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Brabender M, Henriques Pereira DP, Mrnjavac N, Schlikker ML, Kimura ZI, Sucharitakul J, Kleinermanns K, Tüysüz H, Buckel W, Preiner M, Martin WF. Ferredoxin reduction by hydrogen with iron functions as an evolutionary precursor of flavin-based electron bifurcation. Proc Natl Acad Sci U S A 2024; 121:e2318969121. [PMID: 38513105 PMCID: PMC7615787 DOI: 10.1073/pnas.2318969121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 02/14/2024] [Indexed: 03/23/2024] Open
Abstract
Autotrophic theories for the origin of metabolism posit that the first cells satisfied their carbon needs from CO2 and were chemolithoautotrophs that obtained their energy and electrons from H2. The acetyl-CoA pathway of CO2 fixation is central to that view because of its antiquity: Among known CO2 fixing pathways it is the only one that is i) exergonic, ii) occurs in both bacteria and archaea, and iii) can be functionally replaced in full by single transition metal catalysts in vitro. In order to operate in cells at a pH close to 7, however, the acetyl-CoA pathway requires complex multi-enzyme systems capable of flavin-based electron bifurcation that reduce low potential ferredoxin-the physiological donor of electrons in the acetyl-CoA pathway-with electrons from H2. How can the acetyl-CoA pathway be primordial if it requires flavin-based electron bifurcation? Here, we show that native iron (Fe0), but not Ni0, Co0, Mo0, NiFe, Ni2Fe, Ni3Fe, or Fe3O4, promotes the H2-dependent reduction of aqueous Clostridium pasteurianum ferredoxin at pH 8.5 or higher within a few hours at 40 °C, providing the physiological function of flavin-based electron bifurcation, but without the help of enzymes or organic redox cofactors. H2-dependent ferredoxin reduction by iron ties primordial ferredoxin reduction and early metabolic evolution to a chemical process in the Earth's crust promoted by solid-state iron, a metal that is still deposited in serpentinizing hydrothermal vents today.
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Affiliation(s)
- Max Brabender
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Düsseldorf40225, Germany
| | - Delfina P. Henriques Pereira
- Microcosm Earth Center, Research Group for Geochemical Protozymes, Max Planck Institute for Terrestrial Microbiology and Philipps University, Marburg35032, Germany
| | - Natalia Mrnjavac
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Düsseldorf40225, Germany
| | - Manon Laura Schlikker
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Düsseldorf40225, Germany
| | - Zen-Ichiro Kimura
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Düsseldorf40225, Germany
- Department of Civil and Environmental Engineering, National Institute of Technology, Kure College, Kure, Hiroshima737-8506, Japan
| | - Jeerus Sucharitakul
- Department of Biochemistry, Chulalongkorn University, Patumwan, Bangkok10330, Thailand
| | - Karl Kleinermanns
- Institute for Physical Chemistry, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Düsseldorf40225, Germany
| | - Harun Tüysüz
- Max Planck Institute for Coal Research, Department of Heterogeneous Catalysis, Mülheim an der Ruhr45470, Germany
| | - Wolfgang Buckel
- Max Planck Institute for Terrestrial Microbiology, Marburg35043, Germany
- Laboratory for Microbiology, Department of Biology, Philipps University, Marburg35043, Germany
- Center for Synthetic Microbiology SYNMIKRO, Philipps University, Marburg35043, Germany
| | - Martina Preiner
- Microcosm Earth Center, Research Group for Geochemical Protozymes, Max Planck Institute for Terrestrial Microbiology and Philipps University, Marburg35032, Germany
| | - William F. Martin
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Düsseldorf40225, Germany
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Moraïs S, Winkler S, Zorea A, Levin L, Nagies FSP, Kapust N, Lamed E, Artan-Furman A, Bolam DN, Yadav MP, Bayer EA, Martin WF, Mizrahi I. Cryptic diversity of cellulose-degrading gut bacteria in industrialized humans. Science 2024; 383:eadj9223. [PMID: 38484069 PMCID: PMC7615765 DOI: 10.1126/science.adj9223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 02/08/2024] [Indexed: 03/19/2024]
Abstract
Humans, like all mammals, depend on the gut microbiome for digestion of cellulose, the main component of plant fiber. However, evidence for cellulose fermentation in the human gut is scarce. We have identified ruminococcal species in the gut microbiota of human populations that assemble functional multienzymatic cellulosome structures capable of degrading plant cell wall polysaccharides. One of these species, which is strongly associated with humans, likely originated in the ruminant gut and was subsequently transferred to the human gut, potentially during domestication where it underwent diversification and diet-related adaptation through the acquisition of genes from other gut microbes. Collectively, these species are abundant and widespread among ancient humans, hunter-gatherers, and rural populations but are rare in populations from industrialized societies thus indicating potential disappearance in response to the westernized lifestyle.
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Affiliation(s)
- Sarah Moraïs
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
- The Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Sarah Winkler
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
- The Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Alvah Zorea
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
- The Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Liron Levin
- Bioinformatics Core Facility, llse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Falk S. P. Nagies
- Department of Biology, Institute for Molecular Evolution, Heinrich-Heine-Universität Düsseldorf, D-40225, Düsseldorf, Germany
| | - Nils Kapust
- Department of Biology, Institute for Molecular Evolution, Heinrich-Heine-Universität Düsseldorf, D-40225, Düsseldorf, Germany
| | - Eva Lamed
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001 Israel
| | - Avital Artan-Furman
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001 Israel
| | - David N. Bolam
- Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Madhav P. Yadav
- US Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, 600 East Mermaid Lane, Wyndmoor, PA 19038, USA
| | - Edward A. Bayer
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001 Israel
| | - William F. Martin
- Department of Biology, Institute for Molecular Evolution, Heinrich-Heine-Universität Düsseldorf, D-40225, Düsseldorf, Germany
| | - Itzhak Mizrahi
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
- The Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
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Mrnjavac N, Wimmer JLE, Brabender M, Schwander L, Martin WF. The Moon-Forming Impact and the Autotrophic Origin of Life. Chempluschem 2023; 88:e202300270. [PMID: 37812146 PMCID: PMC7615287 DOI: 10.1002/cplu.202300270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 09/29/2023] [Accepted: 10/03/2023] [Indexed: 10/10/2023]
Abstract
The Moon-forming impact vaporized part of Earth's mantle, and turned the rest into a magma ocean, from which carbon dioxide degassed into the atmosphere, where it stayed until water rained out to form the oceans. The rain dissolved CO2 and made it available to react with transition metal catalysts in the Earth's crust so as to ultimately generate the organic compounds that form the backbone of microbial metabolism. The Moon-forming impact was key in building a planet with the capacity to generate life in that it converted carbon on Earth into a homogeneous and accessible substrate for organic synthesis. Today all ecosystems, without exception, depend upon primary producers, organisms that fix CO2 . According to theories of autotrophic origin, it has always been that way, because autotrophic theories posit that the first forms of life generated all the molecules needed to build a cell from CO2 , forging a direct line of continuity between Earth's initial CO2 -rich atmosphere and the first microorganisms. By modern accounts these were chemolithoautotrophic archaea and bacteria that initially colonized the crust and still inhabit that environment today.
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Affiliation(s)
- Natalia Mrnjavac
- Department of Biology Institute for Molecular Evolution Heinrich Heine University Duesseldorf Universitaetsstr. 1, 40225 Düsseldorf (Germany)
| | - Jessica L. E. Wimmer
- Department of Biology Institute for Molecular Evolution Heinrich Heine University Duesseldorf Universitaetsstr. 1, 40225 Düsseldorf (Germany)
| | - Max Brabender
- Department of Biology Institute for Molecular Evolution Heinrich Heine University Duesseldorf Universitaetsstr. 1, 40225 Düsseldorf (Germany)
| | - Loraine Schwander
- Department of Biology Institute for Molecular Evolution Heinrich Heine University Duesseldorf Universitaetsstr. 1, 40225 Düsseldorf (Germany)
| | - William F. Martin
- Department of Biology Institute for Molecular Evolution Heinrich Heine University Duesseldorf Universitaetsstr. 1, 40225 Düsseldorf (Germany)
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Schwander L, Brabender M, Mrnjavac N, Wimmer JLE, Preiner M, Martin WF. Serpentinization as the source of energy, electrons, organics, catalysts, nutrients and pH gradients for the origin of LUCA and life. Front Microbiol 2023; 14:1257597. [PMID: 37854333 PMCID: PMC10581274 DOI: 10.3389/fmicb.2023.1257597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 09/04/2023] [Indexed: 10/20/2023] Open
Abstract
Serpentinization in hydrothermal vents is central to some autotrophic theories for the origin of life because it generates compartments, reductants, catalysts and gradients. During the process of serpentinization, water circulates through hydrothermal systems in the crust where it oxidizes Fe (II) in ultramafic minerals to generate Fe (III) minerals and H2. Molecular hydrogen can, in turn, serve as a freely diffusible source of electrons for the reduction of CO2 to organic compounds, provided that suitable catalysts are present. Using catalysts that are naturally synthesized in hydrothermal vents during serpentinization H2 reduces CO2 to formate, acetate, pyruvate, and methane. These compounds represent the backbone of microbial carbon and energy metabolism in acetogens and methanogens, strictly anaerobic chemolithoautotrophs that use the acetyl-CoA pathway of CO2 fixation and that inhabit serpentinizing environments today. Serpentinization generates reduced carbon, nitrogen and - as newer findings suggest - reduced phosphorous compounds that were likely conducive to the origins process. In addition, it gives rise to inorganic microcompartments and proton gradients of the right polarity and of sufficient magnitude to support chemiosmotic ATP synthesis by the rotor-stator ATP synthase. This would help to explain why the principle of chemiosmotic energy harnessing is more conserved (older) than the machinery to generate ion gradients via pumping coupled to exergonic chemical reactions, which in the case of acetogens and methanogens involve H2-dependent CO2 reduction. Serpentinizing systems exist in terrestrial and deep ocean environments. On the early Earth they were probably more abundant than today. There is evidence that serpentinization once occurred on Mars and is likely still occurring on Saturn's icy moon Enceladus, providing a perspective on serpentinization as a source of reductants, catalysts and chemical disequilibrium for life on other worlds.
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Affiliation(s)
- Loraine Schwander
- Institute of Molecular Evolution, Biology Department, Math. -Nat. Faculty, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Max Brabender
- Institute of Molecular Evolution, Biology Department, Math. -Nat. Faculty, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Natalia Mrnjavac
- Institute of Molecular Evolution, Biology Department, Math. -Nat. Faculty, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Jessica L. E. Wimmer
- Institute of Molecular Evolution, Biology Department, Math. -Nat. Faculty, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Martina Preiner
- Microcosm Earth Center, Max Planck Institute for Terrestrial Microbiology and Philipps-Universität, Marburg, Germany
| | - William F. Martin
- Institute of Molecular Evolution, Biology Department, Math. -Nat. Faculty, Heinrich-Heine-Universität, Düsseldorf, Germany
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Beyazay T, Martin WF, Tüysüz H. Direct Synthesis of Formamide from CO 2 and H 2O with Nickel-Iron Nitride Heterostructures under Mild Hydrothermal Conditions. J Am Chem Soc 2023; 145:19768-19779. [PMID: 37642297 PMCID: PMC7615090 DOI: 10.1021/jacs.3c05412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Formamide can serve as a key building block for the synthesis of organic molecules relevant to premetabolic processes. Natural pathways for its synthesis from CO2 under early earth conditions are lacking. Here, we report the thermocatalytic conversion of CO2 and H2O to formate and formamide over Ni-Fe nitride heterostructures in the absence of synthetic H2 and N2 under mild hydrothermal conditions. While water molecules act as both a solvent and hydrogen source, metal nitrides serve as nitrogen sources to produce formamide in the temperature range of 25-100 °C under 5-50 bar. Longer reaction times promote the C-C bond coupling and formation of acetate and acetamide as additional products. Besides liquid products, methane and ethane are also produced as gas-phase products. Postreaction characterization of Ni-Fe nitride particles reveals structural alteration and provides insights into the potential reaction mechanism. The findings indicate that gaseous CO2 can serve as a carbon source for the formation of C-N bonds in formamide and acetamide over the Ni-Fe nitride heterostructure under simulated hydrothermal vent conditions.
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Affiliation(s)
- Tuğçe Beyazay
- Max-Planck-Institut fur Kohlenforschung, 45470 Mulheim an der Ruhr, Germany
| | - William F. Martin
- Institute of Molecular Evolution, University of Dusseldorf, 40225 Dusseldorf, Germany
| | - Harun Tüysüz
- Max-Planck-Institut fur Kohlenforschung, 45470 Mulheim an der Ruhr, Germany
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Raval PK, Martin WF, Gould SB. Mitochondrial evolution: Gene shuffling, endosymbiosis, and signaling. Sci Adv 2023; 9:eadj4493. [PMID: 37556561 PMCID: PMC10411874 DOI: 10.1126/sciadv.adj4493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
Genes for cardiolipin and ceramide synthesis occur in some alphaproteobacterial genomes. They shed light on mitochondrial origin and signaling in the first eukaryotic cells.
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Affiliation(s)
- Parth K. Raval
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - William F. Martin
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Sven B. Gould
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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Beyazay T, Ochoa-Hernández C, Song Y, Belthle K, Martin WF, Tüysüz H. Influence of Composition of Nickel-Iron Nanoparticles for Abiotic CO2 Conversion to Early Prebiotic Organics. Angew Chem Int Ed Engl 2023; 62:e202218189. [PMID: 36951652 DOI: 10.1002/anie.202218189] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 03/10/2023] [Accepted: 03/23/2023] [Indexed: 03/24/2023]
Abstract
Abiotic synthesis of formate and short hydrocarbons takes place in serpentinizing vents where some members of vent microbial communities live on abiotic formate as their main carbon source. To better understand the catalytic properties of Ni-Fe minerals that naturally exist in hydrothermal vents, we have investigated the ability of synthetic Ni-Fe based nanoparticular solids to catalyze the H2-dependent reduction of CO2, the first step required for the beginning of pre-biotic chemistry. Mono and bimetallic Ni-Fe nanoparticles with varied Ni-to-Fe ratios transform CO2 and H2 into intermediates and products of the acetyl-coenzyme A pathway - formate, acetate, and pyruvate - in mM range under mild hydrothermal conditions. Furthermore, Ni-Fe catalysts converted CO2 to similar products without molecular H2 by using water as a hydrogen source. Both CO2 chemisorption analysis and post-reaction characterization of materials indicate that Ni and Fe metals play complementary roles for CO2 fixation.
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Affiliation(s)
- Tugce Beyazay
- Max-Planck-Institut für Kohlenforschung: Max-Planck-Institut fur Kohlenforschung, Heterogeneous Catalysis, GERMANY
| | - Cristina Ochoa-Hernández
- Max-Planck-Institut für Kohlenforschung: Max-Planck-Institut fur Kohlenforschung, Heterogeneous Catalysis, GERMANY
| | - Youngdong Song
- Max-Planck-Institut für Kohlenforschung: Max-Planck-Institut fur Kohlenforschung, Heterogeneous Catalysis, GERMANY
| | - Kendra Belthle
- Max-Planck-Institute für Kohlenforschung: Max-Planck-Institut fur Kohlenforschung, Heterogeneous Catalysis, GERMANY
| | - William F Martin
- Heinrich-Heine-Universität Düsseldorf: Heinrich-Heine-Universitat Dusseldorf, Institute of Molecular Evolution, GERMANY
| | - Harun Tüysüz
- Max-Planck-Institut für Kohlenforschung: Max-Planck-Institut fur Kohlenforschung, Heterogeneous Catalysis, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, GERMANY
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Bremer N, Tria FDK, Skejo J, Martin WF. The Ancestral Mitotic State: Closed Orthomitosis With Intranuclear Spindles in the Syncytial Last Eukaryotic Common Ancestor. Genome Biol Evol 2023; 15:7031494. [PMID: 36752808 PMCID: PMC9985178 DOI: 10.1093/gbe/evad016] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 01/26/2023] [Accepted: 02/03/2023] [Indexed: 02/09/2023] Open
Abstract
All eukaryotes have linear chromosomes that are distributed to daughter nuclei during mitotic division, but the ancestral state of nuclear division in the last eukaryotic common ancestor (LECA) is so far unresolved. To address this issue, we have employed ancestral state reconstructions for mitotic states that can be found across the eukaryotic tree concerning the intactness of the nuclear envelope during mitosis (open or closed), the position of spindles (intranuclear or extranuclear), and the symmetry of spindles being either axial (orthomitosis) or bilateral (pleuromitosis). The data indicate that the LECA possessed closed orthomitosis with intranuclear spindles. Our reconstruction is compatible with recent findings indicating a syncytial state of the LECA, because it decouples three main processes: chromosome division, chromosome partitioning, and cell division (cytokinesis). The possession of closed mitosis using intranuclear spindles adds to the number of cellular traits that can now be attributed to LECA, providing insights into the lifestyle of this otherwise elusive biological entity at the origin of eukaryotic cells. Closed mitosis in a syncytial eukaryotic common ancestor would buffer mutations arising at the origin of mitotic division by allowing nuclei with viable chromosome sets to complement defective nuclei via mRNA in the cytosol.
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Affiliation(s)
- Nico Bremer
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Fernando D K Tria
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Josip Skejo
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - William F Martin
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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Fan L, Wu D, Goremykin V, Trost K, Knopp M, Zhang C, Martin WF, Zhu R. Reply to: Phylogenetic affiliation of mitochondria with Alpha-II and Rickettsiales is an artefact. Nat Ecol Evol 2022; 6:1832-1835. [PMID: 36280779 DOI: 10.1038/s41559-022-01896-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 09/01/2022] [Indexed: 12/15/2022]
Affiliation(s)
- Lu Fan
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology (SUSTech), Shenzhen, China.
| | - Dingfeng Wu
- The Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Vadim Goremykin
- Research and Innovation Centre, Fondazione E. Mach, San Michele all'Adige, Italy
| | - Katharina Trost
- Institute of Molecular Evolution, Heinrich Heine University, Düsseldorf, Germany
| | - Michael Knopp
- Institute of Molecular Evolution, Heinrich Heine University, Düsseldorf, Germany
| | - Chuanlun Zhang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology (SUSTech), Shenzhen, China
| | - William F Martin
- Institute of Molecular Evolution, Heinrich Heine University, Düsseldorf, Germany.
| | - Ruixin Zhu
- The Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China.
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Belthle KS, Beyazay T, Ochoa-Hernández C, Miyazaki R, Foppa L, Martin WF, Tüysüz H. Effects of Silica Modification (Mg, Al, Ca, Ti, and Zr) on Supported Cobalt Catalysts for H 2-Dependent CO 2 Reduction to Metabolic Intermediates. J Am Chem Soc 2022; 144:21232-21243. [DOI: 10.1021/jacs.2c08845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Kendra S. Belthle
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Tuğçe Beyazay
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Cristina Ochoa-Hernández
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Ray Miyazaki
- The NOMAD Laboratory at the FHI of the Max-Planck-Gesellschaft and IRIS-Adlershof of the Humboldt-Universität zu Berlin, Faradayweg 4-6, 14195 Berlin, Germany
| | - Lucas Foppa
- The NOMAD Laboratory at the FHI of the Max-Planck-Gesellschaft and IRIS-Adlershof of the Humboldt-Universität zu Berlin, Faradayweg 4-6, 14195 Berlin, Germany
| | - William F. Martin
- Institute of Molecular Evolution, University of Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Harun Tüysüz
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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Song B, Modjewski LD, Kapust N, Mizrahi I, Martin WF. The origin and distribution of the main oxygen sensing mechanism across metazoans. Front Physiol 2022; 13:977391. [PMID: 36324306 PMCID: PMC9618697 DOI: 10.3389/fphys.2022.977391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 10/07/2022] [Indexed: 11/13/2022] Open
Abstract
Oxygen sensing mechanisms are essential for metazoans, their origin and evolution in the context of oxygen in Earth history are of interest. To trace the evolution of a main oxygen sensing mechanism among metazoans, the hypoxia induced factor, HIF, we investigated the phylogenetic distribution and phylogeny of 11 of its components across 566 eukaryote genomes. The HIF based oxygen sensing machinery in eukaryotes can be traced as far back as 800 million years (Ma) ago, likely to the last metazoan common ancestor (LMCA), and arose at a time when the atmospheric oxygen content corresponded roughly to the Pasteur point, or roughly 1% of present atmospheric level (PAL). By the time of the Cambrian explosion (541–485 Ma) as oxygen levels started to approach those of the modern atmosphere, the HIF system with its key components HIF1α, HIF1β, PHD1, PHD4, FIH and VHL was well established across metazoan lineages. HIF1α is more widely distributed and therefore may have evolved earlier than HIF2α and HIF3α, and HIF1β and is more widely distributed than HIF2β in invertebrates. PHD1, PHD4, FIH, and VHL appear in all 13 metazoan phyla. The O2 consuming enzymes of the pathway, PHDs and FIH, have a lower substrate affinity, Km, for O2 than terminal oxidases in the mitochondrial respiratory chain, in line with their function as an environmental signal to switch to anaerobic energy metabolic pathways. The ancient HIF system has been conserved and widespread during the period when metazoans evolved and diversified together with O2 during Earth history.
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Affiliation(s)
- Bing Song
- Department of Biology, Institute for Molecular Evolution, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Luca David Modjewski
- Department of Biology, Institute for Molecular Evolution, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Nils Kapust
- Department of Biology, Institute for Molecular Evolution, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Itzhak Mizrahi
- Department of Life Sciences, Ben-Gurion University of the Negev and the National Institute for Biotechnology in the Negev, Marcus Family Campus, Be’er-Sheva, Israel
| | - William F. Martin
- Department of Biology, Institute for Molecular Evolution, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
- *Correspondence: William F. Martin,
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12
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Subedi BP, Schofield LR, Carbone V, Wolf M, Martin WF, Ronimus RS, Sutherland-Smith AJ. Structural characterisation of methanogen pseudomurein cell wall peptide ligases homologous to bacterial MurE/F murein peptide ligases. Microbiology (Reading) 2022; 168. [PMID: 36178458 DOI: 10.1099/mic.0.001235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Archaea have diverse cell wall types, yet none are identical to bacterial peptidoglycan (murein). Methanogens Methanobacteria and Methanopyrus possess cell walls of pseudomurein, a structural analogue of murein. Pseudomurein differs from murein in containing the unique archaeal sugar N-acetyltalosaminuronic acid instead of N-acetylmuramic acid, β-1,3 glycosidic bonds in place of β-1,4 bonds and only l-amino acids in the peptide cross-links. We have determined crystal structures of methanogen pseudomurein peptide ligases (termed pMurE) from Methanothermus fervidus (Mfer762) and Methanothermobacter thermautotrophicus (Mth734) that are structurally most closely related to bacterial MurE peptide ligases. The homology of the archaeal pMurE and bacterial MurE enzymes is clear both in the overall structure and at the level of each of the three domains. In addition, we identified two UDP-binding sites in Mfer762 pMurE, one at the exterior surface of the interface of the N-terminal and middle domains, and a second site at an inner surface continuous with the highly conserved interface of the three domains. Residues involved in ATP binding in MurE are conserved in pMurE, suggesting that a similar ATP-binding pocket is present at the interface of the middle and the C-terminal domains of pMurE. The presence of pMurE ligases in members of the Methanobacteriales and Methanopyrales, that are structurally related to bacterial MurE ligases, supports the idea that the biosynthetic origins of archaeal pseudomurein and bacterial peptidoglycan cell walls are evolutionarily related.
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Affiliation(s)
- Bishwa P Subedi
- AgResearch Ltd, Grasslands, Tennent Drive, Palmerston North, 4442, New Zealand.,School of Natural Sciences, Massey University, Palmerston North 4442, New Zealand.,Present address: Faculty of Medicine, Nursing and Health Sciences, Monash Biomedicine Discovery Institute, Monash University, Victoria 3800, Australia
| | - Linley R Schofield
- AgResearch Ltd, Grasslands, Tennent Drive, Palmerston North, 4442, New Zealand
| | - Vincenzo Carbone
- AgResearch Ltd, Grasslands, Tennent Drive, Palmerston North, 4442, New Zealand
| | - Maximilian Wolf
- AgResearch Ltd, Grasslands, Tennent Drive, Palmerston North, 4442, New Zealand.,Present address: Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology, Centre for Water and Environmental Research, University of Duisburg-Essen, 45141 Essen, Germany
| | - William F Martin
- Institute for Molecular Evolution, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Ron S Ronimus
- AgResearch Ltd, Grasslands, Tennent Drive, Palmerston North, 4442, New Zealand
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13
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Bremer N, Knopp M, Martin WF, Tria FDK. Realistic Gene Transfer to Gene Duplication Ratios Identify Different Roots in the Bacterial Phylogeny Using a Tree Reconciliation Method. Life (Basel) 2022; 12:life12070995. [PMID: 35888084 PMCID: PMC9322720 DOI: 10.3390/life12070995] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 06/29/2022] [Accepted: 07/01/2022] [Indexed: 11/29/2022]
Abstract
The rooting of phylogenetic trees permits important inferences about ancestral states and the polarity of evolutionary events. Recently, methods that reconcile discordance between gene-trees and species-trees—tree reconciliation methods—are becoming increasingly popular for rooting species trees. Rooting via reconciliation requires values for a particular parameter, the gene transfer to gene duplication ratio (T:D), which in current practice is estimated on the fly from discordances observed in the trees. To date, the accuracy of T:D estimates obtained by reconciliation analyses has not been compared to T:D estimates obtained by independent means, hence the effect of T:D upon inferences of species tree roots is altogether unexplored. Here we investigated the issue in detail by performing tree reconciliations of more than 10,000 gene trees under a variety of T:D ratios for two phylogenetic cases: a bacterial (prokaryotic) tree with 265 species and a fungal-metazoan (eukaryotic) tree with 31 species. We show that the T:D ratios automatically estimated by a current tree reconciliation method, ALE, generate virtually identical T:D ratios across bacterial genes and fungal-metazoan genes. The T:D ratios estimated by ALE differ 10- to 100-fold from robust, ALE-independent estimates from real data. More important is our finding that the root inferences using ALE in both datasets are strongly dependent upon T:D. Using more realistic T:D ratios, the number of roots inferred by ALE consistently increases and, in some cases, clearly incorrect roots are inferred. Furthermore, our analyses reveal that gene duplications have a far greater impact on ALE’s preferences for phylogenetic root placement than gene transfers or gene losses do. Overall, we show that obtaining reliable species tree roots with ALE is only possible when gene duplications are abundant in the data and the number of falsely inferred gene duplications is low. Finding a sufficient sample of true gene duplications for rooting species trees critically depends on the T:D ratios used in the analyses. T:D ratios, while being important parameters of genome evolution in their own right, affect the root inferences with tree reconciliations to an unanticipated degree.
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14
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Bremer N, Tria FDK, Skejo J, Garg SG, Martin WF. Ancestral state reconstructions trace mitochondria but not phagocytosis to the last eukaryotic common ancestor. Genome Biol Evol 2022; 14:6596370. [PMID: 35642316 PMCID: PMC9185374 DOI: 10.1093/gbe/evac079] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2022] [Indexed: 11/13/2022] Open
Abstract
Two main theories have been put forward to explain the origin of mitochondria in eukaryotes: phagotrophic engulfment (undigested food) and microbial symbiosis (physiological interactions). The two theories generate mutually exclusive predictions about the order in which mitochondria and phagocytosis arose. To discriminate the alternatives, we have employed ancestral state reconstructions (ASR) for phagocytosis as a trait, phagotrophy as a feeding habit, the presence of mitochondria, the presence of plastids, and the multinucleated organization across major eukaryotic lineages. To mitigate the bias introduced by assuming a particular eukaryotic phylogeny, we reconstructed the appearance of these traits across 1789 different rooted gene trees, each having species from opisthokonts, mycetozoa, hacrobia, excavate, archeplastida, and Stramenopiles, Alveolates and Rhizaria. The trees reflect conflicting relationships and different positions of the root. We employed a novel phylogenomic test that summarizes ASR across trees which reconstructs a last eukaryotic common ancestor that possessed mitochondria, was multinucleated, lacked plastids, and was non-phagotrophic as well as non-phagocytic. This indicates that both phagocytosis and phagotrophy arose subsequent to the origin of mitochondria, consistent with findings from comparative physiology. Furthermore, our ASRs uncovered multiple origins of phagocytosis and of phagotrophy across eukaryotes, indicating that, like wings in animals, these traits are useful but neither ancestral nor homologous across groups. The data indicate that mitochondria preceded the origin of phagocytosis, such that phagocytosis cannot have been the mechanism by which mitochondria were acquired.
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Affiliation(s)
- Nico Bremer
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf 40225 Düsseldorf, Germany
| | - Fernando D K Tria
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf 40225 Düsseldorf, Germany
| | - Josip Skejo
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf 40225 Düsseldorf, Germany
| | - Sriram G Garg
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf 40225 Düsseldorf, Germany
| | - William F Martin
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf 40225 Düsseldorf, Germany
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15
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Toledo FGS, Martin WF, Morrow L, Beysen C, Bajorunas D, Jiang Y, Silverman BL, McDonnell D, Namchuk MN, Newcomer JW, Graham C. Insulin and glucose metabolism with olanzapine and a combination of olanzapine and samidorphan: exploratory phase 1 results in healthy volunteers. Neuropsychopharmacology 2022; 47:696-703. [PMID: 34887529 PMCID: PMC8782841 DOI: 10.1038/s41386-021-01244-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 10/15/2021] [Accepted: 11/19/2021] [Indexed: 02/05/2023]
Abstract
A combination of olanzapine and samidorphan (OLZ/SAM) received US Food and Drug Administration approval in May 2021 for the treatment of adults with schizophrenia or bipolar I disorder. OLZ/SAM provides the efficacy of olanzapine, while mitigating olanzapine-associated weight gain. This exploratory study characterized the metabolic profile of OLZ/SAM in healthy volunteers to gain mechanistic insights. Volunteers received once-daily oral 10 mg/10 mg OLZ/SAM, 10 mg olanzapine, or placebo for 21 days. Assessments included insulin sensitivity during an oral glucose tolerance test (OGTT), hyperinsulinemic-euglycemic clamp, other measures of glucose/lipid metabolism, and adverse event (AE) monitoring. Treatment effects were estimated with analysis of covariance. In total, 60 subjects were randomized (double-blind; placebo, n = 12; olanzapine, n = 24; OLZ/SAM, n = 24). Olanzapine resulted in hyperinsulinemia and reduced insulin sensitivity during an OGTT at day 19, changes not observed with OLZ/SAM or placebo. Insulin sensitivity, measured by hyperinsulinemic-euglycemic clamp, was decreased in all treatment groups relative to baseline, but this effect was greatest with olanzapine and OLZ/SAM. Although postprandial (OGTT) glucose and fasting cholesterol concentrations were similarly increased with olanzapine or OLZ/SAM, other early metabolic effects were distinct, including post-OGTT C-peptide concentrations and aspects of energy metabolism. Forty-nine subjects (81.7%) experienced at least 1 AE, most mild or moderate in severity. OLZ/SAM appeared to mitigate some of olanzapine's unfavorable postprandial metabolic effects (e.g., hyperinsulinemia, elevated C-peptide) in this exploratory study. These findings supplement the body of evidence from completed or ongoing OLZ/SAM clinical trials supporting its role in the treatment of schizophrenia and bipolar I disorder.
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Affiliation(s)
- Frederico G. S. Toledo
- grid.21925.3d0000 0004 1936 9000Division of Endocrinology and Metabolism, Department of Medicine, University of Pittsburgh, Pittsburgh, PA USA
| | | | | | | | - Daiva Bajorunas
- Vault Bioventures, San Diego, CA USA ,Present Address: DBMD Consulting, Pompano Beach, FL USA
| | - Ying Jiang
- grid.422303.40000 0004 0384 9317Alkermes, Inc., Waltham, MA USA
| | | | - David McDonnell
- grid.472773.20000 0004 0384 2510Alkermes Pharma Ireland Limited, Dublin, Ireland
| | - Mark N. Namchuk
- grid.422303.40000 0004 0384 9317Alkermes, Inc., Waltham, MA USA ,grid.38142.3c000000041936754XPresent Address: Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA USA
| | - John W. Newcomer
- Thriving Mind South Florida, Miami, FL USA ,grid.4367.60000 0001 2355 7002Washington University School of Medicine, St. Louis, MO USA
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16
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Hedlund BP, Zhang C, Wang F, Rinke C, Martin WF. Editorial: Ecology, Metabolism and Evolution of Archaea-Perspectives From Proceedings of the International Workshop on Geo-Omics of Archaea. Front Microbiol 2022; 12:827229. [PMID: 35126338 PMCID: PMC8816317 DOI: 10.3389/fmicb.2021.827229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 12/21/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Brian P. Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, NV, United States
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, NV, United States
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Fengping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- School of Oceanography, Shanghai JiaoTong University, Shanghai, China
| | - Christian Rinke
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - William F. Martin
- Institute for Molecular Evolution, University of Dusseldorf Medical School, Düsseldorf, Germany
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17
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Henriques Pereira DP, Leethaus J, Beyazay T, do Nascimento Vieira A, Kleinermanns K, Tüysüz H, Martin WF, Preiner M. Role of geochemical protoenzymes (geozymes) in primordial metabolism: specific abiotic hydride transfer by metals to the biological redox cofactor NAD . FEBS J 2021; 289:3148-3162. [PMID: 34923745 PMCID: PMC9306933 DOI: 10.1111/febs.16329] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/09/2021] [Accepted: 12/17/2021] [Indexed: 12/17/2022]
Abstract
Hydrogen gas, H2, is generated in serpentinizing hydrothermal systems, where it has supplied electrons and energy for microbial communities since there was liquid water on Earth. In modern metabolism, H2 is converted by hydrogenases into organically bound hydrides (H–), for example, the cofactor NADH. It transfers hydrides among molecules, serving as an activated and biologically harnessed form of H2. In serpentinizing systems, minerals can also bind hydrides and could, in principle, have acted as inorganic hydride donors—possibly as a geochemical protoenzyme, a ‘geozyme’— at the origin of metabolism. To test this idea, we investigated the ability of H2 to reduce NAD+ in the presence of iron (Fe), cobalt (Co) and nickel (Ni), metals that occur in serpentinizing systems. In the presence of H2, all three metals specifically reduce NAD+ to the biologically relevant form, 1,4‐NADH, with up to 100% conversion rates within a few hours under alkaline aqueous conditions at 40 °C. Using Henry's law, the partial pressure of H2 in our reactions corresponds to 3.6 mm, a concentration observed in many modern serpentinizing systems. While the reduction of NAD+ by Ni is strictly H2‐dependent, experiments in heavy water (2H2O) indicate that native Fe can reduce NAD+ both with and without H2. The results establish a mechanistic connection between abiotic and biotic hydride donors, indicating that geochemically catalysed, H2‐dependent NAD+ reduction could have preceded the hydrogenase‐dependent reaction in evolution.
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Affiliation(s)
| | - Jana Leethaus
- Institute for Molecular Evolution, Heinrich Heine University, Düsseldorf, Germany
| | - Tugce Beyazay
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany
| | | | - Karl Kleinermanns
- Institute for Physical Chemistry, Heinrich Heine University, Düsseldorf, Germany
| | - Harun Tüysüz
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany
| | - William F Martin
- Institute for Molecular Evolution, Heinrich Heine University, Düsseldorf, Germany
| | - Martina Preiner
- Department of Ocean Systems, Royal Netherlands Institute for Sea Research, Den Burg, The Netherlands.,Department of Earth Sciences, Utrecht University, The Netherlands
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18
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Wimmer JLE, Xavier JC, Vieira ADN, Pereira DPH, Leidner J, Sousa FL, Kleinermanns K, Preiner M, Martin WF. Energy at Origins: Favorable Thermodynamics of Biosynthetic Reactions in the Last Universal Common Ancestor (LUCA). Front Microbiol 2021; 12:793664. [PMID: 34966373 PMCID: PMC8710812 DOI: 10.3389/fmicb.2021.793664] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 11/24/2021] [Indexed: 12/02/2022] Open
Abstract
Though all theories for the origin of life require a source of energy to promote primordial chemical reactions, the nature of energy that drove the emergence of metabolism at origins is still debated. We reasoned that evidence for the nature of energy at origins should be preserved in the biochemical reactions of life itself, whereby changes in free energy, ΔG, which determine whether a reaction can go forward or not, should help specify the source. By calculating values of ΔG across the conserved and universal core of 402 individual reactions that synthesize amino acids, nucleotides and cofactors from H2, CO2, NH3, H2S and phosphate in modern cells, we find that 95-97% of these reactions are exergonic (ΔG ≤ 0 kJ⋅mol-1) at pH 7-10 and 80-100°C under nonequilibrium conditions with H2 replacing biochemical reductants. While 23% of the core's reactions involve ATP hydrolysis, 77% are ATP-independent, thermodynamically driven by ΔG of reactions involving carbon bonds. We identified 174 reactions that are exergonic by -20 to -300 kJ⋅mol-1 at pH 9 and 80°C and that fall into ten reaction types: six pterin dependent alkyl or acyl transfers, ten S-adenosylmethionine dependent alkyl transfers, four acyl phosphate hydrolyses, 14 thioester hydrolyses, 30 decarboxylations, 35 ring closure reactions, 31 aromatic ring formations, and 44 carbon reductions by reduced nicotinamide, flavins, ferredoxin, or formate. The 402 reactions of the biosynthetic core trace to the last universal common ancestor (LUCA), and reveal that synthesis of LUCA's chemical constituents required no external energy inputs such as electric discharge, UV-light or phosphide minerals. The biosynthetic reactions of LUCA uncover a natural thermodynamic tendency of metabolism to unfold from energy released by reactions of H2, CO2, NH3, H2S, and phosphate.
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Affiliation(s)
- Jessica L. E. Wimmer
- Department of Biology, Institute of Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Joana C. Xavier
- Department of Biology, Institute of Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Andrey d. N. Vieira
- Department of Biology, Institute of Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Delfina P. H. Pereira
- Department of Biology, Institute of Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Jacqueline Leidner
- Department of Biology, Institute of Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Filipa L. Sousa
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Karl Kleinermanns
- Department of Chemistry, Institute of Physical Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Martina Preiner
- Department of Biology, Institute of Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - William F. Martin
- Department of Biology, Institute of Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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19
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Wimmer JLE, Kleinermanns K, Martin WF. Pyrophosphate and Irreversibility in Evolution, or why PP i Is Not an Energy Currency and why Nature Chose Triphosphates. Front Microbiol 2021; 12:759359. [PMID: 34759911 PMCID: PMC8575175 DOI: 10.3389/fmicb.2021.759359] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 09/15/2021] [Indexed: 11/13/2022] Open
Abstract
The possible evolutionary significance of pyrophosphate (PPi) has been discussed since the early 1960s. Lipmann suggested that PPi could have been an ancient currency or a possible environmental source of metabolic energy at origins, while Kornberg proposed that PPi vectorializes metabolism because ubiquitous pyrophosphatases render PPi forming reactions kinetically irreversible. To test those ideas, we investigated the reactions that consume phosphoanhydride bonds among the 402 reactions of the universal biosynthetic core that generates amino acids, nucleotides, and cofactors from H2, CO2, and NH3. We find that 36% of the core's phosphoanhydride hydrolyzing reactions generate PPi, while no reactions use PPi as an energy currency. The polymerization reactions that generate ~80% of cell mass - protein, RNA, and DNA synthesis - all generate PPi, while none use PPi as an energy source. In typical prokaryotic cells, aminoacyl tRNA synthetases (AARS) underlie ~80% of PPi production. We show that the irreversibility of the AARS reaction is a kinetic, not a thermodynamic effect. The data indicate that PPi is not an ancient energy currency and probably never was. Instead, PPi hydrolysis is an ancient mechanism that imparts irreversibility, as Kornberg suggested, functioning like a ratchet's pawl to vectorialize the life process toward growth. The two anhydride bonds in nucleoside triphosphates offer ATP-cleaving enzymes an option to impart either thermodynamic control (Pi formation) or kinetic control (PPi formation) upon reactions. This dual capacity explains why nature chose the triphosphate moiety of ATP as biochemistry's universal energy currency.
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Affiliation(s)
- Jessica L. E. Wimmer
- Institute for Molecular Evolution, Department of Biology, Heinrich Heine University Duesseldorf, Duesseldorf, Germany
| | - Karl Kleinermanns
- Institute for Physical Chemistry, Department of Chemistry, Heinrich Heine University Duesseldorf, Duesseldorf, Germany
| | - William F. Martin
- Institute for Molecular Evolution, Department of Biology, Heinrich Heine University Duesseldorf, Duesseldorf, Germany
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20
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Abstract
The contribution of gene duplications to the evolution of eukaryotic genomes is well studied. By contrast, studies of gene duplications in prokaryotes are scarce and generally limited to a handful of genes or careful analysis of a few prokaryotic lineages. Systematic broad-scale studies of prokaryotic genomes that sample available data are lacking, leaving gaps in our understanding of the contribution of gene duplications as a source of genetic novelty in the prokaryotic world. Here, we report conservative and robust estimates for the frequency of recent gene duplications within prokaryotic genomes relative to recent lateral gene transfer (LGT), as mechanisms to generate multiple copies of related sequences in the same genome. We obtain our estimates by focusing on evolutionarily recent events among 5,655 prokaryotic genomes, thereby avoiding vagaries of deep phylogenetic inference and confounding effects of ancient events and differential loss. We find that recent, genome-specific gene duplications are at least 50 times less frequent and probably 100 times less frequent than recent, genome-specific, gene acquisitions via LGT. The frequency of gene duplications varies across lineages and functional categories. The findings improve our understanding of genome evolution in prokaryotes and have far-reaching implications for evolutionary models that entail LGT to gene duplications ratio as a parameter.
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Affiliation(s)
- Fernando D K Tria
- Department of Biology, Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - William F Martin
- Department of Biology, Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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21
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Subedi BP, Martin WF, Carbone V, Duin EC, Cronin B, Sauter J, Schofield LR, Sutherland-Smith AJ, Ronimus RS. Archaeal pseudomurein and bacterial murein cell wall biosynthesis share a common evolutionary ancestry. FEMS Microbes 2021; 2:xtab012. [PMID: 37334239 PMCID: PMC10117817 DOI: 10.1093/femsmc/xtab012] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 08/19/2021] [Indexed: 08/29/2023] Open
Abstract
Bacteria near-universally contain a cell wall sacculus of murein (peptidoglycan), the synthesis of which has been intensively studied for over 50 years. In striking contrast, archaeal species possess a variety of other cell wall types, none of them closely resembling murein. Interestingly though, one type of archaeal cell wall termed pseudomurein found in the methanogen orders Methanobacteriales and Methanopyrales is a structural analogue of murein in that it contains a glycan backbone that is cross-linked by a L-amino acid peptide. Here, we present taxonomic distribution, gene cluster and phylogenetic analyses that confirm orthologues of 13 bacterial murein biosynthesis enzymes in pseudomurein-containing methanogens, most of which are distantly related to their bacterial counterparts. We also present the first structure of an archaeal pseudomurein peptide ligase from Methanothermus fervidus DSM1088 (Mfer336) to a resolution of 2.5 Å and show that it possesses a similar overall tertiary three domain structure to bacterial MurC and MurD type murein peptide ligases. Taken together the data strongly indicate that murein and pseudomurein biosynthetic pathways share a common evolutionary history.
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Affiliation(s)
- Bishwa P Subedi
- AgResearch Ltd. Grasslands, Tennent Drive, Palmerston North 4442, New Zealand
- Massey University, Tennent Drive, Palmerston North 4442, New Zealand
| | - William F Martin
- Institute for Molecular Evolution, Heinrich-Heine University, Düsseldorf Universitätsstraße 1, D-40225, Germany
| | - Vincenzo Carbone
- AgResearch Ltd. Grasslands, Tennent Drive, Palmerston North 4442, New Zealand
| | - Eduardus C Duin
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL 36849, USA
| | - Bryan Cronin
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL 36849, USA
| | - Julia Sauter
- AgResearch Ltd. Grasslands, Tennent Drive, Palmerston North 4442, New Zealand
| | - Linley R Schofield
- AgResearch Ltd. Grasslands, Tennent Drive, Palmerston North 4442, New Zealand
| | | | - Ron S Ronimus
- AgResearch Ltd. Grasslands, Tennent Drive, Palmerston North 4442, New Zealand
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22
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Abstract
Eukaryotes are typically depicted as descendants of archaea, but their genomes are evolutionary chimeras with genes stemming from archaea and bacteria. Which prokaryotic heritage predominates? Here, we have clustered 19,050,992 protein sequences from 5,443 bacteria and 212 archaea with 3,420,731 protein sequences from 150 eukaryotes spanning six eukaryotic supergroups. By downsampling, we obtain estimates for the bacterial and archaeal proportions. Eukaryotic genomes possess a bacterial majority of genes. On average, the majority of bacterial genes is 56% overall, 53% in eukaryotes that never possessed plastids, and 61% in photosynthetic eukaryotic lineages, where the cyanobacterial ancestor of plastids contributed additional genes to the eukaryotic lineage. Intracellular parasites, which undergo reductive evolution in adaptation to the nutrient rich environment of the cells that they infect, relinquish bacterial genes for metabolic processes. Such adaptive gene loss is most pronounced in the human parasite Encephalitozoon intestinalis with 86% archaeal and 14% bacterial derived genes. The most bacterial eukaryote genome sampled is rice, with 67% bacterial and 33% archaeal genes. The functional dichotomy, initially described for yeast, of archaeal genes being involved in genetic information processing and bacterial genes being involved in metabolic processes is conserved across all eukaryotic supergroups.
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Affiliation(s)
- Julia Brueckner
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Germany
| | - William F Martin
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Germany
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23
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Skejo J, Garg SG, Gould SB, Hendriksen M, Tria FDK, Bremer N, Franjević D, Blackstone NW, Martin WF. Evidence for a Syncytial Origin of Eukaryotes from Ancestral State Reconstruction. Genome Biol Evol 2021; 13:evab096. [PMID: 33963405 PMCID: PMC8290118 DOI: 10.1093/gbe/evab096] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/28/2021] [Indexed: 12/11/2022] Open
Abstract
Modern accounts of eukaryogenesis entail an endosymbiotic encounter between an archaeal host and a proteobacterial endosymbiont, with subsequent evolution giving rise to a unicell possessing a single nucleus and mitochondria. The mononucleate state of the last eukaryotic common ancestor (LECA) is seldom, if ever, questioned, even though cells harboring multiple (syncytia, coenocytes, and polykaryons) are surprisingly common across eukaryotic supergroups. Here, we present a survey of multinucleated forms. Ancestral character state reconstruction for representatives of 106 eukaryotic taxa using 16 different possible roots and supergroup sister relationships, indicate that LECA, in addition to being mitochondriate, sexual, and meiotic, was multinucleate. LECA exhibited closed mitosis, which is the rule for modern syncytial forms, shedding light on the mechanics of its chromosome segregation. A simple mathematical model shows that within LECA's multinucleate cytosol, relationships among mitochondria and nuclei were neither one-to-one, nor one-to-many, but many-to-many, placing mitonuclear interactions and cytonuclear compatibility at the evolutionary base of eukaryotic cell origin. Within a syncytium, individual nuclei and individual mitochondria function as the initial lower-level evolutionary units of selection, as opposed to individual cells, during eukaryogenesis. Nuclei within a syncytium rescue each other's lethal mutations, thereby postponing selection for viable nuclei and cytonuclear compatibility to the generation of spores, buffering transitional bottlenecks at eukaryogenesis. The prokaryote-to-eukaryote transition is traditionally thought to have left no intermediates, yet if eukaryogenesis proceeded via a syncytial common ancestor, intermediate forms have persisted to the present throughout the eukaryotic tree as syncytia but have so far gone unrecognized.
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Affiliation(s)
- Josip Skejo
- Institute for Molecular Evolution, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
- Faculty of Science, Division of Zoology, Department of Biology, University of Zagreb, Evolution Lab, Zagreb, Croatia
| | - Sriram G Garg
- Institute for Molecular Evolution, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Sven B Gould
- Institute for Molecular Evolution, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Michael Hendriksen
- Institute for Molecular Evolution, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Fernando D K Tria
- Institute for Molecular Evolution, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Nico Bremer
- Institute for Molecular Evolution, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Damjan Franjević
- Faculty of Science, Division of Zoology, Department of Biology, University of Zagreb, Evolution Lab, Zagreb, Croatia
| | - Neil W Blackstone
- Department of Biological Sciences, Northern Illinois University, DeKalb, IL, USA
| | - William F Martin
- Institute for Molecular Evolution, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
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Tria FDK, Brueckner J, Skejo J, Xavier JC, Kapust N, Knopp M, Wimmer JLE, Nagies FSP, Zimorski V, Gould SB, Garg SG, Martin WF. Gene Duplications Trace Mitochondria to the Onset of Eukaryote Complexity. Genome Biol Evol 2021; 13:evab055. [PMID: 33739376 PMCID: PMC8175051 DOI: 10.1093/gbe/evab055] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/14/2021] [Indexed: 12/15/2022] Open
Abstract
The last eukaryote common ancestor (LECA) possessed mitochondria and all key traits that make eukaryotic cells more complex than their prokaryotic ancestors, yet the timing of mitochondrial acquisition and the role of mitochondria in the origin of eukaryote complexity remain debated. Here, we report evidence from gene duplications in LECA indicating an early origin of mitochondria. Among 163,545 duplications in 24,571 gene trees spanning 150 sequenced eukaryotic genomes, we identify 713 gene duplication events that occurred in LECA. LECA's bacterial-derived genes include numerous mitochondrial functions and were duplicated significantly more often than archaeal-derived and eukaryote-specific genes. The surplus of bacterial-derived duplications in LECA most likely reflects the serial copying of genes from the mitochondrial endosymbiont to the archaeal host's chromosomes. Clustering, phylogenies and likelihood ratio tests for 22.4 million genes from 5,655 prokaryotic and 150 eukaryotic genomes reveal no evidence for lineage-specific gene acquisitions in eukaryotes, except from the plastid in the plant lineage. That finding, and the functions of bacterial genes duplicated in LECA, suggests that the bacterial genes in eukaryotes are acquisitions from the mitochondrion, followed by vertical gene evolution and differential loss across eukaryotic lineages, flanked by concomitant lateral gene transfer among prokaryotes. Overall, the data indicate that recurrent gene transfer via the copying of genes from a resident mitochondrial endosymbiont to archaeal host chromosomes preceded the onset of eukaryotic cellular complexity, favoring mitochondria-early over mitochondria-late hypotheses for eukaryote origin.
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Affiliation(s)
- Fernando D K Tria
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Germany
| | - Julia Brueckner
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Germany
| | - Josip Skejo
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Germany
- Faculty of Science, University of Zagreb, Croatia
| | - Joana C Xavier
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Germany
| | - Nils Kapust
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Germany
| | - Michael Knopp
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Germany
| | - Jessica L E Wimmer
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Germany
| | - Falk S P Nagies
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Germany
| | - Verena Zimorski
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Germany
| | - Sven B Gould
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Germany
| | - Sriram G Garg
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Germany
| | - William F Martin
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Germany
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25
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Xavier JC, Gerhards RE, Wimmer JLE, Brueckner J, Tria FDK, Martin WF. The metabolic network of the last bacterial common ancestor. Commun Biol 2021; 4:413. [PMID: 33772086 PMCID: PMC7997952 DOI: 10.1038/s42003-021-01918-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 02/26/2021] [Indexed: 02/03/2023] Open
Abstract
Bacteria are the most abundant cells on Earth. They are generally regarded as ancient, but due to striking diversity in their metabolic capacities and widespread lateral gene transfer, the physiology of the first bacteria is unknown. From 1089 reference genomes of bacterial anaerobes, we identified 146 protein families that trace to the last bacterial common ancestor, LBCA, and form the conserved predicted core of its metabolic network, which requires only nine genes to encompass all universal metabolites. Our results indicate that LBCA performed gluconeogenesis towards cell wall synthesis, and had numerous RNA modifications and multifunctional enzymes that permitted life with low gene content. In accordance with recent findings for LUCA and LACA, analyses of thousands of individual gene trees indicate that LBCA was rod-shaped and the first lineage to diverge from the ancestral bacterial stem was most similar to modern Clostridia, followed by other autotrophs that harbor the acetyl-CoA pathway.
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Affiliation(s)
- Joana C Xavier
- Institute for Molecular Evolution, Heinrich-Heine-University, 40225, Düsseldorf, Germany.
| | - Rebecca E Gerhards
- Institute for Molecular Evolution, Heinrich-Heine-University, 40225, Düsseldorf, Germany
| | - Jessica L E Wimmer
- Institute for Molecular Evolution, Heinrich-Heine-University, 40225, Düsseldorf, Germany
| | - Julia Brueckner
- Institute for Molecular Evolution, Heinrich-Heine-University, 40225, Düsseldorf, Germany
| | - Fernando D K Tria
- Institute for Molecular Evolution, Heinrich-Heine-University, 40225, Düsseldorf, Germany
| | - William F Martin
- Institute for Molecular Evolution, Heinrich-Heine-University, 40225, Düsseldorf, Germany
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26
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Kowallik KV, Martin WF. The origin of symbiogenesis: An annotated English translation of Mereschkowsky's 1910 paper on the theory of two plasma lineages. Biosystems 2021; 199:104281. [PMID: 33279568 PMCID: PMC7816216 DOI: 10.1016/j.biosystems.2020.104281] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 10/26/2020] [Accepted: 10/26/2020] [Indexed: 02/02/2023]
Abstract
In 1910, the Russian biologist Konstantin Sergejewitch Mereschkowsky (Константин Сергеевич Мережковский, in standard transliterations also written as Konstantin Sergeevič Merežkovskij and Konstantin Sergeevich Merezhkovsky) published a notable synthesis of observations and inferences concerning the origin of life and the origin of nucleated cells. His theory was based on physiology and leaned heavily upon the premise that thermophilic autotrophs were ancient. The ancestors of plants and animals were inferred as ancestrally mesophilic anucleate heterotrophs (Monera) that became complex and diverse through endosymbiosis. He placed a phylogenetic root in the tree of life among anaerobic autotrophic bacteria that lack chlorophyll. His higher level classification of all microbes and macrobes in the living world was based upon the presence or absence of past endosymbiotic events. The paper's primary aim was to demonstrate that all life forms descend from two fundamentally distinct organismal lineages, called mykoplasma and amoeboplasma, whose very nature was so different that, in his view, they could only have arisen independently of one another and at different times during Earth history. The mykoplasma arose at a time when the young Earth was still hot, it later gave rise to cyanobacteria, which in turn gave rise to plastids. The product of the second origin of life, the amoeboplasma, arose after the Earth had cooled and autotrophs had generated substrates for heterotrophic growth. Lineage diversification of that second plasma brought forth, via serial endosymbioses, animals (one symbiosis) and then plants (two symbioses, the second being the plastid). The paper was published in German, rendering it inaccessible to many interested scholars. Here we translate the 1910 paper in full and briefly provide some context.
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Affiliation(s)
- Klaus V Kowallik
- Institute for Molecular Evolution, Heinrich-Heine-University of Düsseldorf, Düsseldorf, Germany.
| | - William F Martin
- Institute for Molecular Evolution, Heinrich-Heine-University of Düsseldorf, Düsseldorf, Germany.
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27
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Garg SG, Kapust N, Lin W, Knopp M, Tria FDK, Nelson-Sathi S, Gould SB, Fan L, Zhu R, Zhang C, Martin WF. Anomalous Phylogenetic Behavior of Ribosomal Proteins in Metagenome-Assembled Asgard Archaea. Genome Biol Evol 2020; 13:5988511. [PMID: 33462601 DOI: 10.1093/gbe/evaa238] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/03/2020] [Indexed: 01/20/2023] Open
Abstract
Metagenomic studies permit the exploration of microbial diversity in a defined habitat, and binning procedures enable phylogenomic analyses, taxon description, and even phenotypic characterizations in the absence of morphological evidence. Such lineages include asgard archaea, which were initially reported to represent archaea with eukaryotic cell complexity, although the first images of such an archaeon show simple cells with prokaryotic characteristics. However, these metagenome-assembled genomes (MAGs) might suffer from data quality problems not encountered in sequences from cultured organisms due to two common analytical procedures of bioinformatics: assembly of metagenomic sequences and binning of assembled sequences on the basis of innate sequence properties and abundance across samples. Consequently, genomic sequences of distantly related taxa, or domains, can in principle be assigned to the same MAG and result in chimeric sequences. The impacts of low-quality or chimeric MAGs on phylogenomic and metabolic prediction remain unknown. Debates that asgard archaeal data are contaminated with eukaryotic sequences are overshadowed by the lack of evidence indicating that individual asgard MAGs stem from the same chromosome. Here, we show that universal proteins including ribosomal proteins of asgard archaeal MAGs fail to meet the basic phylogenetic criterion fulfilled by genome sequences of cultured archaea investigated to date: These proteins do not share common evolutionary histories to the same extent as pure culture genomes do, pointing to a chimeric nature of asgard archaeal MAGs. Our analysis suggests that some asgard archaeal MAGs represent unnatural constructs, genome-like patchworks of genes resulting from assembly and/or the binning process.
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Affiliation(s)
- Sriram G Garg
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Germany
| | - Nils Kapust
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Germany
| | - Weili Lin
- Putuo People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Michael Knopp
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Germany
| | - Fernando D K Tria
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Germany
| | - Shijulal Nelson-Sathi
- Transdisciplinary Biology, Computational Biology Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | - Sven B Gould
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Germany
| | - Lu Fan
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China.,Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China.,SUSTech Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, China
| | - Ruixin Zhu
- Putuo People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China.,Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - William F Martin
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Germany
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28
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Abstract
Lateral gene transfer (LGT) has impacted prokaryotic genome evolution, yet the extent to which LGT compromises vertical evolution across individual genes and individual phyla is unknown, as are the factors that govern LGT frequency across genes. Estimating LGT frequency from tree comparisons is problematic when thousands of genomes are compared, because LGT becomes difficult to distinguish from phylogenetic artefacts. Here we report quantitative estimates for verticality across all genes and genomes, leveraging a well-known property of phylogenetic inference: phylogeny works best at the tips of trees. From terminal (tip) phylum level relationships, we calculate the verticality for 19,050,992 genes from 101,422 clusters in 5,655 prokaryotic genomes and rank them by their verticality. Among functional classes, translation, followed by nucleotide and cofactor biosynthesis, and DNA replication and repair are the most vertical. The most vertically evolving lineages are those rich in ecological specialists such as Acidithiobacilli, Chlamydiae, Chlorobi and Methanococcales. Lineages most affected by LGT are the α-, β-, γ-, and δ- classes of Proteobacteria and the Firmicutes. The 2,587 eukaryotic clusters in our sample having prokaryotic homologues fail to reject eukaryotic monophyly using the likelihood ratio test. The low verticality of α-proteobacterial and cyanobacterial genomes requires only three partners-an archaeal host, a mitochondrial symbiont, and a plastid ancestor-each with mosaic chromosomes, to directly account for the prokaryotic origin of eukaryotic genes. In terms of phylogeny, the 100 most vertically evolving prokaryotic genes are neither representative nor predictive for the remaining 97% of an average genome. In search of factors that govern LGT frequency, we find a simple but natural principle: Verticality correlates strongly with gene distribution density, LGT being least likely for intruding genes that must replace a preexisting homologue in recipient chromosomes. LGT is most likely for novel genetic material, intruding genes that encounter no competing copy.
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Affiliation(s)
- Falk S. P. Nagies
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Julia Brueckner
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Fernando D. K. Tria
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - William F. Martin
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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29
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Abstract
Submarine hydrothermal vents are rich in hydrogen (H2), an ancient source of electrons and chemical energy for life. Geochemical H2 stems from serpentinization, a process in which rock-bound iron reduces water to H2. Reactions involving H2 and carbon dioxide (CO2) in hydrothermal systems generate abiotic methane and formate; these reactions resemble the core energy metabolism of methanogens and acetogens. These organisms are strict anaerobic autotrophs that inhabit hydrothermal vents and harness energy via H2-dependent CO2 reduction. Serpentinization also generates native metals, which can reduce CO2 to formate and acetate in the laboratory. The enzymes that channel H2, CO2, and dinitrogen (N2) into methanogen and acetogen metabolism are the backbone of the most ancient metabolic pathways. Their active sites share carbon-metal bonds which, although rare in biology, are conserved relics of primordial biochemistry present at the origin of life.
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Affiliation(s)
- William F Martin
- Institute for Molecular Evolution, University of Düsseldorf, 40225 Düsseldorf, Germany.
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30
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Cunnane SC, Trushina E, Morland C, Prigione A, Casadesus G, Andrews ZB, Beal MF, Bergersen LH, Brinton RD, de la Monte S, Eckert A, Harvey J, Jeggo R, Jhamandas JH, Kann O, la Cour CM, Martin WF, Mithieux G, Moreira PI, Murphy MP, Nave KA, Nuriel T, Oliet SHR, Saudou F, Mattson MP, Swerdlow RH, Millan MJ. Brain energy rescue: an emerging therapeutic concept for neurodegenerative disorders of ageing. Nat Rev Drug Discov 2020; 19:609-633. [PMID: 32709961 PMCID: PMC7948516 DOI: 10.1038/s41573-020-0072-x] [Citation(s) in RCA: 383] [Impact Index Per Article: 95.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2020] [Indexed: 12/11/2022]
Abstract
The brain requires a continuous supply of energy in the form of ATP, most of which is produced from glucose by oxidative phosphorylation in mitochondria, complemented by aerobic glycolysis in the cytoplasm. When glucose levels are limited, ketone bodies generated in the liver and lactate derived from exercising skeletal muscle can also become important energy substrates for the brain. In neurodegenerative disorders of ageing, brain glucose metabolism deteriorates in a progressive, region-specific and disease-specific manner - a problem that is best characterized in Alzheimer disease, where it begins presymptomatically. This Review discusses the status and prospects of therapeutic strategies for countering neurodegenerative disorders of ageing by improving, preserving or rescuing brain energetics. The approaches described include restoring oxidative phosphorylation and glycolysis, increasing insulin sensitivity, correcting mitochondrial dysfunction, ketone-based interventions, acting via hormones that modulate cerebral energetics, RNA therapeutics and complementary multimodal lifestyle changes.
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Affiliation(s)
- Stephen C Cunnane
- Department of Medicine, Université de Sherbrooke, Sherbrooke, QC, Canada.
- Research Center on Aging, Sherbrooke, QC, Canada.
| | | | - Cecilie Morland
- Department of Pharmaceutical Biosciences, Institute of Pharmacy, University of Oslo, Oslo, Norway
| | - Alessandro Prigione
- Department of General Pediatrics, Neonatology, and Pediatric Cardiology, University of Dusseldorf, Dusseldorf, Germany
| | - Gemma Casadesus
- Department of Biological Sciences, Kent State University, Kent, OH, USA
| | - Zane B Andrews
- Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- Department of Physiology, Monash University, Clayton, VIC, Australia
| | - M Flint Beal
- Department of Neurology, Weill Cornell Medicine, New York, NY, USA
| | - Linda H Bergersen
- Department of Anatomy, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | | | | | | | - Jenni Harvey
- Ninewells Hospital, University of Dundee, Dundee, UK
- Medical School, University of Dundee, Dundee, UK
| | - Ross Jeggo
- Centre for Therapeutic Innovation in Neuropsychiatry, Institut de Recherche Servier, Croissy sur Seine, France
| | - Jack H Jhamandas
- Department of Medicine, University of Albeta, Edmonton, AB, Canada
- Neuroscience and Mental Health Institute, University of Albeta, Edmonton, AB, Canada
| | - Oliver Kann
- Institute of Physiology and Pathophysiology, University of Heidelberg, Heidelberg, Germany
| | - Clothide Mannoury la Cour
- Centre for Therapeutic Innovation in Neuropsychiatry, Institut de Recherche Servier, Croissy sur Seine, France
| | - William F Martin
- Institute of Molecular Evolution, University of Dusseldorf, Dusseldorf, Germany
| | | | - Paula I Moreira
- CNC Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
- Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Michael P Murphy
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Klaus-Armin Nave
- Department of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Tal Nuriel
- Columbia University Medical Center, New York, NY, USA
| | - Stéphane H R Oliet
- Neurocentre Magendie, INSERM U1215, Bordeaux, France
- Université de Bordeaux, Bordeaux, France
| | - Frédéric Saudou
- University of Grenoble Alpes, Grenoble, France
- INSERM U1216, CHU Grenoble Alpes, Grenoble Institute Neurosciences, Grenoble, France
| | - Mark P Mattson
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Mark J Millan
- Centre for Therapeutic Innovation in Neuropsychiatry, Institut de Recherche Servier, Croissy sur Seine, France.
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do Nascimento Vieira A, Kleinermanns K, Martin WF, Preiner M. The ambivalent role of water at the origins of life. FEBS Lett 2020; 594:2717-2733. [PMID: 32416624 DOI: 10.1002/1873-3468.13815] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/29/2020] [Accepted: 05/07/2020] [Indexed: 12/15/2022]
Abstract
Life as we know it would not exist without water. However, water molecules not only serve as a solvent and reactant but can also promote hydrolysis, which counteracts the formation of essential organic molecules. This conundrum constitutes one of the central issues in origin of life. Hydrolysis is an important part of energy metabolism for all living organisms but only because, inside cells, it is a controlled reaction. How could hydrolysis have been regulated under prebiotic settings? Lower water activities possibly provide an answer: geochemical sites with less free and more bound water can supply the necessary conditions for protometabolic reactions. Such conditions occur in serpentinising systems, hydrothermal sites that synthesise hydrogen gas via rock-water interactions. Here, we summarise the parallels between biotic and abiotic means of controlling hydrolysis in order to narrow the gap between biochemical and geochemical reactions and briefly outline how hydrolysis could even have played a constructive role at the origin of molecular self-organisation.
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Affiliation(s)
| | | | - William F Martin
- Institute for Molecular Evolution, University of Düsseldorf, Germany
| | - Martina Preiner
- Institute for Molecular Evolution, University of Düsseldorf, Germany
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32
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Abstract
For decades, microbiologists have viewed the acetyl CoA pathway and organisms that use it for H2-dependent carbon and energy metabolism, acetogens and methanogens, as ancient. Classical evidence and newer evidence indicating the antiquity of the acetyl CoA pathway are summarized here. The acetyl CoA pathway requires approximately 10 enzymes, roughly as many organic cofactors, and more than 500 kDa of combined subunit molecular mass to catalyze the conversion of H2 and CO2 to formate, acetate, and pyruvate in acetogens and methanogens. However, a single hydrothermal vent alloy, awaruite (Ni3Fe), can convert H2 and CO2 to formate, acetate, and pyruvate under mild hydrothermal conditions on its own. The chemical reactions of H2 and CO2 to pyruvate thus have a natural tendency to occur without enzymes, given suitable inorganic catalysts. This suggests that the evolution of the enzymatic acetyl CoA pathway was preceded by-and patterned along-a route of naturally occurring exergonic reactions catalyzed by transition metal minerals that could activate H2 and CO2 by chemisorption. The principle of forward (autotrophic) pathway evolution from preexisting non-enzymatic reactions is generalized to the concept of patterned evolution of pathways. In acetogens, exergonic reduction of CO2 by H2 generates acyl phosphates by highly reactive carbonyl groups undergoing attack by inert inorganic phosphate. In that ancient reaction of biochemical energy conservation, the energy behind formation of the acyl phosphate bond resides in the carbonyl, not in phosphate. The antiquity of the acetyl CoA pathway is usually seen in light of CO2 fixation; its role in primordial energy coupling via acyl phosphates and substrate-level phosphorylation is emphasized here.
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Affiliation(s)
- William F. Martin
- Institute for Molecular Evolution, University of Düsseldorf, Düsseldorf, Germany
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33
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Abstract
Modern cells embody metabolic networks containing thousands of elements and form autocatalytic sets of molecules that produce copies of themselves. How the first self-sustaining metabolic networks arose at life's origin is a major open question. Autocatalytic sets smaller than metabolic networks were proposed as transitory intermediates at the origin of life, but evidence for their role in prebiotic evolution is lacking. Here, we identify reflexively autocatalytic food-generated networks (RAFs)-self-sustaining networks that collectively catalyse all their reactions-embedded within microbial metabolism. RAFs in the metabolism of ancient anaerobic autotrophs that live from H2 and CO2 provided with small-molecule catalysts generate acetyl-CoA as well as amino acids and bases, the monomeric components of protein and RNA, but amino acids and bases without organic catalysts do not generate metabolic RAFs. This suggests that RAFs identify attributes of biochemical origins conserved in metabolic networks. RAFs are consistent with an autotrophic origin of metabolism and furthermore indicate that autocatalytic chemical networks preceded proteins and RNA in evolution. RAFs uncover intermediate stages in the emergence of metabolic networks, narrowing the gaps between early Earth chemistry and life.
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Affiliation(s)
- Joana C. Xavier
- Institut für Molekulare Evolution, Heinrich Heine Universität, 40225 Düsseldorf, Germany
| | - Wim Hordijk
- Konrad Lorenz Institute for Evolution and Cognition Research, 3400 Klosterneuburg, Austria
| | | | - Mike Steel
- Biomathematics Research Centre, University of Canterbury, Christchurch 8041, New Zealand
| | - William F. Martin
- Institut für Molekulare Evolution, Heinrich Heine Universität, 40225 Düsseldorf, Germany
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal
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34
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Abstract
In subseafloor sediment, microbial cell densities exponentially decrease with depth into the fermentation zone. Here, we address the classical question of 'why are cells dying faster than they are growing?' from the standpoint of physiology. The stoichiometries of fermentative ATP production and consumption in the fermentation zone place bounds on the conversion of old cell biomass into new. Most fermentable organic matter in deep subseafloor sediment is amino acids from dead cells because cells are mostly protein by weight. Conversion of carbon from fermented dead cell protein into methanogen protein via hydrogenotrophic and acetoclastic methanogenesis occurs at ratios of ∼200:1 and 100:1, respectively, while fermenters can reach conversion ratios approaching 6:1. Amino acid fermentations become thermodynamically more efficient at lower substrate and product concentrations, but the conversion of carbon from dead cell protein into fermenter protein is low because of the high energetic cost of translation. Low carbon conversion factors within subseafloor anaerobic feeding chains account for exponential declines in cellular biomass in the fermentation zone of anoxic sediments. Our analysis points to the existence of a life-death transition zone in which the last biologically catalyzed life processes are replaced with purely chemical reactions no longer coupled to life.
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Affiliation(s)
- William D Orsi
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
| | - Bernhard Schink
- Department of Biology, University of Konstanz, 78457 Constance, Germany
| | - Wolfgang Buckel
- Department of Biology, Philipps-Universität, 35032 Marburg, Germany
| | - William F Martin
- Institute for Molecular Evolution, Heinrich Heine Universität Düsseldorf, 40225 Düsseldorf, Germany
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Allen JF, Thake B, Martin WF. Nitrogenase Inhibition Limited Oxygenation of Earth's Proterozoic Atmosphere. Trends Plant Sci 2019; 24:1022-1031. [PMID: 31447302 DOI: 10.1016/j.tplants.2019.07.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 07/10/2019] [Accepted: 07/10/2019] [Indexed: 05/24/2023]
Abstract
Cyanobacteria produced the oxygen that began to accumulate on Earth 2.5 billion years ago, at the dawn of the Proterozoic Eon. By 2.4 billion years ago, the Great Oxidation Event (GOE) marked the onset of an atmosphere containing oxygen. The oxygen content of the atmosphere then remained low for almost 2 billion years. Why? Nitrogenase, the sole nitrogen-fixing enzyme on Earth, controls the entry of molecular nitrogen into the biosphere. Nitrogenase is inhibited in air containing more than 2% oxygen: the concentration of oxygen in the Proterozoic atmosphere. We propose that oxygen inhibition of nitrogenase limited Proterozoic global primary production. Oxygen levels increased when upright terrestrial plants isolated nitrogen fixation in soil from photosynthetic oxygen production in shoots and leaves.
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Affiliation(s)
- John F Allen
- Research Department of Genetics, Evolution and Environment, Darwin Building, University College London, Gower Street, London WC1E 6BT, UK.
| | - Brenda Thake
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | - William F Martin
- Institute of Molecular Evolution, Heinrich-Heine-Universitaet Duesseldorf, Universitaetsstr. 1, 40225 Duesseldorf, Germany
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Preiner M, Xavier JC, Vieira ADN, Kleinermanns K, Allen JF, Martin WF. Catalysts, autocatalysis and the origin of metabolism. Interface Focus 2019; 9:20190072. [PMID: 31641438 PMCID: PMC6802133 DOI: 10.1098/rsfs.2019.0072] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 08/30/2019] [Indexed: 12/24/2022] Open
Abstract
If life on Earth started out in geochemical environments like hydrothermal vents, then it started out from gasses like CO2, N2 and H2. Anaerobic autotrophs still live from these gasses today, and they still inhabit the Earth's crust. In the search for connections between abiotic processes in ancient geological systems and biotic processes in biological systems, it becomes evident that chemical activation (catalysis) of these gasses and a constant source of energy are key. The H2–CO2 redox reaction provides a constant source of energy and anabolic inputs, because the equilibrium lies on the side of reduced carbon compounds. Identifying geochemical catalysts that activate these gasses en route to nitrogenous organic compounds and small autocatalytic networks will be an important step towards understanding prebiotic chemistry that operates only on the basis of chemical energy, without input from solar radiation. So, if life arose in the dark depths of hydrothermal vents, then understanding reactions and catalysts that operate under such conditions is crucial for understanding origins.
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Affiliation(s)
- Martina Preiner
- Institute for Molecular Evolution, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | - Joana C Xavier
- Institute for Molecular Evolution, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | | | - Karl Kleinermanns
- Institute for Physical Chemistry, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | - John F Allen
- Research Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - William F Martin
- Institute for Molecular Evolution, Heinrich-Heine-University, 40225 Düsseldorf, Germany
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Wein T, Romero Picazo D, Blow F, Woehle C, Jami E, Reusch TB, Martin WF, Dagan T. Currency, Exchange, and Inheritance in the Evolution of Symbiosis. Trends Microbiol 2019; 27:836-849. [DOI: 10.1016/j.tim.2019.05.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/19/2019] [Accepted: 05/30/2019] [Indexed: 12/28/2022]
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Gould SB, Garg SG, Handrich M, Nelson-Sathi S, Gruenheit N, Tielens AGM, Martin WF. Adaptation to life on land at high O 2 via transition from ferredoxin-to NADH-dependent redox balance. Proc Biol Sci 2019; 286:20191491. [PMID: 31431166 PMCID: PMC6732389 DOI: 10.1098/rspb.2019.1491] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Pyruvate : ferredoxin oxidoreductase (PFO) and iron only hydrogenase ([Fe]-HYD) are common enzymes among eukaryotic microbes that inhabit anaerobic niches. Their function is to maintain redox balance by donating electrons from food oxidation via ferredoxin (Fd) to protons, generating H2 as a waste product. Operating in series, they constitute a soluble electron transport chain of one-electron transfers between FeS clusters. They fulfil the same function—redox balance—served by two electron-transfers in the NADH- and O2-dependent respiratory chains of mitochondria. Although they possess O2-sensitive FeS clusters, PFO, Fd and [Fe]-HYD are also present among numerous algae that produce O2. The evolutionary persistence of these enzymes among eukaryotic aerobes is traditionally explained as adaptation to facultative anaerobic growth. Here, we show that algae express enzymes of anaerobic energy metabolism at ambient O2 levels (21% v/v), Chlamydomonas reinhardtii expresses them with diurnal regulation. High O2 environments arose on Earth only approximately 450 million years ago. Gene presence/absence and gene expression data indicate that during the transition to high O2 environments and terrestrialization, diverse algal lineages retained enzymes of Fd-dependent one-electron-based redox balance, while the land plant and land animal lineages underwent irreversible specialization to redox balance involving the O2-insensitive two-electron carrier NADH.
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Affiliation(s)
- S B Gould
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - S G Garg
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - M Handrich
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - S Nelson-Sathi
- Interdisciplinary Biology, Computational Biology Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | - N Gruenheit
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - A G M Tielens
- Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.,Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - W F Martin
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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Zimorski V, Mentel M, Tielens AGM, Martin WF. Energy metabolism in anaerobic eukaryotes and Earth's late oxygenation. Free Radic Biol Med 2019; 140:279-294. [PMID: 30935869 PMCID: PMC6856725 DOI: 10.1016/j.freeradbiomed.2019.03.030] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 03/21/2019] [Accepted: 03/26/2019] [Indexed: 01/09/2023]
Abstract
Eukaryotes arose about 1.6 billion years ago, at a time when oxygen levels were still very low on Earth, both in the atmosphere and in the ocean. According to newer geochemical data, oxygen rose to approximately its present atmospheric levels very late in evolution, perhaps as late as the origin of land plants (only about 450 million years ago). It is therefore natural that many lineages of eukaryotes harbor, and use, enzymes for oxygen-independent energy metabolism. This paper provides a concise overview of anaerobic energy metabolism in eukaryotes with a focus on anaerobic energy metabolism in mitochondria. We also address the widespread assumption that oxygen improves the overall energetic state of a cell. While it is true that ATP yield from glucose or amino acids is increased in the presence of oxygen, it is also true that the synthesis of biomass costs thirteen times more energy per cell in the presence of oxygen than in anoxic conditions. This is because in the reaction of cellular biomass with O2, the equilibrium lies very far on the side of CO2. The absence of oxygen offers energetic benefits of the same magnitude as the presence of oxygen. Anaerobic and low oxygen environments are ancient. During evolution, some eukaryotes have specialized to life in permanently oxic environments (life on land), other eukaryotes have remained specialized to low oxygen habitats. We suggest that the Km of mitochondrial cytochrome c oxidase of 0.1-10 μM for O2, which corresponds to about 0.04%-4% (avg. 0.4%) of present atmospheric O2 levels, reflects environmental O2 concentrations that existed at the time that the eukaryotes arose.
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Affiliation(s)
- Verena Zimorski
- Institute of Molecular Evolution, Heinrich-Heine-University, 40225, Düsseldorf, Germany.
| | - Marek Mentel
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, 851 04, Bratislava, Slovakia.
| | - Aloysius G M Tielens
- Department of Medical Microbiology and Infectious Diseases, Erasmus Medical Center Rotterdam, The Netherlands; Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.
| | - William F Martin
- Institute of Molecular Evolution, Heinrich-Heine-University, 40225, Düsseldorf, Germany.
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Abstract
The origin of mitochondria was a crucial event in eukaryote evolution. A recent report claimed to provide evidence, based on branch length variation in phylogenetic trees, that the mitochondrion came late in eukaryotic evolution. Here, we reinvestigate their claim with a reanalysis of the published data. We show that the analyses underpinning a late mitochondrial origin suffer from multiple fatal flaws founded in inappropriate statistical methods and analyses, in addition to erroneous interpretations.
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Affiliation(s)
- William F. Martin
- Institute of Molecular Evolution, Heinrich-Heine University, Düsseldorf, Germany
- Corresponding author: E-mail:
| | - Mayo Roettger
- Institute of Molecular Evolution, Heinrich-Heine University, Düsseldorf, Germany
| | - Chuan Ku
- Institute of Molecular Evolution, Heinrich-Heine University, Düsseldorf, Germany
| | - Sriram G. Garg
- Institute of Molecular Evolution, Heinrich-Heine University, Düsseldorf, Germany
| | - Shijulal Nelson-Sathi
- Computational Biology & Bioinformatics Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, Kerala, India
| | - Giddy Landan
- Institute of Microbiology, Christian-Albrechts-University of Kiel, Germany
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Martin WF, Correll CU, Weiden PJ, Jiang Y, Pathak S, DiPetrillo L, Silverman BL, Ehrich EW. Mitigation of Olanzapine-Induced Weight Gain With Samidorphan, an Opioid Antagonist: A Randomized Double-Blind Phase 2 Study in Patients With Schizophrenia. Am J Psychiatry 2019; 176:457-467. [PMID: 30845818 DOI: 10.1176/appi.ajp.2018.18030280] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
OBJECTIVE Preclinical evidence and data from a proof-of-concept study in healthy volunteers suggest that samidorphan, an opioid antagonist, mitigates weight gain associated with olanzapine. This study prospectively compared combination therapy of olanzapine plus either samidorphan or placebo for the treatment of schizophrenia. METHODS This was an international, multicenter, randomized phase 2 study of olanzapine plus samidorphan in patients with schizophrenia. The study had a 1-week open-label olanzapine lead-in period followed by a 12-week double-blind treatment phase in which patients were randomly assigned in a 1:1:1:1 ratio to receive olanzapine plus placebo (N=75) or olanzapine plus 5 mg (N=80), 10 mg (N=86), or 20 mg (N=68) of samidorphan. The primary aims were to confirm that the antipsychotic efficacy of olanzapine plus samidorphan was comparable to olanzapine plus placebo, to assess the effect of combining olanzapine with samidorphan on olanzapine-induced weight gain, and to assess the overall safety and tolerability of olanzapine plus samidorphan. RESULTS Antipsychotic efficacy, as assessed by total score on the Positive and Negative Syndrome Scale (PANSS), was equivalent across all treatment groups. Treatment with olanzapine plus samidorphan resulted in a statistically significant lower weight gain (37% lower weight gain compared with olanzapine plus placebo). The least square mean percent change from baseline in body weight was 4.1% (2.9 kg) for the olanzapine plus placebo group and 2.6% (1.9 kg) for the olanzapine plus samidorphan group (2.8% [2.1 kg] for the 5 mg group, 2.1% [1.5 kg] for the 10 mg group, and 2.9% [2.2 kg] for the 20 mg group). Adverse events reported at a frequency ≥5% in any of the olanzapine plus samidorphan groups and occurring at a rate ≥2 times greater than in the olanzapine plus placebo group were somnolence, sedation, dizziness, and constipation. Other safety measures were comparable between the olanzapine plus samidorphan groups and the olanzapine plus placebo group. CONCLUSIONS The antipsychotic efficacy of olanzapine plus samidorphan was equivalent to that of olanzapine plus placebo, and olanzapine plus samidorphan was associated with clinically meaningful and statistically significant mitigation of weight gain compared with olanzapine plus placebo. Olanzapine plus samidorphan was generally well tolerated, with a safety profile similar to olanzapine plus placebo.
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Affiliation(s)
- William F Martin
- Alkermes, Inc., Waltham, Mass. (Martin, Weiden, Jiang, Pathak, DiPetrillo, Silverman, Ehrich); and Hofstra Northwell School of Medicine, Hempstead, N.Y., and Zucker Hillside Hospital, Psychiatry, Glen Oaks, N.Y. (Correll)
| | - Christoph U Correll
- Alkermes, Inc., Waltham, Mass. (Martin, Weiden, Jiang, Pathak, DiPetrillo, Silverman, Ehrich); and Hofstra Northwell School of Medicine, Hempstead, N.Y., and Zucker Hillside Hospital, Psychiatry, Glen Oaks, N.Y. (Correll)
| | - Peter J Weiden
- Alkermes, Inc., Waltham, Mass. (Martin, Weiden, Jiang, Pathak, DiPetrillo, Silverman, Ehrich); and Hofstra Northwell School of Medicine, Hempstead, N.Y., and Zucker Hillside Hospital, Psychiatry, Glen Oaks, N.Y. (Correll)
| | - Ying Jiang
- Alkermes, Inc., Waltham, Mass. (Martin, Weiden, Jiang, Pathak, DiPetrillo, Silverman, Ehrich); and Hofstra Northwell School of Medicine, Hempstead, N.Y., and Zucker Hillside Hospital, Psychiatry, Glen Oaks, N.Y. (Correll)
| | - Sanjeev Pathak
- Alkermes, Inc., Waltham, Mass. (Martin, Weiden, Jiang, Pathak, DiPetrillo, Silverman, Ehrich); and Hofstra Northwell School of Medicine, Hempstead, N.Y., and Zucker Hillside Hospital, Psychiatry, Glen Oaks, N.Y. (Correll)
| | - Lauren DiPetrillo
- Alkermes, Inc., Waltham, Mass. (Martin, Weiden, Jiang, Pathak, DiPetrillo, Silverman, Ehrich); and Hofstra Northwell School of Medicine, Hempstead, N.Y., and Zucker Hillside Hospital, Psychiatry, Glen Oaks, N.Y. (Correll)
| | - Bernard L Silverman
- Alkermes, Inc., Waltham, Mass. (Martin, Weiden, Jiang, Pathak, DiPetrillo, Silverman, Ehrich); and Hofstra Northwell School of Medicine, Hempstead, N.Y., and Zucker Hillside Hospital, Psychiatry, Glen Oaks, N.Y. (Correll)
| | - Elliot W Ehrich
- Alkermes, Inc., Waltham, Mass. (Martin, Weiden, Jiang, Pathak, DiPetrillo, Silverman, Ehrich); and Hofstra Northwell School of Medicine, Hempstead, N.Y., and Zucker Hillside Hospital, Psychiatry, Glen Oaks, N.Y. (Correll)
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Brunk CF, Martin WF. Archaeal Histone Contributions to the Origin of Eukaryotes. Trends Microbiol 2019; 27:703-714. [PMID: 31076245 DOI: 10.1016/j.tim.2019.04.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 04/01/2019] [Accepted: 04/11/2019] [Indexed: 12/14/2022]
Abstract
The eukaryotic lineage arose from bacterial and archaeal cells that underwent a symbiotic merger. At the origin of the eukaryote lineage, the bacterial partner contributed genes, metabolic energy, and the building blocks of the endomembrane system. What did the archaeal partner donate that made the eukaryotic experiment a success? The archaeal partner provided the potential for complex information processing. Archaeal histones were crucial in that regard by providing the basic functional unit with which eukaryotes organize DNA into nucleosomes, exert epigenetic control of gene expression, transcribe genes with CCAAT-box promoters, and a manifest cell cycle with condensed chromosomes. While mitochondrial energy lifted energetic constraints on eukaryotic protein production, histone-based chromatin organization paved the path to eukaryotic genome complexity, a critical hurdle en route to the evolution of complex cells.
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Affiliation(s)
- Clifford F Brunk
- Department of Ecology and Evolutionary Biology and Molecular Biology Institute University of California Los Angeles, Los Angeles, USA
| | - William F Martin
- Institute of Molecular Evolution Heinrich-Heine-Universitaet Duesseldorf, Dusseldorf, Germany.
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Zajecka JM, Stanford AD, Memisoglu A, Martin WF, Pathak S. Buprenorphine/samidorphan combination for the adjunctive treatment of major depressive disorder: results of a phase III clinical trial (FORWARD-3). Neuropsychiatr Dis Treat 2019; 15:795-808. [PMID: 31040679 PMCID: PMC6459143 DOI: 10.2147/ndt.s199245] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND The endogenous opioid system is a fundamental regulator of mood in humans. Previously reported clinical trials have demonstrated the efficacy of the investigational agent buprenorphine/samidorphan (BUP/SAM) combination, an opioid-system modulator, for the adjunctive treatment of major depressive disorder. We present here a third phase III study of different design. METHODS Adult patients with major depressive disorder and inadequate response to antidepressant therapy were enrolled in this double-blind, placebo-controlled, placebo run-in study to evaluate the efficacy, safety, and tolerability of adjunctive BUP/SAM 2 mg/2 mg. Patients with baseline Hamilton Depression Rating Scale score $20 received double-blind placebo in addition to background antidepressant therapy for 4 weeks. Nonresponders were randomized to receive adjunctive BUP/SAM 2 mg/2 mg or placebo for 6 weeks. The primary end point was change in Montgomery-Åsberg Depression Rating Scale (MADRS)-10 total score from randomization at baseline to the end of the 6-week treatment period. RESULTS Least-squares mean change in MADRS-10 score at end of treatment was -4.8 (SE 0.67) in the BUP/SAM 2 mg/2 mg group and -4.6 (SE 0.66) in the placebo group (mean difference -0.3 [SE 0.95], P=0.782). There were no differences in MADRS-based response or remission rates. Overall, 42.9% of the BUP/SAM 2 mg/2 mg group and 34.5% of the placebo group experienced at least one treatment-emergent adverse event during the 6-week treatment period, most of which were mild or moderate in severity. There were no clinically important changes in laboratory parameters, weight, or vital signs and no evidence of abuse potential during treatment or opiate-withdrawal symptoms post treatment. CONCLUSION Efficacy results in FORWARD-3 measured by change in MADRS-10 score did not meet the primary end point, but postbaseline improvement in MADRS-10 in the BUP/SAM 2 mg/2 mg group was consistent with that seen in previously reported trials. BUP/SAM 2 mg/2 mg was well tolerated.
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Affiliation(s)
- John M Zajecka
- Department of Psychiatry, Rush University Medical Center, Chicago, IL, USA, .,Psychiatric Medicine Associates, LLC, Skokie, IL, USA,
| | | | - Asli Memisoglu
- Department of Biostatistics, Alkermes, Inc., Waltham, MA, USA
| | | | - Sanjeev Pathak
- Department of Clinical Research, Alkermes, Inc., Waltham, MA, USA
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Sudianto E, Wu CS, Leonhard L, Martin WF, Chaw SM. Enlarged and highly repetitive plastome of Lagarostrobos and plastid phylogenomics of Podocarpaceae. Mol Phylogenet Evol 2018; 133:24-32. [PMID: 30553879 DOI: 10.1016/j.ympev.2018.12.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 12/09/2018] [Accepted: 12/10/2018] [Indexed: 11/26/2022]
Abstract
Podocarpaceae is the largest family in cupressophytes (conifers II), but its plastid genomes (plastomes) are poorly studied, with plastome data currently existing for only four of the 19 Podocarpaceous genera. In this study, we sequenced and assembled the complete plastomes from representatives of eight additional genera, including Afrocarpus, Dacrydium, Lagarostrobos, Lepidothamnus, Pherosphaera, Phyllocladus, Prumnopitys, and Saxegothaea. We found that Lagarostrobos, a monotypic genus native to Tasmania, has the largest plastome (151,496 bp) among any cupressophytes studied to date. Plastome enlargement in Lagarostrobos coincides with increased intergenic spacers, repeats, and duplicated genes. Among the Podocarpaceae, Lagarostrobos has the most rearranged plastome, but its substitution rates are modest. Plastid phylogenomic analyses based on 81 plastid genes clarify the positions of previously conflicting Podocarpaceous genera. Tree topologies firmly support the division of Podocarpaceae into two sister clades: (1) the Prumnopityoid clade and (2) the clade containing Podocarpoid, Dacrydioid, Pherosphaera, and Saxegothaea. The Phyllocladus is nested within the Podocarpaceae, thus familial status of the monotypic Phyllocladaceae is not supported.
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Affiliation(s)
- Edi Sudianto
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei 11529, Taiwan; Department of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan; Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Chung-Shien Wu
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Lars Leonhard
- Botanical Garden, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | - William F Martin
- Institute of Molecular Evolution, Heinrich-Heine-University, 40225 Düsseldorf, Germany.
| | - Shu-Miaw Chaw
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei 11529, Taiwan; Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan.
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Kapust N, Nelson-Sathi S, Schönfeld B, Hazkani-Covo E, Bryant D, Lockhart PJ, Röttger M, Xavier JC, Martin WF. Failure to Recover Major Events of Gene Flux in Real Biological Data Due to Method Misapplication. Genome Biol Evol 2018; 10:1198-1209. [PMID: 29718211 PMCID: PMC5928405 DOI: 10.1093/gbe/evy080] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2018] [Indexed: 12/13/2022] Open
Abstract
In prokaryotes, known mechanisms of lateral gene transfer (transformation, transduction, conjugation, and gene transfer agents) generate new combinations of genes among chromosomes during evolution. In eukaryotes, whose host lineage is descended from archaea, lateral gene transfer from organelles to the nucleus occurs at endosymbiotic events. Recent genome analyses studying gene distributions have uncovered evidence for sporadic, discontinuous events of gene transfer from bacteria to archaea during evolution. Other studies have used traditional models designed to investigate gene family size evolution (Count) to support claims that gene transfer to archaea was continuous during evolution, rather than involving occasional periodic mass gene influx events. Here, we show that the methodology used in analyses favoring continuous gene transfers to archaea was misapplied in other studies and does not recover known events of single simultaneous origin for many genes followed by differential loss in real data: plastid genomes. Using the same software and the same settings, we reanalyzed presence/absence pattern data for proteins encoded in plastid genomes and for eukaryotic protein families acquired from plastids. Contrary to expectations under a plastid origin model, we found that the methodology employed inferred that gene acquisitions occurred uniformly across the plant tree. Sometimes as many as nine different acquisitions by plastid DNA were inferred for the same protein family. That is, the methodology that recovered gradual and continuous lateral gene transfer among lineages for archaea obtains the same result for plastids, even though it is known that massive gains followed by gradual differential loss is the true evolutionary process that generated plastid gene distribution data. Our findings caution against the use of models designed to study gene family size evolution for investigating gene transfer processes, especially when transfers involving more than one gene per event are possible.
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Affiliation(s)
- Nils Kapust
- Institute of Molecular Evolution, Heinrich Heine University, Düsseldorf, Germany
| | - Shijulal Nelson-Sathi
- Computational Biology & Bioinformatics Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, Kerala, India
| | | | - Einat Hazkani-Covo
- Department of Natural and Life Sciences, The Open University of Israel, Ra’anana, Israel
| | - David Bryant
- Department of Mathematics and Statistics, University of Otago, Dunedin, New Zealand
| | - Peter J Lockhart
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Mayo Röttger
- Institute of Molecular Evolution, Heinrich Heine University, Düsseldorf, Germany
| | - Joana C Xavier
- Institute of Molecular Evolution, Heinrich Heine University, Düsseldorf, Germany
- Corresponding author: E-mail:
| | - William F Martin
- Institute of Molecular Evolution, Heinrich Heine University, Düsseldorf, Germany
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Portugez S, Martin WF, Hazkani-Covo E. Mosaic mitochondrial-plastid insertions into the nuclear genome show evidence of both non-homologous end joining and homologous recombination. BMC Evol Biol 2018; 18:162. [PMID: 30390623 PMCID: PMC6215612 DOI: 10.1186/s12862-018-1279-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 10/18/2018] [Indexed: 02/06/2023] Open
Abstract
Background Mitochondrial and plastid DNA fragments are continuously transferred into eukaryotic nuclear genomes, giving rise to nuclear copies of mitochondrial DNA (numts) and nuclear copies of plastid DNA (nupts). Numts and nupts are classified as simple if they are composed of a single organelle fragment or as complex if they are composed of multiple fragments. Mosaic insertions are complex insertions composed of fragments of both mitochondrial and plastid DNA. Simple numts and nupts in eukaryotes have been extensively studied, their mechanism of insertion involves non-homologous end joining (NHEJ). Mosaic insertions have been less well-studied and their mechanisms of integration are unknown. Results Here we estimated the number of nuclear mosaic insertions (numins) in nine plant genomes. We show that numins compose up to 10% of the total nuclear insertions of organelle DNA in these plant genomes. The NHEJ hallmarks typical for numts and nupts were also identified in mosaic insertions. However, the number of identified insertions that integrated via NHEJ mechanism is underestimated, as NHEJ signatures are conserved only in recent insertions and mutationally eroded in older ones. A few complex insertions show signatures of long homology that cannot be attributed to NHEJ, a novel observation that implicates gene conversion or single strand annealing mechanisms in organelle nuclear insertions. Conclusions The common NHEJ signature that was identified here reveals that, in plant cells, mitochondria and plastid fragments in numins must meet during or prior to integration into the nuclear genome. Electronic supplementary material The online version of this article (10.1186/s12862-018-1279-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shir Portugez
- Department of Natural and Life Sciences, The Open University of Israel, Ra'anana, Israel.,School of Molecular Cell Biology & Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - William F Martin
- Institute of Molecular Evolution, Heinrich-Heine University, Düsseldorf, Germany
| | - Einat Hazkani-Covo
- Department of Natural and Life Sciences, The Open University of Israel, Ra'anana, Israel.
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48
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Abstract
Carbon dioxide enters metabolism via six known CO2 fixation pathways, of which only one is linear, exergonic in the direction of CO2‐assimilation, and present in both bacterial and archaeal anaerobes – the Wood‐Ljungdahl (WL) or reductive acetyl‐CoA pathway. Carbon monoxide (CO) plays a central role in the WL pathway as an energy rich intermediate. Here, we scan the major biochemical reaction databases for reactions involving CO and CO2. We identified 415 reactions corresponding to enzyme commission (EC) numbers involving CO2, which are non‐randomly distributed across different biochemical pathways. Their taxonomic distribution, reversibility under physiological conditions, cofactors and prosthetic groups are summarized. In contrast to CO2, only 15 reaction classes involving CO were detected. Closer inspection reveals that CO interfaces with metabolism and the carbon cycle at only two enzymes: anaerobic carbon monoxide dehydrogenase (CODH), a Ni‐ and Fe‐containing enzyme that generates CO for CO2 fixation in the WL pathway, and aerobic CODH, a Mo‐ and Cu‐containing enzyme that oxidizes environmental CO as an electron source. The CO‐dependent reaction of the WL pathway involves carbonyl insertion into a methyl carbon‐nickel at the Ni‐Fe‐S A‐cluster of acetyl‐CoA synthase (ACS). It appears that no alternative mechanisms to the CO‐dependent reaction of ACS have evolved in nearly 4 billion years, indicating an ancient and mechanistically essential role for CO at the onset of metabolism.
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Affiliation(s)
- Joana C Xavier
- Institut für Molekulare Evolution, Heinrich Heine Universität Düsseldorf, Germany
| | - Martina Preiner
- Institut für Molekulare Evolution, Heinrich Heine Universität Düsseldorf, Germany
| | - William F Martin
- Institut für Molekulare Evolution, Heinrich Heine Universität Düsseldorf, Germany.,Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
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49
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Barth C, Weiss MC, Roettger M, Martin WF, Unden G. Origin and phylogenetic relationships of [4Fe-4S]-containing O 2 sensors of bacteria. Environ Microbiol 2018; 20:4567-4586. [PMID: 30225854 DOI: 10.1111/1462-2920.14411] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 09/10/2018] [Indexed: 11/28/2022]
Abstract
The advent of environmental O2 about 2.5 billion years ago forced microbes to metabolically adapt and to develop mechanisms for O2 sensing. Sensing of O2 by [4Fe-4S]2+ to [2Fe-2S]2+ cluster conversion represents an ancient mechanism that is used by FNREc (Escherichia coli), FNRBs (Bacillus subtilis), NreBSa (Staphylococcus aureus) and WhiB3Mt (Mycobacterium tuberculosis). The phylogenetic relationship of these sensors was investigated. FNREc homologues are restricted to the proteobacteria and a few representatives from other phyla. Homologues of FNRBs and NreBSa are located within the bacilli, of WhiB3 within the actinobacteria. Archaea contain no homologues. The data reveal no similarity between the FNREc , FNRBs , NreBSa and WhiB3 sensor families on the sequence and structural levels. These O2 sensor families arose independently in phyla that were already present at the time O2 appeared, their members were subsequently distributed by lateral gene transfer. The chemistry of [4Fe-4S] and [2Fe-2S] cluster formation and interconversion appears to be shared by the sensor protein families. The type of signal output is, however, family specific. The homologues of FNREc and NreBSa vary with regard to the number of Cys residues that coordinate the cluster. It is suggested that the variants derive from lateral gene transfer and gained other functions.
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Affiliation(s)
- C Barth
- Microbiology and Wine Research, Institute for Molecular Physiology, Johannes Gutenberg University Mainz, Mainz, Germany
| | - M C Weiss
- Institute for Molecular Evolution, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany
| | - M Roettger
- Institute for Molecular Evolution, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany
| | - W F Martin
- Institute for Molecular Evolution, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany
| | - G Unden
- Microbiology and Wine Research, Institute for Molecular Physiology, Johannes Gutenberg University Mainz, Mainz, Germany
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50
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Gerlitz M, Knopp M, Kapust N, Xavier JC, Martin WF. Elusive data underlying debate at the prokaryote-eukaryote divide. Biol Direct 2018; 13:21. [PMID: 31196150 PMCID: PMC6888934 DOI: 10.1186/s13062-018-0221-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 08/16/2018] [Indexed: 12/11/2022] Open
Abstract
Background The origin of eukaryotic cells was an important transition in evolution. The factors underlying the origin and evolutionary success of the eukaryote lineage are still discussed. One camp argues that mitochondria were essential for eukaryote origin because of the unique configuration of internalized bioenergetic membranes that they conferred to the common ancestor of all known eukaryotic lineages. A recent paper by Lynch and Marinov concluded that mitochondria were energetically irrelevant to eukaryote origin, a conclusion based on analyses of previously published numbers of various molecules and ribosomes per cell and cell volumes as a presumed proxy for the role of mitochondria in evolution. Their numbers were purportedly extracted from the literature. Results We have examined the numbers upon which the recent study was based. We report that for a sample of 80 numbers that were purportedly extracted from the literature and that underlie key inferences of the recent study, more than 50% of the values do not exist in the cited papers to which the numbers are attributed. The published result cannot be independently reproduced. Other numbers that the recent study reports differ inexplicably from those in the literature to which they are ascribed. We list the discrepancies between the recently published numbers and the purported literature sources of those numbers in a head to head manner so that the discrepancies are readily evident, although the source of error underlying the discrepancies remains obscure. Conclusion The data purportedly supporting the view that mitochondria had no impact upon eukaryotic evolution data exhibits notable irregularities. The paper in question evokes the impression that the published numbers are of up to seven significant digit accuracy, when in fact more than half the numbers are nowhere to be found in the literature to which they are attributed. Though the reasons for the discrepancies are unknown, it is important to air these issues, lest the prominent paper in question become a point source of a snowballing error through the literature or become interpreted as a form of evidence that mitochondria were irrelevant to eukaryote evolution. Reviewers This article was reviewed by Eric Bapteste, Jianzhi Zhang and Martin Lercher.
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Affiliation(s)
- Marie Gerlitz
- Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, Universitätsstr. 1, 40225, Düsseldorf, Germany
| | - Michael Knopp
- Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, Universitätsstr. 1, 40225, Düsseldorf, Germany
| | - Nils Kapust
- Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, Universitätsstr. 1, 40225, Düsseldorf, Germany
| | - Joana C Xavier
- Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, Universitätsstr. 1, 40225, Düsseldorf, Germany
| | - William F Martin
- Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, Universitätsstr. 1, 40225, Düsseldorf, Germany.
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