form the cell nucleus and coevolving mitotic apparatus, with numerous genetic eukaryotic novelties inevitable consequences of this compartmentation and novel DNA segregation mechanism. Physical and mutational mechanisms of origin of the nucleus are seldom considered beyond the long-standing assumption that it involved wrapping pre-existing endomembranes around chromatin. Discussions on the origin of sex typically overlook its association with protozoan entry into dormant walled cysts and the likely simultaneous coevolutionary, not sequential, origin of mitosis and meiosis. RESULTS I elucidate nuclear and mitotic coevolution, explaining the origins of dicer and small centromeric RNAs for positionally controlling centromeric heterochromatin, and how 27 major features of the cell nucleus evolved in four logical stages, making both mechanisms and selective advantages explicit: two initial stages (origin of 30 nm chromatin fibres, enabling DNA compaction; and firmer attachment of endomembranes to heterochromatin) protected DNA and nascent RNA from shearing by novel molecular motors mediating vesicle transport, division, and cytoplasmic motility. Then octagonal nuclear pore complexes (NPCs) arguably evolved from COPII coated vesicle proteins trapped in clumps by Ran GTPase-mediated cisternal fusion that generated the fenestrated nuclear envelope, preventing lethal complete cisternal fusion, and allowing passive protein and RNA exchange. Finally, plugging NPC lumens by an FG-nucleoporin meshwork and adopting karyopherins for nucleocytoplasmic exchange conferred compartmentation advantages. These successive changes took place in naked growing cells, probably as indirect consequences of the origin of phagotrophy. The first eukaryote had 1-2 cilia and also walled resting cysts; I outline how encystation may have promoted the origin of meiotic sex. I also explain why many alternative ideas are inadequate. CONCLUSION Nuclear pore complexes are evolutionary chimaeras of endomembrane- and mitosis-related chromatin-associated proteins. The keys to understanding eukaryogenesis are a proper phylogenetic context and understanding organelle coevolution: how innovations in one cell component caused repercussions on others.
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Foster PG, Cox CJ, Embley TM. The primary divisions of life: a phylogenomic approach employing composition-heterogeneous methods. Philos Trans R Soc Lond B Biol Sci 2009; 364:2197-207. [PMID: 19571240 DOI: 10.1098/rstb.2009.0034] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The three-domains tree, which depicts eukaryotes and archaebacteria as monophyletic sister groups, is the dominant model for early eukaryotic evolution. By contrast, the 'eocyte hypothesis', where eukaryotes are proposed to have originated from within the archaebacteria as sister to the Crenarchaeota (also called the eocytes), has been largely neglected in the literature. We have investigated support for these two competing hypotheses from molecular sequence data using methods that attempt to accommodate the across-site compositional heterogeneity and across-tree compositional and rate matrix heterogeneity that are manifest features of these data. When ribosomal RNA genes were analysed using standard methods that do not adequately model these kinds of heterogeneity, the three-domains tree was supported. However, this support was eroded or lost when composition-heterogeneous models were used, with concomitant increase in support for the eocyte tree for eukaryotic origins. Analysis of combined amino acid sequences from 41 protein-coding genes supported the eocyte tree, whether or not composition-heterogeneous models were used. The possible effects of substitutional saturation of our data were examined using simulation; these results suggested that saturation is delayed by among-site rate variation in the sequences, and that phylogenetic signal for ancient relationships is plausibly present in these data.
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Affiliation(s)
- Peter G Foster
- Department of Zoology, Natural History Museum, London, UK
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25
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Lake JA, Skophammer RG, Herbold CW, Servin JA. Genome beginnings: rooting the tree of life. Philos Trans R Soc Lond B Biol Sci 2009; 364:2177-85. [PMID: 19571238 DOI: 10.1098/rstb.2009.0035] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
A rooted tree of life provides a framework to answer central questions about the evolution of life. Here we review progress on rooting the tree of life and introduce a new root of life obtained through the analysis of indels, insertions and deletions, found within paralogous gene sets. Through the analysis of indels in eight paralogous gene sets, the root is localized to the branch between the clade consisting of the Actinobacteria and the double-membrane (Gram-negative) prokaryotes and one consisting of the archaebacteria and the firmicutes. This root provides a new perspective on the habitats of early life, including the evolution of methanogenesis, membranes and hyperthermophily, and the speciation of major prokaryotic taxa. Our analyses exclude methanogenesis as a primitive metabolism, in contrast to previous findings. They parsimoniously imply that the ether archaebacterial lipids are not primitive and that the cenancestral prokaryotic population consisted of organisms enclosed by a single, ester-linked lipid membrane, covered by a peptidoglycan layer. These results explain the similarities previously noted by others between the lipid synthesis pathways in eubacteria and archaebacteria. The new root also implies that the last common ancestor was not hyperthermophilic, although moderate thermophily cannot be excluded.
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Affiliation(s)
- James A Lake
- Department of Molecular, Cellular and Developmental Biology, University of California, Los Angeles, CA 90095, USA.
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Abstract
Endosymbioses have dramatically altered eukaryotic life, but are thought to have negligibly affected prokaryotic evolution. Here, by analysing the flows of protein families, I present evidence that the double-membrane, gram-negative prokaryotes were formed as the result of a symbiosis between an ancient actinobacterium and an ancient clostridium. The resulting taxon has been extraordinarily successful, and has profoundly altered the evolution of life by providing endosymbionts necessary for the emergence of eukaryotes and by generating Earth's oxygen atmosphere. Their double-membrane architecture and the observed genome flows into them suggest a common evolutionary mechanism for their origin: an endosymbiosis between a clostridium and actinobacterium.
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Affiliation(s)
- James A Lake
- Department of Molecular, Cellular and Developmental Biology, University of California, Los Angeles, California 90095, USA.
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27
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Valas RE, Bourne PE. Structural analysis of polarizing indels: an emerging consensus on the root of the tree of life. Biol Direct 2009; 4:30. [PMID: 19706177 PMCID: PMC3224940 DOI: 10.1186/1745-6150-4-30] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Accepted: 08/25/2009] [Indexed: 11/18/2022] Open
Abstract
Background The root of the tree of life has been a holy grail ever since Darwin first used the tree as a metaphor for evolution. New methods seek to narrow down the location of the root by excluding it from branches of the tree of life. This is done by finding traits that must be derived, and excluding the root from the taxa those traits cover. However the two most comprehensive attempts at this strategy, performed by Cavalier-Smith and Lake et al., have excluded each other's rootings. Results The indel polarizations of Lake et al. rely on high quality alignments between paralogs that diverged before the last universal common ancestor (LUCA). Therefore, sequence alignment artifacts may skew their conclusions. We have reviewed their data using protein structure information where available. Several of the conclusions are quite different when viewed in the light of structure which is conserved over longer evolutionary time scales than sequence. We argue there is no polarization that excludes the root from all Gram-negatives, and that polarizations robustly exclude the root from the Archaea. Conclusion We conclude that there is no contradiction between the polarization datasets. The combination of these datasets excludes the root from every possible position except near the Chloroflexi. Reviewers This article was reviewed by Greg Fournier (nominated by J. Peter Gogarten), Purificación López-García, and Eugene Koonin.
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Affiliation(s)
- Ruben E Valas
- Bioinformatics Program, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
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28
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Gupta RS. Protein signatures (molecular synapomorphies) that are distinctive characteristics of the major cyanobacterial clades. Int J Syst Evol Microbiol 2009; 59:2510-26. [DOI: 10.1099/ijs.0.005678-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Dong CK, Patel V, Yang JC, Dvorin JD, Duraisingh MT, Clardy J, Wirth DF. Type II NADH dehydrogenase of the respiratory chain of Plasmodium falciparum and its inhibitors. Bioorg Med Chem Lett 2009; 19:972-5. [PMID: 19097788 PMCID: PMC4422330 DOI: 10.1016/j.bmcl.2008.11.071] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2008] [Revised: 11/17/2008] [Accepted: 11/19/2008] [Indexed: 10/21/2022]
Abstract
Plasmodium falciparum NDH2 (pfNDH2) is a non-proton pumping, rotenone-insensitive alternative enzyme to the multi-subunit NADH:ubiquinone oxidoreductases (Complex I) of many other eukaryotes. Recombinantly expressed pfNDH2 prefers coenzyme CoQ(0) as an acceptor substrate, and can also use the artificial electron acceptors, menadione and dichlorophenol-indophenol (DCIP). Previously characterized NDH2 inhibitors, dibenziodolium chloride (DPI), diphenyliodonium chloride (IDP), and 1-hydroxy-2-dodecyl-4(1H)quinolone (HDQ) do not inhibit pfNDH2 activity. Here, we provide evidence that HDQ likely targets another P. falciparum mitochondrial enzyme, dihydroorotate dehydrogenase (pfDHOD), which is essential for de novo pyrimidine biosynthesis.
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Affiliation(s)
- Carolyn K. Dong
- Department of Immunology and Infectious Disease, Harvard School of Public Health, Building 1, Boston, MA 02115, USA
| | - Vishal Patel
- Department of Immunology and Infectious Disease, Harvard School of Public Health, Building 1, Boston, MA 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Jimmy C. Yang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- The Broad Institute of Harvard and MIT, Infectious Disease Initiative, Cambridge, MA 02142, USA
| | - Jeffrey D. Dvorin
- Department of Immunology and Infectious Disease, Harvard School of Public Health, Building 1, Boston, MA 02115, USA
- Children’s Hospital Boston, Division of Infectious Diseases, Boston, MA 02115, USA
| | - Manoj T. Duraisingh
- Department of Immunology and Infectious Disease, Harvard School of Public Health, Building 1, Boston, MA 02115, USA
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- The Broad Institute of Harvard and MIT, Infectious Disease Initiative, Cambridge, MA 02142, USA
| | - Dyann F. Wirth
- Department of Immunology and Infectious Disease, Harvard School of Public Health, Building 1, Boston, MA 02115, USA
- The Broad Institute of Harvard and MIT, Infectious Disease Initiative, Cambridge, MA 02142, USA
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30
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Patel V, Booker M, Kramer M, Ross L, Celatka CA, Kennedy LM, Dvorin JD, Duraisingh MT, Sliz P, Wirth DF, Clardy J. Identification and characterization of small molecule inhibitors of Plasmodium falciparum dihydroorotate dehydrogenase. J Biol Chem 2008; 283:35078-85. [PMID: 18842591 PMCID: PMC2596402 DOI: 10.1074/jbc.m804990200] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2008] [Revised: 10/06/2008] [Indexed: 11/06/2022] Open
Abstract
Plasmodium falciparum causes the most deadly form of malaria and accounts for over one million deaths annually. The malaria parasite is unable to salvage pyrimidines and relies on de novo biosynthesis for survival. Dihydroorotate dehydrogenase (DHOD), a mitochondrially localized flavoenzyme, catalyzes the rate-limiting step of this pathway and is therefore an attractive antimalarial chemotherapeutic target. Using a target-based high throughput screen, we have identified a series of potent, species-specific inhibitors of P. falciparum DHOD (pfDHOD) that are also efficacious against three cultured strains (3D7, HB3, and Dd2) of P. falciparum. The primary antimalarial mechanism of action of these compounds was confirmed to be inhibition of pfDHOD through a secondary assay with transgenic malaria parasites, and the structural basis for enzyme inhibition was explored through in silico structure-based docking and site-directed mutagenesis. Compound-mediated cytotoxicity was not observed with human dermal fibroblasts or renal epithelial cells. These data validate pfDHOD as an antimalarial drug target and provide chemical scaffolds with which to begin medicinal chemistry efforts.
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Affiliation(s)
- Vishal Patel
- Department of Biological
Chemistry and Molecular Pharmacology, Harvard Medical School, Boston,
Massachusetts 02115, the Department
of Immunology and Infectious Disease, Harvard School of Public Health, Boston,
Massachusetts 02115, Drug and
Biomaterial Research and Development, Genzyme Corporation, Waltham,
Massachusetts 02451, Division of
Infectious Diseases, Children's Hospital Boston, Boston, Massachusetts 02115,
and the Department of Pediatrics, Harvard
Medical School, Boston, Massachusetts 02115
| | - Michael Booker
- Department of Biological
Chemistry and Molecular Pharmacology, Harvard Medical School, Boston,
Massachusetts 02115, the Department
of Immunology and Infectious Disease, Harvard School of Public Health, Boston,
Massachusetts 02115, Drug and
Biomaterial Research and Development, Genzyme Corporation, Waltham,
Massachusetts 02451, Division of
Infectious Diseases, Children's Hospital Boston, Boston, Massachusetts 02115,
and the Department of Pediatrics, Harvard
Medical School, Boston, Massachusetts 02115
| | - Martin Kramer
- Department of Biological
Chemistry and Molecular Pharmacology, Harvard Medical School, Boston,
Massachusetts 02115, the Department
of Immunology and Infectious Disease, Harvard School of Public Health, Boston,
Massachusetts 02115, Drug and
Biomaterial Research and Development, Genzyme Corporation, Waltham,
Massachusetts 02451, Division of
Infectious Diseases, Children's Hospital Boston, Boston, Massachusetts 02115,
and the Department of Pediatrics, Harvard
Medical School, Boston, Massachusetts 02115
| | - Leila Ross
- Department of Biological
Chemistry and Molecular Pharmacology, Harvard Medical School, Boston,
Massachusetts 02115, the Department
of Immunology and Infectious Disease, Harvard School of Public Health, Boston,
Massachusetts 02115, Drug and
Biomaterial Research and Development, Genzyme Corporation, Waltham,
Massachusetts 02451, Division of
Infectious Diseases, Children's Hospital Boston, Boston, Massachusetts 02115,
and the Department of Pediatrics, Harvard
Medical School, Boston, Massachusetts 02115
| | - Cassandra A. Celatka
- Department of Biological
Chemistry and Molecular Pharmacology, Harvard Medical School, Boston,
Massachusetts 02115, the Department
of Immunology and Infectious Disease, Harvard School of Public Health, Boston,
Massachusetts 02115, Drug and
Biomaterial Research and Development, Genzyme Corporation, Waltham,
Massachusetts 02451, Division of
Infectious Diseases, Children's Hospital Boston, Boston, Massachusetts 02115,
and the Department of Pediatrics, Harvard
Medical School, Boston, Massachusetts 02115
| | - Leah M. Kennedy
- Department of Biological
Chemistry and Molecular Pharmacology, Harvard Medical School, Boston,
Massachusetts 02115, the Department
of Immunology and Infectious Disease, Harvard School of Public Health, Boston,
Massachusetts 02115, Drug and
Biomaterial Research and Development, Genzyme Corporation, Waltham,
Massachusetts 02451, Division of
Infectious Diseases, Children's Hospital Boston, Boston, Massachusetts 02115,
and the Department of Pediatrics, Harvard
Medical School, Boston, Massachusetts 02115
| | - Jeffrey D. Dvorin
- Department of Biological
Chemistry and Molecular Pharmacology, Harvard Medical School, Boston,
Massachusetts 02115, the Department
of Immunology and Infectious Disease, Harvard School of Public Health, Boston,
Massachusetts 02115, Drug and
Biomaterial Research and Development, Genzyme Corporation, Waltham,
Massachusetts 02451, Division of
Infectious Diseases, Children's Hospital Boston, Boston, Massachusetts 02115,
and the Department of Pediatrics, Harvard
Medical School, Boston, Massachusetts 02115
| | - Manoj T. Duraisingh
- Department of Biological
Chemistry and Molecular Pharmacology, Harvard Medical School, Boston,
Massachusetts 02115, the Department
of Immunology and Infectious Disease, Harvard School of Public Health, Boston,
Massachusetts 02115, Drug and
Biomaterial Research and Development, Genzyme Corporation, Waltham,
Massachusetts 02451, Division of
Infectious Diseases, Children's Hospital Boston, Boston, Massachusetts 02115,
and the Department of Pediatrics, Harvard
Medical School, Boston, Massachusetts 02115
| | - Piotr Sliz
- Department of Biological
Chemistry and Molecular Pharmacology, Harvard Medical School, Boston,
Massachusetts 02115, the Department
of Immunology and Infectious Disease, Harvard School of Public Health, Boston,
Massachusetts 02115, Drug and
Biomaterial Research and Development, Genzyme Corporation, Waltham,
Massachusetts 02451, Division of
Infectious Diseases, Children's Hospital Boston, Boston, Massachusetts 02115,
and the Department of Pediatrics, Harvard
Medical School, Boston, Massachusetts 02115
| | - Dyann F. Wirth
- Department of Biological
Chemistry and Molecular Pharmacology, Harvard Medical School, Boston,
Massachusetts 02115, the Department
of Immunology and Infectious Disease, Harvard School of Public Health, Boston,
Massachusetts 02115, Drug and
Biomaterial Research and Development, Genzyme Corporation, Waltham,
Massachusetts 02451, Division of
Infectious Diseases, Children's Hospital Boston, Boston, Massachusetts 02115,
and the Department of Pediatrics, Harvard
Medical School, Boston, Massachusetts 02115
| | - Jon Clardy
- Department of Biological
Chemistry and Molecular Pharmacology, Harvard Medical School, Boston,
Massachusetts 02115, the Department
of Immunology and Infectious Disease, Harvard School of Public Health, Boston,
Massachusetts 02115, Drug and
Biomaterial Research and Development, Genzyme Corporation, Waltham,
Massachusetts 02451, Division of
Infectious Diseases, Children's Hospital Boston, Boston, Massachusetts 02115,
and the Department of Pediatrics, Harvard
Medical School, Boston, Massachusetts 02115
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Abstract
The origin of the eukaryotic genetic apparatus is thought to be central to understanding the evolution of the eukaryotic cell. Disagreement about the source of the relevant genes has spawned competing hypotheses for the origins of the eukaryote nuclear lineage. The iconic rooted 3-domains tree of life shows eukaryotes and archaebacteria as separate groups that share a common ancestor to the exclusion of eubacteria. By contrast, the eocyte hypothesis has eukaryotes originating within the archaebacteria and sharing a common ancestor with a particular group called the Crenarchaeota or eocytes. Here, we have investigated the relative support for each hypothesis from analysis of 53 genes spanning the 3 domains, including essential components of the eukaryotic nucleic acid replication, transcription, and translation apparatus. As an important component of our analysis, we investigated the fit between model and data with respect to composition. Compositional heterogeneity is a pervasive problem for reconstruction of ancient relationships, which, if ignored, can produce an incorrect tree with strong support. To mitigate its effects, we used phylogenetic models that allow for changing nucleotide or amino acid compositions over the tree and data. Our analyses favor a topology that supports the eocyte hypothesis rather than archaebacterial monophyly and the 3-domains tree of life.
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Lake JA, Servin JA, Herbold CW, Skophammer RG. Evidence for a New Root of the Tree of Life. Syst Biol 2008; 57:835-43. [DOI: 10.1080/10635150802555933] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Affiliation(s)
- James A. Lake
- Department of Molecular, Cellular, and Developmental Biology, University of California Los Angeles, California 90095, USA; E-mail: (J.A.L.)
- Molecular Biology Institute, University of California Los Angeles, California 90095, USA
- Department of Human Genetics, University of California Los Angeles, California 90095, USA
- UCLA Astrobiology Institute, University of California Los Angeles, California 90095, USA
| | - Jacqueline A. Servin
- Molecular Biology Institute, University of California Los Angeles, California 90095, USA
- UCLA Astrobiology Institute, University of California Los Angeles, California 90095, USA
| | - Craig W. Herbold
- Molecular Biology Institute, University of California Los Angeles, California 90095, USA
- UCLA Astrobiology Institute, University of California Los Angeles, California 90095, USA
| | - Ryan G. Skophammer
- Department of Molecular, Cellular, and Developmental Biology, University of California Los Angeles, California 90095, USA; E-mail: (J.A.L.)
- UCLA Astrobiology Institute, University of California Los Angeles, California 90095, USA
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Cavalier-Smith T. Predation and eukaryote cell origins: a coevolutionary perspective. Int J Biochem Cell Biol 2008; 41:307-22. [PMID: 18935970 DOI: 10.1016/j.biocel.2008.10.002] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2008] [Revised: 10/06/2008] [Accepted: 10/08/2008] [Indexed: 12/23/2022]
Abstract
Cells are of only two kinds: bacteria, with DNA segregated by surface membrane motors, dating back approximately 3.5Gy; and eukaryotes, which evolved from bacteria, possibly as recently as 800-850My ago. The last common ancestor of eukaryotes was a sexual phagotrophic protozoan with mitochondria, one or two centrioles and cilia. Conversion of bacteria (=prokaryotes) into a eukaryote involved approximately 60 major innovations. Numerous contradictory ideas about eukaryogenesis fail to explain fundamental features of eukaryotic cell biology or conflict with phylogeny. Data are best explained by the intracellular coevolutionary theory, with three basic tenets: (1) the eukaryotic cytoskeleton and endomembrane system originated through cooperatively enabling the evolution of phagotrophy; (2) phagocytosis internalised DNA-membrane attachments, unavoidably disrupting bacterial division; recovery entailed the evolution of the nucleus and mitotic cycle; (3) the symbiogenetic origin of mitochondria immediately followed the perfection of phagotrophy and intracellular digestion, contributing greater energy efficiency and group II introns as precursors of spliceosomal introns. Eukaryotes plus their archaebacterial sisters form the clade neomura, which evolved from a radically modified derivative of an actinobacterial posibacterium that had replaced the ancestral eubacterial murein peptidoglycan by N-linked glycoproteins, radically modified its DNA-handling enzymes, and evolved cotranslational protein secretion, but not the isoprenoid-ether lipids of archaebacteria. I focus on this phylogenetic background and on explaining how in response to novel phagotrophic selective pressures and ensuing genome internalisation this prekaryote evolved efficient digestion of prey proteins by retrotranslocation and 26S proteasomes, then internal digestion by phagocytosis, lysosomes, and peroxisomes, and eukaryotic vesicle trafficking and intracellular compartmentation.
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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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Larson MA, Bressani R, Sayood K, Corn JE, Berger JM, Griep MA, Hinrichs SH. Hyperthermophilic Aquifex aeolicus initiates primer synthesis on a limited set of trinucleotides comprised of cytosines and guanines. Nucleic Acids Res 2008; 36:5260-9. [PMID: 18684998 PMCID: PMC2532735 DOI: 10.1093/nar/gkn461] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The placement of the extreme thermophile Aquifex aeolicus in the bacterial phylogenetic tree has evoked much controversy. We investigated whether adaptations for growth at high temperatures would alter a key functional component of the replication machinery, specifically DnaG primase. Although the structure of bacterial primases is conserved, the trinucleotide initiation specificity for A. aeolicus was hypothesized to differ from other microbes as an adaptation to a geothermal milieu. To determine the full range of A. aeolicus primase activity, two oligonucleotides were designed that comprised all potential trinucleotide initiation sequences. One of the screening templates supported primer synthesis and the lengths of the resulting primers were used to predict possible initiation trinucleotides. Use of trinucleotide-specific templates demonstrated that the preferred initiation trinucleotide sequence for A. aeolicus primase was 5′-d(CCC)-3′. Two other sequences, 5′-d(GCC)-3′ and d(CGC)-3′, were also capable of supporting initiation, but to a much lesser degree. None of these trinucleotides were known to be recognition sequences used by other microbial primases. These results suggest that the initiation specificity of A. aeolicus primase may represent an adaptation to a thermophilic environment.
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Affiliation(s)
- Marilynn A Larson
- Department of Microbiology and Pathology, University of Nebraska Medical Center, Omaha, NE 68198-6495, USA
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Meyer J. Iron-sulfur protein folds, iron-sulfur chemistry, and evolution. J Biol Inorg Chem 2007; 13:157-70. [PMID: 17992543 DOI: 10.1007/s00775-007-0318-7] [Citation(s) in RCA: 173] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2007] [Accepted: 10/25/2007] [Indexed: 11/28/2022]
Abstract
An inventory of unique local protein folds around Fe-S clusters has been derived from the analysis of protein structure databases. Nearly 50 such folds have been identified, and over 90% of them harbor low-potential [2Fe-2S](2+,+) or [4Fe-4S](2+,+) clusters. In contrast, high-potential Fe-S clusters, notwithstanding their structural diversity, occur in only three different protein folds. These observations suggest that the extant population of Fe-S protein folds has to a large extent been shaped in the reducing iron- and sulfur-rich environment that is believed to have predominated on this planet until approximately two billion years ago. High-potential active sites are then surmised to be rarer because they emerged later, in a more oxidizing biosphere, in conditions where iron and sulfide had become poorly available, Fe-S clusters were less stable, and in addition faced competition from heme iron and copper active sites. Among the low-potential Fe-S active sites, protein folds hosting [4Fe-4S](2+,+) clusters outnumber those with [2Fe-2S](2+,+) ones by a factor of 3 at least. This is in keeping with the higher chemical stability and versatility of the tetranuclear clusters, compared with the binuclear ones. It is therefore suggested that, at least while novel Fe-S sites are evolving within proteins, the intrinsic chemical stability of the inorganic moiety may be more important than the stabilizing effect of the polypeptide chain. The discovery rate of novel Fe-S-containing protein folds underwent a sharp increase around 1995, and has remained stable to this day. The current trend suggests that the mapping of the Fe-S fold space is not near completion, in agreement with predictions made for protein folds in general. Altogether, the data collected and analyzed here suggest that the extant structural landscape of Fe-S proteins has been shaped to a large extent by primeval geochemical conditions on one hand, and iron-sulfur chemistry on the other.
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Affiliation(s)
- Jacques Meyer
- Commissariat à l'Energie Atomique, Université Joseph Fourier, UMR5249, CEA-Grenoble, 38054, Grenoble, France.
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