1
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Cuevas-Zuviría B, Adam ZR, Goldman AD, Kaçar B. Informatic Capabilities of Translation and Its Implications for the Origins of Life. J Mol Evol 2023; 91:567-569. [PMID: 37526692 DOI: 10.1007/s00239-023-10125-0] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 06/22/2023] [Indexed: 08/02/2023]
Abstract
The ability to encode and convert heritable information into molecular function is a defining feature of life as we know it. The conversion of information into molecular function is performed by the translation process, in which triplets of nucleotides in a nucleic acid polymer (mRNA) encode specific amino acids in a protein polymer that folds into a three-dimensional structure. The folded protein then performs one or more molecular activities, often as one part of a complex and coordinated physiological network. Prebiotic systems, lacking the ability to explicitly translate information between genotype and phenotype, would have depended upon either chemosynthetic pathways to generate its components-constraining its complexity and evolvability- or on the ambivalence of RNA as both carrier of information and of catalytic functions-a possibility which is still supported by a very limited set of catalytic RNAs. Thus, the emergence of translation during early evolutionary history may have allowed life to unmoor from the setting of its origin. The origin of translation machinery also represents an entirely novel and distinct threshold of behavior for which there is no abiotic counterpart-it could be the only known example of computing that emerged naturally at the chemical level. Here we describe translation machinery's decoding system as the basis of cellular translation's information-processing capabilities, and the four operation types that find parallels in computer systems engineering that this biological machinery exhibits.
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Affiliation(s)
- Bruno Cuevas-Zuviría
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Madrid, Spain.
| | - Zachary R Adam
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Department of Geosciences, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Betül Kaçar
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
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2
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Goldman AD, Weber JM, LaRowe DE, Barge LM. Electron transport chains as a window into the earliest stages of evolution. Proc Natl Acad Sci U S A 2023; 120:e2210924120. [PMID: 37579147 PMCID: PMC10451490 DOI: 10.1073/pnas.2210924120] [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] [Indexed: 08/16/2023] Open
Abstract
The origin and early evolution of life is generally studied under two different paradigms: bottom up and top down. Prebiotic chemistry and early Earth geochemistry allow researchers to explore possible origin of life scenarios. But for these "bottom-up" approaches, even successful experiments only amount to a proof of principle. On the other hand, "top-down" research on early evolutionary history is able to provide a historical account about ancient organisms, but is unable to investigate stages that occurred during and just after the origin of life. Here, we consider ancient electron transport chains (ETCs) as a potential bridge between early evolutionary history and a protocellular stage that preceded it. Current phylogenetic evidence suggests that ancestors of several extant ETC components were present at least as late as the last universal common ancestor of life. In addition, recent experiments have shown that some aspects of modern ETCs can be replicated by minerals, protocells, or organic cofactors in the absence of biological proteins. Here, we discuss the diversity of ETCs and other forms of chemiosmotic energy conservation, describe current work on the early evolution of membrane bioenergetics, and advocate for several lines of research to enhance this understanding by pairing top-down and bottom-up approaches.
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Affiliation(s)
- Aaron D. Goldman
- Department of Biology, Oberlin College, Oberlin, OH44074
- Blue Marble Space Institute of Science, Seattle, WA98154
| | - Jessica M. Weber
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA91109
| | - Douglas E. LaRowe
- Department of Earth Sciences, University of Southern California, Los Angeles, CA90089
| | - Laura M. Barge
- Blue Marble Space Institute of Science, Seattle, WA98154
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA91109
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3
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Goldman AD. How did life become cellular? Proc Biol Sci 2023; 290:20222327. [PMID: 36750189 PMCID: PMC9904939 DOI: 10.1098/rspb.2022.2327] [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: 02/09/2023] Open
Affiliation(s)
- Aaron D. Goldman
- Department of Biology, Oberlin College, Oberlin, OH, USA,Blue Marble Space Institute of Science, Seattle, WA, USA
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4
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Abstract
The universal ancestor at the root of the species tree of life depicts a population of organisms with a surprising degree of complexity, posessing genomes and translation systems much like that of microbial life today. As the first life forms were most likely to have been simple replicators, considerable evolutionary change must have taken place prior to the last universal common ancestor. It is often assumed that the lack of earlier branches on the tree of life is due to a prevalence of random horizontal gene transfer that obscured the delineations between lineages and hindered their divergence. Therefore, principles of microbial evolution and ecology may give us some insight into these early stages in the history of life. Here, we synthesize the current understanding of organismal and genome evolution from the perspective of microbial ecology and apply these evolutionary principles to the earliest stages of life on Earth. We focus especially on broad evolutionary modes pertaining to horizontal gene transfer, pangenome structure, and microbial mat communities.
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Affiliation(s)
- Aaron D Goldman
- Department of Biology, Oberlin College and Conservatory, Oberlin, Ohio, USA
| | - Betül Kaçar
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
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5
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Krishnamurthy R, Goldman AD, Liberles DA, Rogers KL, Tor Y. Nucleobases in Meteorites to Nucleobases in RNA and DNA? J Mol Evol 2022; 90:328-331. [PMID: 35960316 DOI: 10.1007/s00239-022-10069-x] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 07/29/2022] [Indexed: 10/16/2022]
Abstract
Nucleic acids likely played a foundational role in the origin of life. However, the prebiotic chemistry of nucleoside and nucleotide synthesis has proved challenging on a number of fronts. The recent discovery of both pyrimidine and purine nucleobases in carbonaceous chondrite meteorites has garnered much attention from both the popular press and the scientific community. Here, we discuss these findings in the context of nucleoside/nucleotide prebiotic chemistry. We consider that the main challenge of prebiotic nucleoside synthesis, that of nucleosidic bond formation, is not addressed by the identification nucleobases in meteorites. We further discuss issues of selection that arise from the observation that such meteorites contain both canonical and non-canonical nucleobases. In sum, we argue that, despite the major analytical achievement of identifying and characterizing nucleobases in meteorites, this observation does little to advance our understanding of the prebiotic chemistry that could have led to the first genetic molecules that gave rise to us.
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Affiliation(s)
- Ramanarayanan Krishnamurthy
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA. .,NSF-NASA Center for Chemical Evolution, Atlanta, GA, USA.
| | - Aaron D Goldman
- Department of Biology, Oberlin College and Conservatory, Oberlin, OH, USA.,Blue Marble Space Institute of Science, Seattle, WA, USA
| | - David A Liberles
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, USA
| | - Karyn L Rogers
- Department of Earth and Environmental Sciences and Rensselaer Astrobiology Research and Education Center, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, CA, USA
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6
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Crapitto AJ, Campbell A, Harris AJ, Goldman AD. A consensus view of the proteome of the last universal common ancestor. Ecol Evol 2022; 12:e8930. [PMID: 35784055 PMCID: PMC9165204 DOI: 10.1002/ece3.8930] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 01/29/2022] [Revised: 04/11/2022] [Accepted: 04/14/2022] [Indexed: 12/30/2022] Open
Abstract
The availability of genomic and proteomic data from across the tree of life has made it possible to infer features of the genome and proteome of the last universal common ancestor (LUCA). A number of studies have done so, all using a unique set of methods and bioinformatics databases. Here, we compare predictions across eight such studies and measure both their agreement with one another and with the consensus predictions among them. We find that some LUCA genome studies show a strong agreement with the consensus predictions of the others, but that no individual study shares a high or even moderate degree of similarity with any other individual study. From these observations, we conclude that the consensus among studies provides a more accurate depiction of the core proteome of the LUCA and its functional repertoire. The set of consensus LUCA protein family predictions between all of these studies portrays a LUCA genome that, at minimum, encoded functions related to protein synthesis, amino acid metabolism, nucleotide metabolism, and the use of common, nucleotide‐derived organic cofactors.
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Affiliation(s)
| | - Amy Campbell
- Perelman School of Medicine University of Pennsylvania Philadelphia Pennsylvania USA
| | - AJ Harris
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization South China Botanical Garden Chinese Academy of Sciences Guangzhou China
| | - Aaron D. Goldman
- Department of Biology Oberlin College Oberlin Ohio USA
- Blue Marble Space Institute of Science Seattle Washington USA
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7
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Weber JM, Henderson BL, LaRowe DE, Goldman AD, Perl SM, Billings K, Barge LM. Testing Abiotic Reduction of NAD + Directly Mediated by Iron/Sulfur Minerals. Astrobiology 2022; 22:25-34. [PMID: 34591607 DOI: 10.1089/ast.2021.0035] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Life emerged in a geochemical context, possibly in the midst of mineral substrates. However, it is not known to what extent minerals and dissolved inorganic ions could have facilitated the evolution of biochemical reactions. Herein, we have experimentally shown that iron sulfide minerals can act as electron transfer agents for the reduction of the ubiquitous biological protein cofactor nicotinamide adenine dinucleotide (NAD+) under anaerobic prebiotic conditions, observing the NAD+/NADH redox transition by using ultraviolet-visible spectroscopy and 1H nuclear magnetic resonance. This reaction was mediated with iron sulfide minerals, which were likely abundant on early Earth in seafloor and hydrothermal settings; and the NAD+/NADH redox reaction occurred in the absence of UV light, peptide ligand(s), or dissolved mediators. To better understand this reaction, thermodynamic modeling was also performed. The ability of an iron sulfide mineral to transfer electrons to a biochemical cofactor that is found in every living cell demonstrates how geologic materials could have played a direct role in the evolution of certain cofactor-driven metabolic pathways.
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Affiliation(s)
- Jessica M Weber
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Bryana L Henderson
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Douglas E LaRowe
- Department of Earth Sciences, University of Southern California, Los Angeles, California, USA
| | - Aaron D Goldman
- Blue Marble Space Institute of Science, Seattle, Washington, United States of America
- Department of Biology, Oberlin College, Oberlin, Ohio, USA
| | - Scott M Perl
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Keith Billings
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Laura M Barge
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
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8
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Affiliation(s)
- Aaron D Goldman
- Department of Biology, Oberlin College and Conservatory, Oberlin, OH, 44074, USA.
- Blue Marble Space Institute of Science, Seattle, WA, 98154, USA.
| | - David A Liberles
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, 19122, USA.
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9
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Abstract
The RNA World is one of the most widely accepted hypotheses explaining the origin of the genetic system used by all organisms today. It proposes that the tripartite system of DNA, RNA, and proteins was preceded by one consisting solely of RNA, which both stored genetic information and performed the molecular functions encoded by that genetic information. Current research into a potential RNA World revolves around the catalytic properties of RNA-based enzymes, or ribozymes. Well before the discovery of ribozymes, Harold White proposed that evidence for a precursor RNA world could be found within modern proteins in the form of coenzymes, the majority of which contain nucleobases or nucleoside moieties, such as Coenzyme A and S-adenosyl methionine, or are themselves nucleotides, such as ATP and NADH (a dinucleotide). These coenzymes, White suggested, had been the catalytic active sites of ancient ribozymes, which transitioned to their current forms after the surrounding ribozyme scaffolds had been replaced by protein apoenzymes during the evolution of translation. Since its proposal four decades ago, this groundbreaking hypothesis has garnered support from several different research disciplines and motivated similar hypotheses about other classes of cofactors, most notably iron-sulfur cluster cofactors as remnants of the geochemical setting of the origin of life. Evidence from prebiotic geochemistry, ribozyme biochemistry, and evolutionary biology, increasingly supports these hypotheses. Certain coenzymes and cofactors may bridge modern biology with the past and can thus provide insights into the elusive and poorly-recorded period of the origin and early evolution of life.
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Affiliation(s)
- Aaron D Goldman
- Department of Biology, Oberlin College and Conservatory, Oberlin, OH, 44074, USA. .,Blue Marble Space Institute of Science, Seattle, WA, 98154, USA.
| | - Betul Kacar
- Blue Marble Space Institute of Science, Seattle, WA, 98154, USA. .,Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, 85721, USA. .,Lunar and Planetary Laboratory and Department of Astronomy, University of Arizona, Tucson, AZ, 85721, USA. .,Earth-Life Science Institute, Tokyo Institute of Technology, Meguro, Tokyo, 152-8550, Japan.
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10
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Takagi YA, Nguyen DH, Wexler TB, Goldman AD. The Coevolution of Cellularity and Metabolism Following the Origin of Life. J Mol Evol 2020; 88:598-617. [PMID: 32809045 PMCID: PMC7445158 DOI: 10.1007/s00239-020-09961-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 01/31/2020] [Accepted: 07/27/2020] [Indexed: 01/09/2023]
Abstract
The emergence of cellular organisms occurred sometime between the origin of life and the evolution of the last universal common ancestor and represents one of the major transitions in evolutionary history. Here we describe a series of artificial life simulations that reveal a close relationship between the evolution of cellularity, the evolution of metabolism, and the richness of the environment. When environments are rich in processing energy, a resource that the digital organisms require to both process their genomes and replicate, populations evolve toward a state of non-cellularity. But when processing energy is not readily available in the environment and organisms must produce their own processing energy from food puzzles, populations always evolve both a proficient metabolism and a high level of cellular impermeability. Even between these two environmental extremes, the population-averaged values of cellular impermeability and metabolic proficiency exhibit a very strong correlation with one another. Further investigations show that non-cellularity is selectively advantageous when environmental processing energy is abundant because it allows organisms to access the available energy, while cellularity is selectively advantageous when environmental processing energy is scarce because it affords organisms the genetic fidelity required to incrementally evolve efficient metabolisms. The selection pressures favoring either non-cellularity or cellularity can be reversed when the environment transitions from one of abundant processing energy to one of scarce processing energy. These results have important implications for when and why cellular organisms evolved following the origin of life.
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Affiliation(s)
- Yuta A Takagi
- Department of Biology, Oberlin College, Oberlin, OH, 44074, USA
| | - Diep H Nguyen
- Department of Biology, Oberlin College, Oberlin, OH, 44074, USA.,Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Tom B Wexler
- Department of Computer Science, Oberlin College, Oberlin, OH, 44074, USA.,Verily Life Sciences, Cambridge, MA, USA
| | - Aaron D Goldman
- Department of Biology, Oberlin College, Oberlin, OH, 44074, USA. .,Blue Marble Space Institute of Science, Seattle, WA, 98154, USA.
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11
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Maltais TR, VanderVelde D, LaRowe DE, Goldman AD, Barge LM. Reactivity of Metabolic Intermediates and Cofactor Stability under Model Early Earth Conditions. ORIGINS LIFE EVOL B 2020; 50:35-55. [PMID: 31981046 DOI: 10.1007/s11084-019-09590-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 12/30/2019] [Indexed: 01/24/2023]
Abstract
Understanding the emergence of metabolic pathways is key to unraveling the factors that promoted the origin of life. One popular view is that protein cofactors acted as catalysts prior to the evolution of the protein enzymes with which they are now associated. We investigated the stability of acetyl coenzyme A (Acetyl Co-A, the group transfer cofactor in citric acid synthesis in the TCA cycle) under early Earth conditions, as well as whether Acetyl Co-A or its small molecule analogs thioacetate or acetate can catalyze the transfer of an acetyl group onto oxaloacetate in the absence of the citrate synthase enzyme. Several different temperatures, pH ranges, and compositions of aqueous environments were tested to simulate the Earth's early ocean and its possible components; the effect of these variables on oxaloacetate and cofactor chemistry were assessed under ambient and anoxic conditions. The cofactors tested are chemically stable under early Earth conditions, but none of the three compounds (Acetyl Co-A, thioacetate, or acetate) promoted synthesis of citric acid from oxaloacetate under the conditions tested. Oxaloacetate reacted with itself and/or decomposed to form a sequence of other products under ambient conditions, and under anoxic conditions was more stable; under ambient conditions the specific chemical pathways observed depended on the environmental conditions such as pH and presence/absence of bicarbonate or salt ions in early Earth ocean simulants. This work demonstrates the stability of these metabolic intermediates under anoxic conditions. However, even though free cofactors may be stable in a geological environmental setting, an enzyme or other mechanism to promote reaction specificity would likely be necessary for at least this particular reaction to proceed.
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Affiliation(s)
- Thora R Maltais
- NASA Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, CA, 91109, USA
| | - David VanderVelde
- Department of Chemistry, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA, 91125, USA
| | - Douglas E LaRowe
- Department of Earth Sciences, University of Southern California, 3651 Trousdale Pkwy, Los Angeles, CA, 90089, USA
| | - Aaron D Goldman
- Department of Biology, Oberlin College, Science Center K123 119 Woodland St., Oberlin, OH, 44074, USA.,Blue Marble Space Institute for Science, Seattle, Washington, 98154, USA
| | - Laura M Barge
- NASA Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, CA, 91109, USA.
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12
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Domagal-Goldman SD, Wright KE, Adamala K, Arina de la Rubia L, Bond J, Dartnell LR, Goldman AD, Lynch K, Naud ME, Paulino-Lima IG, Singer K, Walther-Antonio M, Abrevaya XC, Anderson R, Arney G, Atri D, Azúa-Bustos A, Bowman JS, Brazelton WJ, Brennecka GA, Carns R, Chopra A, Colangelo-Lillis J, Crockett CJ, DeMarines J, Frank EA, Frantz C, de la Fuente E, Galante D, Glass J, Gleeson D, Glein CR, Goldblatt C, Horak R, Horodyskyj L, Kaçar B, Kereszturi A, Knowles E, Mayeur P, McGlynn S, Miguel Y, Montgomery M, Neish C, Noack L, Rugheimer S, Stüeken EE, Tamez-Hidalgo P, Imari Walker S, Wong T. The Astrobiology Primer v2.0. Astrobiology 2016; 16:561-653. [PMID: 27532777 PMCID: PMC5008114 DOI: 10.1089/ast.2015.1460] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 06/06/2016] [Indexed: 05/09/2023]
Affiliation(s)
- Shawn D Domagal-Goldman
- 1 NASA Goddard Space Flight Center , Greenbelt, Maryland, USA
- 2 Virtual Planetary Laboratory , Seattle, Washington, USA
| | - Katherine E Wright
- 3 University of Colorado at Boulder , Colorado, USA
- 4 Present address: UK Space Agency, UK
| | - Katarzyna Adamala
- 5 Department of Genetics, Cell Biology and Development, University of Minnesota , Minneapolis, Minnesota, USA
| | | | - Jade Bond
- 7 Department of Physics, University of New South Wales , Sydney, Australia
| | | | | | - Kennda Lynch
- 10 Division of Biological Sciences, University of Montana , Missoula, Montana, USA
| | - Marie-Eve Naud
- 11 Institute for research on exoplanets (iREx) , Université de Montréal, Montréal, Canada
| | - Ivan G Paulino-Lima
- 12 Universities Space Research Association , Mountain View, California, USA
- 13 Blue Marble Space Institute of Science , Seattle, Washington, USA
| | - Kelsi Singer
- 14 Southwest Research Institute , Boulder, Colorado, USA
| | | | - Ximena C Abrevaya
- 16 Instituto de Astronomía y Física del Espacio (IAFE) , UBA-CONICET, Ciudad Autónoma de Buenos Aires, Argentina
| | - Rika Anderson
- 17 Department of Biology, Carleton College , Northfield, Minnesota, USA
| | - Giada Arney
- 18 University of Washington Astronomy Department and Astrobiology Program , Seattle, Washington, USA
| | - Dimitra Atri
- 13 Blue Marble Space Institute of Science , Seattle, Washington, USA
| | | | - Jeff S Bowman
- 19 Lamont-Doherty Earth Observatory, Columbia University , Palisades, New York, USA
| | | | | | - Regina Carns
- 22 Polar Science Center, Applied Physics Laboratory, University of Washington , Seattle, Washington, USA
| | - Aditya Chopra
- 23 Planetary Science Institute, Research School of Earth Sciences, Research School of Astronomy and Astrophysics, The Australian National University , Canberra, Australia
| | - Jesse Colangelo-Lillis
- 24 Earth and Planetary Science, McGill University , and the McGill Space Institute, Montréal, Canada
| | | | - Julia DeMarines
- 13 Blue Marble Space Institute of Science , Seattle, Washington, USA
| | | | - Carie Frantz
- 27 Department of Geosciences, Weber State University , Ogden, Utah, USA
| | - Eduardo de la Fuente
- 28 IAM-Departamento de Fisica, CUCEI , Universidad de Guadalajara, Guadalajara, México
| | - Douglas Galante
- 29 Brazilian Synchrotron Light Laboratory , Campinas, Brazil
| | - Jennifer Glass
- 30 School of Earth and Atmospheric Sciences, Georgia Institute of Technology , Atlanta, Georgia , USA
| | | | | | - Colin Goldblatt
- 33 School of Earth and Ocean Sciences, University of Victoria , Victoria, Canada
| | - Rachel Horak
- 34 American Society for Microbiology , Washington, DC, USA
| | | | - Betül Kaçar
- 36 Harvard University , Organismic and Evolutionary Biology, Cambridge, Massachusetts, USA
| | - Akos Kereszturi
- 37 Research Centre for Astronomy and Earth Sciences , Hungarian Academy of Sciences, Budapest, Hungary
| | - Emily Knowles
- 38 Johnson & Wales University , Denver, Colorado, USA
| | - Paul Mayeur
- 39 Rensselaer Polytechnic Institute , Troy, New York, USA
| | - Shawn McGlynn
- 40 Earth Life Science Institute, Tokyo Institute of Technology , Tokyo, Japan
| | - Yamila Miguel
- 41 Laboratoire Lagrange, UMR 7293, Université Nice Sophia Antipolis , CNRS, Observatoire de la Côte d'Azur, Nice, France
| | | | - Catherine Neish
- 43 Department of Earth Sciences, The University of Western Ontario , London, Canada
| | - Lena Noack
- 44 Royal Observatory of Belgium , Brussels, Belgium
| | - Sarah Rugheimer
- 45 Department of Astronomy, Harvard University , Cambridge, Massachusetts, USA
- 46 University of St. Andrews , St. Andrews, UK
| | - Eva E Stüeken
- 47 University of Washington , Seattle, Washington, USA
- 48 University of California , Riverside, California, USA
| | | | - Sara Imari Walker
- 13 Blue Marble Space Institute of Science , Seattle, Washington, USA
- 50 School of Earth and Space Exploration and Beyond Center for Fundamental Concepts in Science, Arizona State University , Tempe, Arizona, USA
| | - Teresa Wong
- 51 Department of Earth and Planetary Sciences, Washington University in St. Louis , St. Louis, Missouri, USA
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13
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Stüeken EE, Anderson RE, Bowman JS, Brazelton WJ, Colangelo-Lillis J, Goldman AD, Som SM, Baross JA. Did life originate from a global chemical reactor? Geobiology 2013; 11:101-126. [PMID: 23331348 DOI: 10.1111/gbi.12025] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2012] [Accepted: 12/03/2012] [Indexed: 06/01/2023]
Abstract
Many decades of experimental and theoretical research on the origin of life have yielded important discoveries regarding the chemical and physical conditions under which organic compounds can be synthesized and polymerized. However, such conditions often seem mutually exclusive, because they are rarely encountered in a single environmental setting. As such, no convincing models explain how living cells formed from abiotic constituents. Here, we propose a new approach that considers the origin of life within the global context of the Hadean Earth. We review previous ideas and synthesize them in four central hypotheses: (i) Multiple microenvironments contributed to the building blocks of life, and these niches were not necessarily inhabitable by the first organisms; (ii) Mineral catalysts were the backbone of prebiotic reaction networks that led to modern metabolism; (iii) Multiple local and global transport processes were essential for linking reactions occurring in separate locations; (iv) Global diversity and local selection of reactants and products provided mechanisms for the generation of most of the diverse building blocks necessary for life. We conclude that no single environmental setting can offer enough chemical and physical diversity for life to originate. Instead, any plausible model for the origin of life must acknowledge the geological complexity and diversity of the Hadean Earth. Future research may therefore benefit from identifying further linkages between organic precursors, minerals, and fluids in various environmental contexts.
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Affiliation(s)
- E E Stüeken
- Department of Earth and Space Sciences, University of Washington, Seattle, WA, USA.
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14
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Swart EC, Bracht JR, Magrini V, Minx P, Chen X, Zhou Y, Khurana JS, Goldman AD, Nowacki M, Schotanus K, Jung S, Fulton RS, Ly A, McGrath S, Haub K, Wiggins JL, Storton D, Matese JC, Parsons L, Chang WJ, Bowen MS, Stover NA, Jones TA, Eddy SR, Herrick GA, Doak TG, Wilson RK, Mardis ER, Landweber LF. The Oxytricha trifallax macronuclear genome: a complex eukaryotic genome with 16,000 tiny chromosomes. PLoS Biol 2013; 11:e1001473. [PMID: 23382650 PMCID: PMC3558436 DOI: 10.1371/journal.pbio.1001473] [Citation(s) in RCA: 157] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 12/12/2012] [Indexed: 01/03/2023] Open
Abstract
With more chromosomes than any other sequenced genome, the macronuclear genome of Oxytricha trifallax has a unique and complex architecture, including alternative fragmentation and predominantly single-gene chromosomes. The macronuclear genome of the ciliate Oxytricha trifallax displays an extreme and unique eukaryotic genome architecture with extensive genomic variation. During sexual genome development, the expressed, somatic macronuclear genome is whittled down to the genic portion of a small fraction (∼5%) of its precursor “silent” germline micronuclear genome by a process of “unscrambling” and fragmentation. The tiny macronuclear “nanochromosomes” typically encode single, protein-coding genes (a small portion, 10%, encode 2–8 genes), have minimal noncoding regions, and are differentially amplified to an average of ∼2,000 copies. We report the high-quality genome assembly of ∼16,000 complete nanochromosomes (∼50 Mb haploid genome size) that vary from 469 bp to 66 kb long (mean ∼3.2 kb) and encode ∼18,500 genes. Alternative DNA fragmentation processes ∼10% of the nanochromosomes into multiple isoforms that usually encode complete genes. Nucleotide diversity in the macronucleus is very high (SNP heterozygosity is ∼4.0%), suggesting that Oxytricha trifallax may have one of the largest known effective population sizes of eukaryotes. Comparison to other ciliates with nonscrambled genomes and long macronuclear chromosomes (on the order of 100 kb) suggests several candidate proteins that could be involved in genome rearrangement, including domesticated MULE and IS1595-like DDE transposases. The assembly of the highly fragmented Oxytricha macronuclear genome is the first completed genome with such an unusual architecture. This genome sequence provides tantalizing glimpses into novel molecular biology and evolution. For example, Oxytricha maintains tens of millions of telomeres per cell and has also evolved an intriguing expansion of telomere end-binding proteins. In conjunction with the micronuclear genome in progress, the O. trifallax macronuclear genome will provide an invaluable resource for investigating programmed genome rearrangements, complementing studies of rearrangements arising during evolution and disease. The macronuclear genome of the ciliate Oxytricha trifallax, contained in its somatic nucleus, has a unique genome architecture. Unlike its diploid germline genome, which is transcriptionally inactive during normal cellular growth, the macronuclear genome is fragmented into at least 16,000 tiny (∼3.2 kb mean length) chromosomes, most of which encode single actively transcribed genes and are differentially amplified to a few thousand copies each. The smallest chromosome is just 469 bp, while the largest is 66 kb and encodes a single enormous protein. We found considerable variation in the genome, including frequent alternative fragmentation patterns, generating chromosome isoforms with shared sequence. We also found limited variation in chromosome amplification levels, though insufficient to explain mRNA transcript level variation. Another remarkable feature of Oxytricha's macronuclear genome is its inordinate fondness for telomeres. In conjunction with its possession of tens of millions of chromosome-ending telomeres per macronucleus, we show that Oxytricha has evolved multiple putative telomere-binding proteins. In addition, we identified two new domesticated transposase-like protein classes that we propose may participate in the process of genome rearrangement. The macronuclear genome now provides a crucial resource for ongoing studies of genome rearrangement processes that use Oxytricha as an experimental or comparative model.
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Affiliation(s)
- Estienne C. Swart
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
| | - John R. Bracht
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Vincent Magrini
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Patrick Minx
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Xiao Chen
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Yi Zhou
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Jaspreet S. Khurana
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Aaron D. Goldman
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Mariusz Nowacki
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Klaas Schotanus
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Seolkyoung Jung
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
| | - Robert S. Fulton
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Amy Ly
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Sean McGrath
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Kevin Haub
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Jessica L. Wiggins
- Sequencing Core Facility, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Donna Storton
- Sequencing Core Facility, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - John C. Matese
- Sequencing Core Facility, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Lance Parsons
- Bioinformatics Group, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Wei-Jen Chang
- Department of Biology, Hamilton College, Clinton, New York, United States of America
| | - Michael S. Bowen
- Biology Department, Bradley University, Peoria, Illinois, United States of America
| | - Nicholas A. Stover
- Biology Department, Bradley University, Peoria, Illinois, United States of America
| | - Thomas A. Jones
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
| | - Sean R. Eddy
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
| | - Glenn A. Herrick
- Biology Department, University of Utah, Salt Lake City, Utah, United States of America
| | - Thomas G. Doak
- Department of Biology, University of Indiana, Bloomington, Indiana, United States of America
| | - Richard K. Wilson
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Elaine R. Mardis
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Laura F. Landweber
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
- * E-mail:
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15
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Goldman AD, Samudrala R, Baross JA. The evolution and functional repertoire of translation proteins following the origin of life. Biol Direct 2010; 5:15. [PMID: 20377891 PMCID: PMC2873265 DOI: 10.1186/1745-6150-5-15] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [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: 03/24/2010] [Accepted: 04/08/2010] [Indexed: 11/11/2022] Open
Abstract
Background The RNA world hypothesis posits that the earliest genetic system consisted of informational RNA molecules that directed the synthesis of modestly functional RNA molecules. Further evidence suggests that it was within this RNA-based genetic system that life developed the ability to synthesize proteins by translating genetic code. Here we investigate the early development of the translation system through an evolutionary survey of protein architectures associated with modern translation. Results Our analysis reveals a structural expansion of translation proteins immediately following the RNA world and well before the establishment of the DNA genome. Subsequent functional annotation shows that representatives of the ten most ancestral protein architectures are responsible for all of the core protein functions found in modern translation. Conclusions We propose that this early robust translation system evolved by virtue of a positive feedback cycle in which the system was able to create increasingly complex proteins to further enhance its own function. Reviewers This article was reviewed by Janet Siefert, George Fox, and Antonio Lazcano (nominated by Laura Landweber)
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Affiliation(s)
- Aaron D Goldman
- Department of Microbiology, University of Washington, Box 357242, Seattle, WA 98195, USA.
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16
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Borlee BR, Goldman AD, Murakami K, Samudrala R, Wozniak DJ, Parsek MR. Pseudomonas aeruginosa uses a cyclic-di-GMP-regulated adhesin to reinforce the biofilm extracellular matrix. Mol Microbiol 2010; 75:827-42. [PMID: 20088866 PMCID: PMC2847200 DOI: 10.1111/j.1365-2958.2009.06991.x] [Citation(s) in RCA: 350] [Impact Index Per Article: 25.0] [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] [Indexed: 11/30/2022]
Abstract
Pseudomonas aeruginosa, the principal pathogen of cystic fibrosis patients, forms antibiotic-resistant biofilms promoting chronic colonization of the airways. The extracellular (EPS) matrix is a crucial component of biofilms that provides the community multiple benefits. Recent work suggests that the secondary messenger, cyclic-di-GMP, promotes biofilm formation. An analysis of factors specifically expressed in P. aeruginosa under conditions of elevated c-di-GMP, revealed functions involved in the production and maintenance of the biofilm extracellular matrix. We have characterized one of these components, encoded by the PA4625 gene, as a putative adhesin and designated it cdrA. CdrA shares structural similarities to extracellular adhesins that belong to two-partner secretion systems. The cdrA gene is in a two gene operon that also encodes a putative outer membrane transporter, CdrB. The cdrA gene encodes a 220 KDa protein that is predicted to be rod-shaped protein harbouring a β-helix structural motif. Western analysis indicates that the CdrA is produced as a 220 kDa proprotein and processed to 150 kDa before secretion into the extracellular medium. We demonstrated that cdrAB expression is minimal in liquid culture, but is elevated in biofilm cultures. CdrAB expression was found to promote biofilm formation and auto-aggregation in liquid culture. Aggregation mediated by CdrA is dependent on the Psl polysaccharide and can be disrupted by adding mannose, a key structural component of Psl. Immunoprecipitation of Psl present in culture supernatants resulted in co-immunoprecipitation of CdrA, providing additional evidence that CdrA directly binds to Psl. A mutation in cdrA caused a decrease in biofilm biomass and resulted in the formation of biofilms exhibiting decreased structural integrity. Psl-specific lectin staining suggests that CdrA either cross-links Psl polysaccharide polymers and/or tethers Psl to the cells, resulting in increased biofilm structural stability. Thus, this study identifies a key protein structural component of the P. aeruginosa EPS matrix.
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Affiliation(s)
- Bradley R Borlee
- Department of Microbiology, University of Washington, Box 357242, Seattle, WA 98195-7242, USA
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17
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Goldman AD, Leigh JA, Samudrala R. Comprehensive computational analysis of Hmd enzymes and paralogs in methanogenic Archaea. BMC Evol Biol 2009; 9:199. [PMID: 19671178 PMCID: PMC2739858 DOI: 10.1186/1471-2148-9-199] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [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: 11/24/2008] [Accepted: 08/11/2009] [Indexed: 11/29/2022] Open
Abstract
Background Methanogenesis is the sole means of energy production in methanogenic Archaea. H2-forming methylenetetrahydromethanopterin dehydrogenase (Hmd) catalyzes a step in the hydrogenotrophic methanogenesis pathway in class I methanogens. At least one hmd paralog has been identified in nine of the eleven complete genome sequences of class I hydrogenotrophic methanogens. The products of these paralog genes have thus far eluded any detailed functional characterization. Results Here we present a thorough computational analysis of Hmd enzymes and paralogs that includes state of the art phylogenetic inference, structure prediction, and functional site prediction techniques. We determine that the Hmd enzymes are phylogenetically distinct from Hmd paralogs but share a common overall structure. We predict that the active site of the Hmd enzyme is conserved as a functional site in Hmd paralogs and use this observation to propose possible molecular functions of the paralog that are consistent with previous experimental evidence. We also identify an uncharacterized site in the N-terminal domains of both proteins that is predicted by our methods to directly impart function. Conclusion This study contributes to our understanding of the evolutionary history, structural conservation, and functional roles, of the Hmd enzymes and paralogs. The results of our phylogenetic and structural analysis constitute datasets that will aid in the future study of the Hmd protein family. Our functional site predictions generate several testable hypotheses that will guide further experimental characterization of the Hmd paralog. This work also represents a novel approach to protein function prediction in which multiple computational methods are integrated to achieve a detailed characterization of proteins that are not well understood.
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Affiliation(s)
- Aaron D Goldman
- Department of Microbiology, University of Washington, Seattle, WA, USA.
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18
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Kramer BC, Goldman AD, Mytilineou C. Glial cell line derived neurotrophic factor promotes the recovery of dopamine neurons damaged by 6-hydroxydopamine in vitro. Brain Res 1999; 851:221-7. [PMID: 10642847 DOI: 10.1016/s0006-8993(99)02191-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Glial cell line derived neurotrophic factor (GDNF) has been shown to be a potent neurotrophic factor for dopamine neurons in culture and to prevent the loss of substantia nigra dopamine neurons following in vivo lesions with 6-hydroxydopamine (6-OHDA). In this study we used mesencephalic cultures containing both neurons and glia to examine whether GDNF protects dopamine neurons from 6-OHDA toxicity in vitro. Our data show that GDNF does not prevent the loss of dopamine neurons caused by treatment with 6-OHDA in vitro. However, continuous exposure to GDNF increases the high affinity dopamine uptake in cultures treated with 6-OHDA, suggesting that it enhances the growth of damaged dopamine neurons. We also show that in vitro treatment with 6-OHDA causes widespread cell death in mesencephalic cultures, which is not restricted to dopamine neurons. The lack of selectivity of 6-OHDA toxicity when applied in vitro may explain the inability of GDNF to prevent the loss of dopamine neurons in mesencephalic cultures. The stimulation of the growth of 6-OHDA damaged dopamine neurons by GDNF, observed in our study, suggests that it may prove beneficial in the treatment of injured dopamine neurons.
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Affiliation(s)
- B C Kramer
- Fishberg Center for Neurobiology, Mount Sinai School of Medicine, New York, NY 10029, USA
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Taylor JV, Roh L, Goldman AD. Metropolitan Forensic Anthropology Team (MFAT) case studies in identification: 2. Identification of a Vietnamese trophy skull. J Forensic Sci 1984; 29:1253-9. [PMID: 6502122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
A Vietnamese trophy skull, apparently a victim of the Vietnam war, was recently received for analysis in a New York State homicide case. The skull, which is well preserved except for the missing mandible and maxillary dentition, is compared to trophy skulls of Japanese military personnel, also brought back to the United States by American soldiers following wartime duty in Asia.
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Taylor JV, DiBennardo R, Linares GH, Goldman AD, DeForest PR. Metropolitan Forensic Anthropology Team (MFAT) studies in identification: 1. Race and sex assessment by discriminant function analysis of the postcranial skeleton. J Forensic Sci 1984; 29:798-805. [PMID: 6747580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
A case study is presented to demonstrate the utility of the team approach to the identification of human remains, and to illustrate a methodological innovation developed by MFAT. Case 1 represents the first of several planned case studies, each designed to present new methodological solutions to standard problems in identification. The present case describes a test, by application, of race and sex assessment of the postcranial skeleton by discriminant function analysis.
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