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Lyons TW, Tino CJ, Fournier GP, Anderson RE, Leavitt WD, Konhauser KO, Stüeken EE. Co-evolution of early Earth environments and microbial life. Nat Rev Microbiol 2024; 22:572-586. [PMID: 38811839 DOI: 10.1038/s41579-024-01044-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2024] [Indexed: 05/31/2024]
Abstract
Two records of Earth history capture the evolution of life and its co-evolving ecosystems with interpretable fidelity: the geobiological and geochemical traces preserved in rocks and the evolutionary histories captured within genomes. The earliest vestiges of life are recognized mostly in isotopic fingerprints of specific microbial metabolisms, whereas fossils and organic biomarkers become important later. Molecular biology provides lineages that can be overlayed on geologic and geochemical records of evolving life. All these data lie within a framework of biospheric evolution that is primarily characterized by the transition from an oxygen-poor to an oxygen-rich world. In this Review, we explore the history of microbial life on Earth and the degree to which it shaped, and was shaped by, fundamental transitions in the chemical properties of the oceans, continents and atmosphere. We examine the diversity and evolution of early metabolic processes, their couplings with biogeochemical cycles and their links to the oxygenation of the early biosphere. We discuss the distinction between the beginnings of metabolisms and their subsequent proliferation and their capacity to shape surface environments on a planetary scale. The evolution of microbial life and its ecological impacts directly mirror the Earth's chemical and physical evolution through cause-and-effect relationships.
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Affiliation(s)
- Timothy W Lyons
- Department of Earth and Planetary Sciences, University of California, Riverside, CA, USA.
- Virtual Planetary Laboratory, University of Washington, Seattle, WA, USA.
| | - Christopher J Tino
- Department of Earth and Planetary Sciences, University of California, Riverside, CA, USA.
| | - Gregory P Fournier
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Rika E Anderson
- Virtual Planetary Laboratory, University of Washington, Seattle, WA, USA
- Biology Department, Carleton College, Northfield, MN, USA
| | - William D Leavitt
- Department of Earth Sciences, Dartmouth College, Hanover, NH, USA
- Department of Chemistry, Dartmouth College, Hanover, NH, USA
| | - Kurt O Konhauser
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Eva E Stüeken
- Virtual Planetary Laboratory, University of Washington, Seattle, WA, USA
- School of Earth and Environmental Sciences, University of St Andrews, St Andrews, UK
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2
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Ribeiro GC, Mogollón-García HD, Moraes ACID, Dias GS, Viana GDB, Milbradt EL, Andreatti-Filho RL, Okamoto AS. Research Note: The effects of a Lactobacillus helveticus ATCC 15009-derived postbiotic mitigating Salmonella Gallinarum colonization in commercial layer chicks. Poult Sci 2023; 102:103095. [PMID: 37832187 PMCID: PMC10568553 DOI: 10.1016/j.psj.2023.103095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/28/2023] [Accepted: 09/05/2023] [Indexed: 10/15/2023] Open
Abstract
This study aimed to assess the effects of a Lactobacillus helveticus ATCC 15009-derived postbiotic in mitigating experimental Salmonella Gallinarum infection. For this purpose, a sample of Lactobacillus sp. was inoculated in 2 different media, each containing different postbiotics (sensitized and nonsensitized). Both inocula had their antagonistic effect over S. Gallinarum tested through the spot-on-the-lawn method. It revealed that the sensitized postbiotic had a higher action potential over Lactobacillus sp. than the nonsensitized one (P < 0.05). Then, 48 day of hatch chicks were divided into 4 groups: A = Lactobacillus sp. (109 CFU/mL) inoculum on the 18th day; B = Lactobacillus sp. (109 CFU/mL) inoculum on the 18th day and postbiotic inoculum on the 19th day; C = postbiotic inoculum on the 19th day; and D = sterile saline inoculum on 18th and 19th days. On the 21st day, all chicks were infected with S. Gallinarum (109 CFU/mL). On the 23rd day, the animals were euthanized by cervical dislocation, and the ceca and liver were aseptically removed. Bacterial count of S. Gallinarum with serial decimal dilution was performed with these organs. It revealed that the prophylactic treatment with the postbiotic that modulates the intestinal microbiota was as efficient as the probiotic administration in reducing S. Gallinarum in the cecum and liver of chicks (P < 0.05). These data point to a new range of alternatives for preventing S. Gallinarum, which might help the poultry industry produce safer food for human consumption.
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Affiliation(s)
- Gabriella Costa Ribeiro
- Veterinary Clinic Department, School of Veterinary Medicine and Animal Science of the São Paulo State University (FMVZ/ UNESP), Botucatu, São Paulo, Brazil.
| | | | - Ana Carolina Izidoro de Moraes
- Veterinary Clinic Department, School of Veterinary Medicine and Animal Science of the São Paulo State University (FMVZ/ UNESP), Botucatu, São Paulo, Brazil
| | - Gabriele Silva Dias
- Veterinary Clinic Department, School of Veterinary Medicine and Animal Science of the São Paulo State University (FMVZ/ UNESP), Botucatu, São Paulo, Brazil
| | - Guilherme de Brito Viana
- Veterinary Clinic Department, School of Veterinary Medicine and Animal Science of the São Paulo State University (FMVZ/ UNESP), Botucatu, São Paulo, Brazil
| | - Elisane Lenita Milbradt
- Veterinary Clinic Department, School of Veterinary Medicine and Animal Science of the São Paulo State University (FMVZ/ UNESP), Botucatu, São Paulo, Brazil
| | - Raphael Lucio Andreatti-Filho
- Veterinary Clinic Department, School of Veterinary Medicine and Animal Science of the São Paulo State University (FMVZ/ UNESP), Botucatu, São Paulo, Brazil
| | - Adriano Sakai Okamoto
- Veterinary Clinic Department, School of Veterinary Medicine and Animal Science of the São Paulo State University (FMVZ/ UNESP), Botucatu, São Paulo, Brazil
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3
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Volov VT. Fractal-Cluster Theory and Its Applications for the Description of Biological Organisms. ENTROPY (BASEL, SWITZERLAND) 2023; 25:1433. [PMID: 37895554 PMCID: PMC10606124 DOI: 10.3390/e25101433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/23/2023] [Accepted: 09/25/2023] [Indexed: 10/29/2023]
Abstract
This article presents an overview of an alternative approach to the systematization and evolution of biological organisms on the basis of the fractal-cluster theory. It presents the foundations of the fractal-cluster theory for the self-organizing systems of the organism class. Static and dynamic efficiency criteria based on the fractal-cluster relations and the analytical apparatus of nonequilibrium thermodynamics are presented. We introduce a highly sensitive static criterion, D, which determines the deviation in the value of the clusters and subclusters of the fractal-cluster system structures from their reference values. Other static criteria are the fractal-cluster entropy H and the free energy F of an organism. The dynamic criterion is based on Prigogine's theorem and is determined by the second differential of the temporal trend of the fractal-cluster entropy H. By using simulations of the cluster variations for biological organisms in the (H, D, F)-space, the criteria for the fractal-cluster stochastics as well as for energy and evolution laws are obtained. The relationship between the traditional and fractal-cluster approaches for identifying an organism is discussed.
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Affiliation(s)
- Vyacheslav Theodorovich Volov
- Natural Science Department, Samara State University of Railway Transport, Perviy Bezimyaniy Pereulok 18, 443066 Samara, Russia
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4
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Riggi VS, Watson EB, Steele A, Rogers KL. Mineral-Mediated Oligoribonucleotide Condensation: Broadening the Scope of Prebiotic Possibilities on the Early Earth. Life (Basel) 2023; 13:1899. [PMID: 37763303 PMCID: PMC10532843 DOI: 10.3390/life13091899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/01/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
The origin of life on earth requires the synthesis of protobiopolymers in realistic geologic environments along strictly abiotic pathways that rely on inorganic phases (such as minerals) instead of cellular machinery to promote condensation. One such class of polymer central to biochemistry is the polynucleotides, and oligomerization of activated ribonucleotides has been widely studied. Nonetheless, the range of laboratory conditions tested to date is limited and the impact of realistic early Earth conditions on condensation reactions remains unexplored. Here, we investigate the potential for a variety of minerals to enhance oligomerization using ribonucleotide monomers as one example to model condensation under plausible planetary conditions. The results show that several minerals differing in both structure and composition enhance oligomerization. Sulfide minerals yielded oligomers of comparable lengths to those formed in the presence of clays, with galena being the most effective, yielding oligonucleotides up to six bases long. Montmorillonite continues to excel beyond other clays. Chemical pretreatment of the clay was not required, though maximum oligomer lengths decreased from ~11 to 6 bases. These results demonstrate the diversity of mineral phases that can impact condensation reactions and highlight the need for greater consideration of environmental context when assessing prebiotic synthesis and the origin of life.
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Affiliation(s)
- Vincent S. Riggi
- Rensselaer Astrobiology Research and Education Center, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; (E.B.W.); (A.S.); (K.L.R.)
- Department of Earth and Environmental Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - E. Bruce Watson
- Rensselaer Astrobiology Research and Education Center, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; (E.B.W.); (A.S.); (K.L.R.)
- Department of Earth and Environmental Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Andrew Steele
- Rensselaer Astrobiology Research and Education Center, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; (E.B.W.); (A.S.); (K.L.R.)
- Earth and Planets Laboratory, Carnegie Institution for Science, 5251 Broad Branch Rd NW, Washington, DC 20015, USA
| | - Karyn L. Rogers
- Rensselaer Astrobiology Research and Education Center, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; (E.B.W.); (A.S.); (K.L.R.)
- Department of Earth and Environmental Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
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5
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Gollo G. On the emergence of eukaryotes and other enigmas. Biosystems 2023; 231:104958. [PMID: 37442362 DOI: 10.1016/j.biosystems.2023.104958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 05/20/2023] [Accepted: 06/15/2023] [Indexed: 07/15/2023]
Abstract
The origin of eukaryotes is one of the most fundamental problems in the entire history of life. How did eukaryotes arise? Previous attempts to solve the problem are very far from an answer, at best they propose a solution to one of the various innovations that ended up culminating in eukaryotes. Based on a hypothetical-deductive methodology, as usual in evolutionary issues, I propose that eukaryotes emerged from the endosymbiotic association between a flagellate parasite and its host, of which the sperm is the main vestige. The hypothesis unifies the solution to the vast array of acquisitions shared by eukaryotes that differentiate them from other beings, remarkably cell nucleus, mitosis, meiosis and sexual reproduction. The solution has a deep impact on understanding the origin and functioning of all complex life forms.
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Affiliation(s)
- Gustavo Gollo
- Universidade de Brasília, Eecologia, Brasilia, DF, Brazil.
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6
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Peters S, Semenov DA, Hochleitner R, Trapp O. Synthesis of prebiotic organics from CO 2 by catalysis with meteoritic and volcanic particles. Sci Rep 2023; 13:6843. [PMID: 37231067 DOI: 10.1038/s41598-023-33741-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 04/18/2023] [Indexed: 05/27/2023] Open
Abstract
The emergence of prebiotic organics was a mandatory step toward the origin of life. The significance of the exogenous delivery versus the in-situ synthesis from atmospheric gases is still under debate. We experimentally demonstrate that iron-rich meteoritic and volcanic particles activate and catalyse the fixation of CO2, yielding the key precursors of life-building blocks. This catalysis is robust and produces selectively aldehydes, alcohols, and hydrocarbons, independent of the redox state of the environment. It is facilitated by common minerals and tolerates a broad range of the early planetary conditions (150-300 °C, ≲ 10-50 bar, wet or dry climate). We find that up to 6 × 108 kg/year of prebiotic organics could have been synthesized by this planetary-scale process from the atmospheric CO2 on Hadean Earth.
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Affiliation(s)
- Sophia Peters
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, Munich, Germany
- Max Planck Institute for Astronomy, Königstuhl 17, 69117, Heidelberg, Germany
| | - Dmitry A Semenov
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, Munich, Germany
- Max Planck Institute for Astronomy, Königstuhl 17, 69117, Heidelberg, Germany
| | - Rupert Hochleitner
- Mineralogische Staatssammlung München, Theresienstr. 41, 80333, Munich, Germany
| | - Oliver Trapp
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, Munich, Germany.
- Max Planck Institute for Astronomy, Königstuhl 17, 69117, Heidelberg, Germany.
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7
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Rabitz H, Russell B, Ho TS. The Surprising Ease of Finding Optimal Solutions for Controlling Nonlinear Phenomena in Quantum and Classical Complex Systems. J Phys Chem A 2023; 127:4224-4236. [PMID: 37142303 DOI: 10.1021/acs.jpca.3c01896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
This Perspective addresses the often observed surprising ease of achieving optimal control of nonlinear phenomena in quantum and classical complex systems. The circumstances involved are wide-ranging, with scenarios including manipulation of atomic scale processes, maximization of chemical and material properties or synthesis yields, Nature's optimization of species' populations by natural selection, and directed evolution. Natural evolution will mainly be discussed in terms of laboratory experiments with microorganisms, and the field is also distinct from the other domains where a scientist specifies the goal(s) and oversees the control process. We use the word "control" in reference to all of the available variables, regardless of the circumstance. The empirical observations on the ease of achieving at least good, if not excellent, control in diverse domains of science raise the question of why this occurs despite the generally inherent complexity of the systems in each scenario. The key to addressing the question lies in examining the associated control landscape, which is defined as the optimization objective as a function of the control variables that can be as diverse as the phenomena under consideration. Controls may range from laser pulses, chemical reagents, chemical processing conditions, out to nucleic acids in the genome and more. This Perspective presents a conjecture, based on present findings, that the systematics of readily finding good outcomes from controlled phenomena may be unified through consideration of control landscapes with the same common set of three underlying assumptions─the existence of an optimal solution, the ability for local movement on the landscape, and the availability of sufficient control resources─whose validity needs assessment in each scenario. In practice, many cases permit using myopic gradient-like algorithms while other circumstances utilize algorithms having some elements of stochasticity or introduced noise, depending on whether the landscape is locally smooth or rough. The overarching observation is that only relatively short searches are required despite the common high dimensionality of the available controls in typical scenarios.
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Affiliation(s)
- Herschel Rabitz
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Benjamin Russell
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Tak-San Ho
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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8
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Kobayashi K, Ise JI, Aoki R, Kinoshita M, Naito K, Udo T, Kunwar B, Takahashi JI, Shibata H, Mita H, Fukuda H, Oguri Y, Kawamura K, Kebukawa Y, Airapetian VS. Formation of Amino Acids and Carboxylic Acids in Weakly Reducing Planetary Atmospheres by Solar Energetic Particles from the Young Sun. Life (Basel) 2023; 13:life13051103. [PMID: 37240748 DOI: 10.3390/life13051103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 04/11/2023] [Accepted: 04/12/2023] [Indexed: 05/28/2023] Open
Abstract
Life most likely started during the Hadean Eon; however, the environmental conditions which contributed to the complexity of its chemistry are poorly known. A better understanding of various environmental conditions, including global (heliospheric) and local (atmospheric, surface, and oceanic), along with the internal dynamic conditions of the early Earth, are required to understand the onset of abiogenesis. Herein, we examine the contributions of galactic cosmic rays (GCRs) and solar energetic particles (SEPs) associated with superflares from the young Sun to the formation of amino acids and carboxylic acids in weakly reduced gas mixtures representing the early Earth's atmosphere. We also compare the products with those introduced by lightning events and solar ultraviolet light (UV). In a series of laboratory experiments, we detected and characterized the formation of amino acids and carboxylic acids via proton irradiation of a mixture of carbon dioxide, methane, nitrogen, and water in various mixing ratios. These experiments show the detection of amino acids after acid hydrolysis when 0.5% (v/v) of initial methane was introduced to the gas mixture. In the set of experiments with spark discharges (simulation of lightning flashes) performed for the same gas mixture, we found that at least 15% methane was required to detect the formation of amino acids, and no amino acids were detected in experiments via UV irradiation, even when 50% methane was used. Carboxylic acids were formed in non-reducing gas mixtures (0% methane) by proton irradiation and spark discharges. Hence, we suggest that GCRs and SEP events from the young Sun represent the most effective energy sources for the prebiotic formation of biologically important organic compounds from weakly reducing atmospheres. Since the energy flux of space weather, which generated frequent SEPs from the young Sun in the first 600 million years after the birth of the solar system, was expected to be much greater than that of GCRs, we conclude that SEP-driven energetic protons are the most promising energy sources for the prebiotic production of bioorganic compounds in the atmosphere of the Hadean Earth.
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Affiliation(s)
- Kensei Kobayashi
- Department of Chemistry and Life Science, Graduate School of Engineering Science, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Jun-Ichi Ise
- Department of Chemistry and Life Science, Graduate School of Engineering Science, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Ryohei Aoki
- Department of Chemistry and Life Science, Graduate School of Engineering Science, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Miei Kinoshita
- Department of Chemistry and Life Science, Graduate School of Engineering Science, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Koki Naito
- Department of Chemistry and Life Science, Graduate School of Engineering Science, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Takumi Udo
- Department of Chemistry and Life Science, Graduate School of Engineering Science, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Bhagawati Kunwar
- Chubu Institute of Advanced Studies, Chubu University, 1200 Matsumoto-cho, Kasugai 487-8501, Japan
| | - Jun-Ichi Takahashi
- Department of Chemistry and Life Science, Graduate School of Engineering Science, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Hiromi Shibata
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Ibaraki 567-0047, Japan
| | - Hajime Mita
- Department of Life, Environment and Applied Chemistry, Faculty of Engineering, Fukuoka Institute of Technology, Fukuoka 811-0295, Japan
| | - Hitoshi Fukuda
- Open Facility Center, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Yoshiyuki Oguri
- Institute of Innovative Research, Tokyo Institute of Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Kimitaka Kawamura
- Chubu Institute of Advanced Studies, Chubu University, 1200 Matsumoto-cho, Kasugai 487-8501, Japan
| | - Yoko Kebukawa
- Department of Chemistry and Life Science, Graduate School of Engineering Science, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Vladimir S Airapetian
- NASA Goddard Space Flight Center/Sellers Exoplanetary Environments Collaboration, Greenbelt, MD 20771, USA
- Department of Physics, American University, Washington, DC 20016, USA
- Graduate School of Advanced Integrated Studies in Human Survivability, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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9
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McGuinness KN, Klau GW, Morrison SM, Moore EK, Seipp J, Falkowski PG, Nanda V. Evaluating Mineral Lattices as Evolutionary Proxies for Metalloprotein Evolution. ORIGINS LIFE EVOL B 2022; 52:263-275. [DOI: 10.1007/s11084-022-09630-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 10/03/2022] [Indexed: 11/17/2022]
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10
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Fuentes-Carreón CA, Cruz-Castañeda JA, Mateo-Martí E, Negrón-Mendoza A. Stability of DL-Glyceraldehyde under Simulated Hydrothermal Conditions: Synthesis of Sugar-like Compounds in an Iron(III)-Oxide-Hydroxide-Rich Environment under Acidic Conditions. Life (Basel) 2022; 12:life12111818. [PMID: 36362973 PMCID: PMC9696992 DOI: 10.3390/life12111818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/04/2022] [Accepted: 11/06/2022] [Indexed: 11/10/2022] Open
Abstract
Researchers have suggested that the condensation of low-molecular-weight aldehydes under basic conditions (e.g., pH > 11) is the prebiotic reaction responsible for the abiotic formation of carbohydrates. It has also been suggested that surface hydrothermal systems were ubiquitous during the early Archean period. Therefore, the catalysis of prebiotic carbohydrate synthesis by metallic oxide minerals under acidic conditions in these environments seems considerably more probable than the more widely hypothesized reaction routes. This study investigates the stability of DL-glyceraldehyde and its reaction products under the simulated conditions of an Archean surface hydrothermal system. The Hveradalur geothermal area in Iceland was selected as an analog of such a system. HPLC-ESIMS, UV−Vis spectroscopy, Raman spectroscopy and XPS spectroscopy were used to analyze the reaction products. In hot (323 K) and acidic (pH 2) solutions under the presence of suspended iron(III) oxide hydroxide powder, DL-glyceraldehyde readily decomposes into low-molecular-weight compounds and transforms into sugar-like molecules via condensation reactions.
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Affiliation(s)
- Claudio Alejandro Fuentes-Carreón
- Posgrado en Ciencias de la Tierra, Instituto de Ciencias Nucleares, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
- Instituto de Ciencias Nucleares, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
- Correspondence:
| | | | - Eva Mateo-Martí
- Centro de Astrobiología (CAB) CSIC-INTA, Ctra. de Ajalvir km 4, 28850 Torrejón de Ardoz, Spain
| | - Alicia Negrón-Mendoza
- Instituto de Ciencias Nucleares, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
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11
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Ślesak I, Mazur Z, Ślesak H. Genes encoding the photosystem II proteins are under purifying selection: an insight into the early evolution of oxygenic photosynthesis. PHOTOSYNTHESIS RESEARCH 2022; 153:163-175. [PMID: 35648248 DOI: 10.1007/s11120-022-00917-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/28/2022] [Indexed: 06/15/2023]
Abstract
The molecular evolution concerns coding sequences (CDSs) of genes and may affect the structure and function of proteins. Non-uniform use of synonymous codons during translation, known as codon usage bias (CUB), depends on the balance between mutations bias and natural selection. We estimated different CUB indices, i.e. the effective number of codons (ENC), G + C content in the 3rd codon positions (GC3), and codon adaptation index for CDSs of intrinsic proteins of photosystem II (PSII), such as psbA (D1), psbD (D2), psbB (CP47), psbC (CP43), and CDSs of the extrinsic protein psbO (PsbO). These genes occur in all organisms that perform oxygenic photosynthesis (OP) on Earth: cyanobacteria, algae and plants. Comparatively, a similar analysis of codon bias for CDSs of L and M subunits that constitute the core proteins of the type II reaction centre (RCII) in anoxygenic bacteria was performed. Analysis of CUB indices and determination of the number of synonymous (dS) and nonsynonymous substitutions (dN) in all analysed CDSs indicated that the crucial PSII and RCII proteins were under strong purifying (negative) selection in course of evolution. Purifying selection was also estimated for CDSs of atpA, the α subunit of ATP synthase, an enzyme that was most likely already present in the last universal common ancestor (LUCA). The data obtained point to an ancient origin of OP, even in the earliest stages of the evolution of life on Earth.
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Affiliation(s)
- Ireneusz Ślesak
- The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek 21, 30-239, Kraków, Poland.
| | - Zofia Mazur
- The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek 21, 30-239, Kraków, Poland
| | - Halina Ślesak
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 9, 30-387, Kraków, Poland
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12
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Ikehara K. How Did Life Emerge in Chemically Complex Messy Environments? Life (Basel) 2022; 12:life12091319. [PMID: 36143356 PMCID: PMC9503616 DOI: 10.3390/life12091319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/18/2022] [Accepted: 08/25/2022] [Indexed: 11/18/2022] Open
Abstract
One of the problems that make it difficult to solve the mystery of the origin of life is determining how life emerged in chemically complex messy environments on primitive Earth. In this article, the “chemically complex messy environments” that are focused on are a mixed state of various organic compounds produced via prebiotic means and accumulated on primitive earth. The five factors described below are thought to have contributed to opening the way for the emergence of life: (1) A characteristic inherent in [GADV]-amino acids, which are easily produced via prebiotic means. [GADV] stands for four amino acids, Gly [G], Ala [A], Asp [D] and Val [V], which are indicated by a one-letter symbol. (2) The protein 0th-order structure or a [GADV]-amino acid composition generating water-soluble globular protein with some flexibility, which can be produced even by the random joining of [GADV]-amino acids. (3) The formation of versatile [GADV]-microspheres, which can grow, divide and proliferate even without a genetic system, was the emergence of proto-life. (4) The [GADV]-microspheres with a higher proliferation ability than others were able to be selected. Proto-Darwin evolution made it possible to proceed forward to the creation of a core life system composed of the (GNC)n gene, anticodon stem-loop tRNA or AntiC-SL tRNA (GNC genetic code), and [GADV]-protein. (5) Eventually, the first genuine life with a core life system emerged. Thus, the formation processes of [GADV]-protein and the (GNC)n gene in chemically complex messy environments were the steps to the emergence of genuine life.
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Affiliation(s)
- Kenji Ikehara
- G&L Kyosei Institute, The Keihanna Academy of Science and Culture (KASC), Keihanna Interaction Plaza, Lab. Wing 3F, 1-7 Hikaridai, Seika-cho, Souraku, Kyoto 619-0237, Japan; ; Tel.: +81-774-73-4478
- International Institute for Advanced Studies, Kizugawadai 9-3, Kizugawa, Kyoto 619-0225, Japan
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13
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Malaterre C, Jeancolas C, Nghe P. The Origin of Life: What Is the Question? ASTROBIOLOGY 2022; 22:851-862. [PMID: 35594335 PMCID: PMC9298494 DOI: 10.1089/ast.2021.0162] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 03/12/2022] [Indexed: 06/15/2023]
Abstract
The question of the origin of life is a tenacious question that challenges many branches of science but is also extremely multifaceted. While prebiotic chemistry and micropaleontology reformulate the question as that of explaining the appearance of life on Earth in the deep past, systems chemistry and synthetic biology typically understand the question as that of demonstrating the synthesis of novel living matter from nonliving matter independently of historical constraints. The objective of this contribution is to disentangle the different readings of the origin-of-life question found in science. We identify three main dimensions along which the question can be differently constrained depending on context: historical adequacy, natural spontaneity, and similarity to life-as-we-know-it. We argue that the epistemic status of what needs to be explained-the explanandum-varies from approximately true when the origin-of-life question is the most constrained to entirely speculative when the constraints are the most relaxed. This difference in epistemic status triggers a shift in the nature of the origin-of-life question from an explanation-seeking question in the most constrained case to a fact-establishing question in the lesser-constrained ones. We furthermore explore how answers to some interpretations of the origin-of-life questions matter for other interpretations.
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Affiliation(s)
- Christophe Malaterre
- Département de philosophie, Université du Québec à Montréal (UQAM), Montréal, Canada
- Centre interuniversitaire de recherche sur la science et la technologie (CIRST), Université du Québec à Montréal (UQAM), Montréal, Canada
| | - Cyrille Jeancolas
- Laboratoire Biophysique et Évolution, UMR Chimie Biologie Innovation 8231, ESPCI Paris, Université PSL, CNRS, Paris, France
- Laboratoire d'Anthropologie Sociale, Collège de France, Paris, France
| | - Philippe Nghe
- Laboratoire Biophysique et Évolution, UMR Chimie Biologie Innovation 8231, ESPCI Paris, Université PSL, CNRS, Paris, France
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14
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Fried SD, Fujishima K, Makarov M, Cherepashuk I, Hlouchova K. Peptides before and during the nucleotide world: an origins story emphasizing cooperation between proteins and nucleic acids. J R Soc Interface 2022; 19:20210641. [PMID: 35135297 PMCID: PMC8833103 DOI: 10.1098/rsif.2021.0641] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 01/05/2022] [Indexed: 12/14/2022] Open
Abstract
Recent developments in Origins of Life research have focused on substantiating the narrative of an abiotic emergence of nucleic acids from organic molecules of low molecular weight, a paradigm that typically sidelines the roles of peptides. Nevertheless, the simple synthesis of amino acids, the facile nature of their activation and condensation, their ability to recognize metals and cofactors and their remarkable capacity to self-assemble make peptides (and their analogues) favourable candidates for one of the earliest functional polymers. In this mini-review, we explore the ramifications of this hypothesis. Diverse lines of research in molecular biology, bioinformatics, geochemistry, biophysics and astrobiology provide clues about the progression and early evolution of proteins, and lend credence to the idea that early peptides served many central prebiotic roles before they were encodable by a polynucleotide template, in a putative 'peptide-polynucleotide stage'. For example, early peptides and mini-proteins could have served as catalysts, compartments and structural hubs. In sum, we shed light on the role of early peptides and small proteins before and during the nucleotide world, in which nascent life fully grasped the potential of primordial proteins, and which has left an imprint on the idiosyncratic properties of extant proteins.
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Affiliation(s)
- Stephen D. Fried
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21212, USA
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21212, USA
| | - Kosuke Fujishima
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo 1528550, Japan
- Graduate School of Media and Governance, Keio University, Fujisawa 2520882, Japan
| | - Mikhail Makarov
- Department of Cell Biology, Faculty of Science, Charles University, BIOCEV, Prague 12800, Czech Republic
| | - Ivan Cherepashuk
- Department of Cell Biology, Faculty of Science, Charles University, BIOCEV, Prague 12800, Czech Republic
| | - Klara Hlouchova
- Department of Cell Biology, Faculty of Science, Charles University, BIOCEV, Prague 12800, Czech Republic
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 16610, Czech Republic
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15
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From iron to bacterial electroconductive filaments: Exploring cytochrome diversity using Geobacter bacteria. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2021.214284] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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16
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Evolutionary Origins of DNA Repair Pathways: Role of Oxygen Catastrophe in the Emergence of DNA Glycosylases. Cells 2021; 10:cells10071591. [PMID: 34202661 PMCID: PMC8307549 DOI: 10.3390/cells10071591] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/17/2021] [Accepted: 06/18/2021] [Indexed: 11/23/2022] Open
Abstract
It was proposed that the last universal common ancestor (LUCA) evolved under high temperatures in an oxygen-free environment, similar to those found in deep-sea vents and on volcanic slopes. Therefore, spontaneous DNA decay, such as base loss and cytosine deamination, was the major factor affecting LUCA’s genome integrity. Cosmic radiation due to Earth’s weak magnetic field and alkylating metabolic radicals added to these threats. Here, we propose that ancient forms of life had only two distinct repair mechanisms: versatile apurinic/apyrimidinic (AP) endonucleases to cope with both AP sites and deaminated residues, and enzymes catalyzing the direct reversal of UV and alkylation damage. The absence of uracil–DNA N-glycosylases in some Archaea, together with the presence of an AP endonuclease, which can cleave uracil-containing DNA, suggests that the AP endonuclease-initiated nucleotide incision repair (NIR) pathway evolved independently from DNA glycosylase-mediated base excision repair. NIR may be a relic that appeared in an early thermophilic ancestor to counteract spontaneous DNA damage. We hypothesize that a rise in the oxygen level in the Earth’s atmosphere ~2 Ga triggered the narrow specialization of AP endonucleases and DNA glycosylases to cope efficiently with a widened array of oxidative base damage and complex DNA lesions.
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17
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Clark BC, Kolb VM, Steele A, House CH, Lanza NL, Gasda PJ, VanBommel SJ, Newsom HE, Martínez-Frías J. Origin of Life on Mars: Suitability and Opportunities. Life (Basel) 2021; 11:539. [PMID: 34207658 PMCID: PMC8227854 DOI: 10.3390/life11060539] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/28/2021] [Accepted: 06/01/2021] [Indexed: 02/07/2023] Open
Abstract
Although the habitability of early Mars is now well established, its suitability for conditions favorable to an independent origin of life (OoL) has been less certain. With continued exploration, evidence has mounted for a widespread diversity of physical and chemical conditions on Mars that mimic those variously hypothesized as settings in which life first arose on Earth. Mars has also provided water, energy sources, CHNOPS elements, critical catalytic transition metal elements, as well as B, Mg, Ca, Na and K, all of which are elements associated with life as we know it. With its highly favorable sulfur abundance and land/ocean ratio, early wet Mars remains a prime candidate for its own OoL, in many respects superior to Earth. The relatively well-preserved ancient surface of planet Mars helps inform the range of possible analogous conditions during the now-obliterated history of early Earth. Continued exploration of Mars also contributes to the understanding of the opportunities for settings enabling an OoL on exoplanets. Favoring geochemical sediment samples for eventual return to Earth will enhance assessments of the likelihood of a Martian OoL.
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Affiliation(s)
| | - Vera M. Kolb
- Department of Chemistry, University of Wisconsin—Parkside, Kenosha, WI 53141, USA;
| | - Andrew Steele
- Earth and Planetary Laboratory, Carnegie Institution for Science, Washington, DC 20015, USA;
| | - Christopher H. House
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, State College, PA 16807, USA;
| | - Nina L. Lanza
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA; (N.L.L.); (P.J.G.)
| | - Patrick J. Gasda
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA; (N.L.L.); (P.J.G.)
| | - Scott J. VanBommel
- Department of Earth and Planetary Sciences, Washington University in St. Louis, St. Louis, MO 63130, USA;
| | - Horton E. Newsom
- Institute of Meteoritics, Department of Earth and Planetary Sciences, University of New Mexico, Albuquerque, NM 88033, USA;
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18
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Neidhöfer C. On the Evolution of the Biological Framework for Insight. PHILOSOPHIES 2021; 6:43. [DOI: 10.3390/philosophies6020043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
The details of abiogenesis, to date, remain a matter of debate and constitute a key mystery in science and philosophy. The prevailing scientific hypothesis implies an evolutionary process of increasing complexity on Earth starting from (self-) replicating polymers. Defining the cut-off point where life begins is another moot point beyond the scope of this article. We will instead walk through the known evolutionary steps that led from these first exceptional polymers to the vast network of living biomatter that spans our world today, focusing in particular on perception, from simple biological feedback mechanisms to the complexity that allows for abstract thought. We will then project from the well-known to the unknown to gain a glimpse into what the universe aims to accomplish with living matter, just to find that if the universe had ever planned to be comprehended, evolution still has a long way to go.
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19
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Mojarro A, Jin L, Szostak JW, Head JW, Zuber MT. In search of the RNA world on Mars. GEOBIOLOGY 2021; 19:307-321. [PMID: 33565260 PMCID: PMC8248371 DOI: 10.1111/gbi.12433] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 01/22/2021] [Accepted: 01/23/2021] [Indexed: 05/17/2023]
Abstract
Advances in origins of life research and prebiotic chemistry suggest that life as we know it may have emerged from an earlier RNA World. However, it has been difficult to reconcile the conditions used in laboratory experiments with real-world geochemical environments that may have existed on the early Earth and hosted the origin(s) of life. This challenge is due to geologic resurfacing and recycling that have erased the overwhelming majority of the Earth's prebiotic history. We therefore propose that Mars, a planet frozen in time, comprised of many surfaces that have remained relatively unchanged since their formation > 4 Gya, is the best alternative to search for environments consistent with geochemical requirements imposed by the RNA world. In this study, we synthesize in situ and orbital observations of Mars and modeling of its early atmosphere into solutions containing a range of pHs and concentrations of prebiotically relevant metals (Fe2+ , Mg2+ , and Mn2+ ) spanning various candidate aqueous environments. We then experimentally determine RNA degradation kinetics due to metal-catalyzed hydrolysis (cleavage) and evaluate whether early Mars could have been permissive toward the accumulation of long-lived RNA polymers. Our results indicate that a Mg2+ -rich basalt sourcing metals to a slightly acidic (pH 5.4) environment mediates the slowest rates of RNA cleavage, though geologic evidence and basalt weathering models suggest aquifers on Mars would be near neutral (pH ~ 7). Moreover, the early onset of oxidizing conditions on Mars has major consequences regarding the availability of oxygen-sensitive metals (i.e., Fe2+ and Mn2+ ) due to increased RNA degradation rates and precipitation. Overall, (a) low pH decreases RNA cleavage at high metal concentrations; (b) acidic to neutral pH environments with Fe2+ or Mn2+ cleave more RNA than Mg2+ ; and (c) alkaline environments with Mg2+ dramatically cleaves more RNA while precipitates were observed for Fe2+ and Mn2+ .
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Affiliation(s)
- Angel Mojarro
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Lin Jin
- Department of Molecular Biology, and Center for Computational and Integrative BiologyMassachusetts General HospitalBostonMAUSA
| | - Jack W. Szostak
- Department of Molecular Biology, and Center for Computational and Integrative BiologyMassachusetts General HospitalBostonMAUSA
| | - James W. Head
- Department of Earth, Environmental and Planetary SciencesBrown UniversityProvidenceRIUSA
| | - Maria T. Zuber
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
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20
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Snyder-Beattie AE, Sandberg A, Drexler KE, Bonsall MB. The Timing of Evolutionary Transitions Suggests Intelligent Life is Rare. ASTROBIOLOGY 2021; 21:265-278. [PMID: 33216655 PMCID: PMC7997718 DOI: 10.1089/ast.2019.2149] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 09/29/2020] [Indexed: 06/11/2023]
Abstract
It is unknown how abundant extraterrestrial life is, or whether such life might be complex or intelligent. On Earth, the emergence of complex intelligent life required a preceding series of evolutionary transitions such as abiogenesis, eukaryogenesis, and the evolution of sexual reproduction, multicellularity, and intelligence itself. Some of these transitions could have been extraordinarily improbable, even in conducive environments. The emergence of intelligent life late in Earth's lifetime is thought to be evidence for a handful of rare evolutionary transitions, but the timing of other evolutionary transitions in the fossil record is yet to be analyzed in a similar framework. Using a simplified Bayesian model that combines uninformative priors and the timing of evolutionary transitions, we demonstrate that expected evolutionary transition times likely exceed the lifetime of Earth, perhaps by many orders of magnitude. Our results corroborate the original argument suggested by Brandon Carter that intelligent life in the Universe is exceptionally rare, assuming that intelligent life elsewhere requires analogous evolutionary transitions. Arriving at the opposite conclusion would require exceptionally conservative priors, evidence for much earlier transitions, multiple instances of transitions, or an alternative model that can explain why evolutionary transitions took hundreds of millions of years without appealing to rare chance events. Although the model is simple, it provides an initial basis for evaluating how varying biological assumptions and fossil record data impact the probability of evolving intelligent life, and also provides a number of testable predictions, such as that some biological paradoxes will remain unresolved and that planets orbiting M dwarf stars are uninhabitable.
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Affiliation(s)
| | - Anders Sandberg
- Future of Humanity Institute, University of Oxford, Oxford, United Kingdom
| | - K. Eric Drexler
- Future of Humanity Institute, University of Oxford, Oxford, United Kingdom
| | - Michael B. Bonsall
- Mathematical Ecology Research Group, University of Oxford, Oxford, United Kingdom
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21
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Harris AJ, Goldman AD. The very early evolution of protein translocation across membranes. PLoS Comput Biol 2021; 17:e1008623. [PMID: 33684113 PMCID: PMC7987157 DOI: 10.1371/journal.pcbi.1008623] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 03/23/2021] [Accepted: 12/10/2020] [Indexed: 11/18/2022] Open
Abstract
In this study, we used a computational approach to investigate the early evolutionary history of a system of proteins that, together, embed and translocate other proteins across cell membranes. Cell membranes comprise the basis for cellularity, which is an ancient, fundamental organizing principle shared by all organisms and a key innovation in the evolution of life on Earth. Two related requirements for cellularity are that organisms are able to both embed proteins into membranes and translocate proteins across membranes. One system that accomplishes these tasks is the signal recognition particle (SRP) system, in which the core protein components are the paralogs, FtsY and Ffh. Complementary to the SRP system is the Sec translocation channel, in which the primary channel-forming protein is SecY. We performed phylogenetic analyses that strongly supported prior inferences that FtsY, Ffh, and SecY were all present by the time of the last universal common ancestor of life, the LUCA, and that the ancestor of FtsY and Ffh existed before the LUCA. Further, we combined ancestral sequence reconstruction and protein structure and function prediction to show that the LUCA had an SRP system and Sec translocation channel that were similar to those of extant organisms. We also show that the ancestor of Ffh and FtsY that predated the LUCA was more similar to FtsY than Ffh but could still have comprised a rudimentary protein translocation system on its own. Duplication of the ancestor of FtsY and Ffh facilitated the specialization of FtsY as a membrane bound receptor and Ffh as a cytoplasmic protein that could bind nascent proteins with specific membrane-targeting signal sequences. Finally, we analyzed amino acid frequencies in our ancestral sequence reconstructions to infer that the ancestral Ffh/FtsY protein likely arose prior to or just after the completion of the canonical genetic code. Taken together, our results offer a window into the very early evolutionary history of cellularity.
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Affiliation(s)
- AJ Harris
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Department of Biology, Oberlin College and Conservatory, K123 Science Center, Oberlin, Ohio, United States of America
| | - Aaron David Goldman
- Department of Biology, Oberlin College and Conservatory, K123 Science Center, Oberlin, Ohio, United States of America
- Blue Marble Space Institute of Science, Seattle, Washington, United States of America
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22
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Ślesak I, Ślesak H. The activity of RubisCO and energy demands for its biosynthesis. Comparative studies with CO 2-reductases. JOURNAL OF PLANT PHYSIOLOGY 2021; 257:153337. [PMID: 33421837 DOI: 10.1016/j.jplph.2020.153337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 10/14/2020] [Accepted: 11/24/2020] [Indexed: 06/12/2023]
Abstract
Most CO2 on Earth is fixed into organic matter via reactions catalysed by enzymes called carboxylases. CO2-fixation via carboxylases occurs in the Calvin-Benson-Bassham (CBB) cycle, and the crucial role in this cycle is played by RubisCO (D-ribulose 1,5-bisphosphate carboxylase/oxygenase). CO2 can also be fixed by pathways, where a reduction of CO2 to formate or carbon monoxide (CO) occurs. The latter reactions are performed by so-called CO2-reductases e.g. formate dehydrogenase (FDH), carbon-monooxide (CO) dehydrogenase (CODH), and crotonyl-CoA reductase/carboxylase (CCR). In general, a simple model of enzymatic activity based only on a turnover rate of an enzyme for an appropriate substrate (kcat) is insufficient. Based on estimated metabolic costs of each amino acid, the average energetic costs of amino acid biosynthesis (Eaa), and the total costs (ET) for selected CO2-fixing enzymes were analyzed concerning 1) kcat for CO2 (kC), and 2) specificity factor (Srel) for RubisCO. A comparison of Eaa and ET to their kC showed that CODH and FDHs do not need to be more efficient enzymes in CO2 capturing pathways than some forms of RubisCO. CCR was the only both low-cost and highly active CO2-fixing enzyme. The obtained results showed also that there exists an evolutionarily conserved trade-off between Srel of RubisCOs and the energetic demands needed for their biosynthesis. Phylogenetic analysis demonstrated that RubisCO, CODH, FDH, and CCR are enzymes formed as a result of parallel evolution. Moreover, the kinetic parameters (kC) of CO2-fixing enzymes were plausibly optimized already at the early stages of life evolution on Earth.
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Affiliation(s)
- Ireneusz Ślesak
- The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek 21, 30-239, Kraków, Poland.
| | - Halina Ślesak
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 9, 30-387 Kraków, Poland
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23
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Gebauer S, Grenfell JL, Lammer H, de Vera JPP, Sproß L, Airapetian VS, Sinnhuber M, Rauer H. Atmospheric Nitrogen When Life Evolved on Earth. ASTROBIOLOGY 2020; 20:1413-1426. [PMID: 33121251 DOI: 10.1089/ast.2019.2212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The amount of nitrogen (N2) present in the atmosphere when life evolved on our planet is central for understanding the production of prebiotic molecules and, hence, is a fundamental quantity to constrain. Estimates of atmospheric molecular nitrogen partial surface pressures during the Archean, however, widely vary in the literature. In this study, we apply a model that combines newly gained insights into atmospheric escape, magma ocean duration, and outgassing evolution. Results suggest <420 mbar surface molecular nitrogen at the time when life originated, which is much lower compared with estimates in previous works and hence could impact our understanding of the production rate of prebiotic molecules such as hydrogen cyanide. Our revised values provide new input for atmospheric chamber experiments that simulate prebiotic chemistry on the early Earth. Our results that assume negligible nitrogen escape rates are in agreement with research based on solidified gas bubbles and the oxidation of iron in micrometeorites at 2.7 Gyr ago, which suggest that the atmospheric pressure was probably less than half the present-day value. Our results contradict previous studies that assume N2 partial surface pressures during the Archean were higher than those observed today and suggest that, if the N2 partial pressure were low in the Archean, it would likely be low in the Hadean as well. Furthermore, our results imply a biogenic nitrogen fixation rate from 9 to 14 Teragram N2 per year (Tg N2/year), which is consistent with modern marine biofixation rates and, hence, indicate an oceanic origin of this fixation process.
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Affiliation(s)
- Stefanie Gebauer
- Institute for Planetary Research (PF), German Aerospace Centre (DLR), Berlin, Germany
| | - John Lee Grenfell
- Institute for Planetary Research (PF), German Aerospace Centre (DLR), Berlin, Germany
| | - Helmut Lammer
- Space Research Institute, Austrian Academy of Sciences, Graz, Austria
| | | | - Laurenz Sproß
- Space Research Institute, Austrian Academy of Sciences, Graz, Austria
- Institute for Physics, University of Graz, Graz, Austria
| | - Vladimir S Airapetian
- NASA Goddard Space Flight Center (GSFC), Greenbelt, Maryland, USA
- American University, NW Washington, District of Columbia, USA
| | - Miriam Sinnhuber
- Institute for Meteorology and Climate Research, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Heike Rauer
- Institute for Planetary Research (PF), German Aerospace Centre (DLR), Berlin, Germany
- Institute for Geological Sciences, Planetology and Remote Sensing, Freie Universität Berlin (FUB), Berlin, Germany
- Centre for Astronomy and Astrophysics, Technische Universität Berlin (TUB), Berlin, Germany
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24
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Clark BC, Kolb VM. Macrobiont: Cradle for the Origin of Life and Creation of a Biosphere. Life (Basel) 2020; 10:life10110278. [PMID: 33198206 PMCID: PMC7697624 DOI: 10.3390/life10110278] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 11/09/2020] [Accepted: 11/09/2020] [Indexed: 02/06/2023] Open
Abstract
Although the cellular microorganism is the fundamental unit of biology, the origin of life (OoL) itself is unlikely to have occurred in a microscale environment. The macrobiont (MB) is the macro-scale setting where life originated. Guided by the methodologies of Systems Analysis, we focus on subaerial ponds of scale 3 to 300 m diameter. Within such ponds, there can be substantial heterogeneity, on the vertical, horizontal, and temporal scales, which enable multi-pot prebiotic chemical evolution. Pond size-sensitivities for several figures of merit are mathematically formulated, leading to the expectation that the optimum pond size for the OoL is intermediate, but biased toward smaller sizes. Sensitivities include relative access to nutrients, energy sources, and catalysts, as sourced from geological, atmospheric, hydrospheric, and astronomical contributors. Foreshores, especially with mudcracks, are identified as a favorable component for the success of the macrobiont. To bridge the gap between inanimate matter and a planetary-scale biosphere, five stages of evolution within the macrobiont are hypothesized: prebiotic chemistry → molecular replicator → protocell → macrobiont cell → colonizer cell. Comparison of ponds with other macrobionts, including hydrothermal and meteorite settings, allows a conclusion that more than one possible macrobiont locale could enable an OoL.
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Affiliation(s)
- Benton C. Clark
- Space Science Institute, Boulder, CO 80301, USA
- Correspondence:
| | - Vera M. Kolb
- Department of Chemistry, University of Wisconsin—Parkside, Kenosha, WI 53141, USA;
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25
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Kunnev D. Origin of Life: The Point of No Return. Life (Basel) 2020; 10:life10110269. [PMID: 33153087 PMCID: PMC7693465 DOI: 10.3390/life10110269] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/01/2020] [Accepted: 11/01/2020] [Indexed: 12/13/2022] Open
Abstract
Origin of life research is one of the greatest scientific frontiers of mankind. Many hypotheses have been proposed to explain how life began. Although different hypotheses emphasize different initial phenomena, all of them agree around one important concept: at some point, along with the chain of events toward life, Darwinian evolution emerged. There is no consensus, however, how this occurred. Frequently, the mechanism leading to Darwinian evolution is not addressed and it is assumed that this problem could be solved later, with experimental proof of the hypothesis. Here, the author first defines the minimum components required for Darwinian evolution and then from this standpoint, analyzes some of the hypotheses for the origin of life. Distinctive features of Darwinian evolution and life rooted in the interaction between information and its corresponding structure/function are then reviewed. Due to the obligatory dependency of the information and structure subject to Darwinian evolution, these components must be locked in their origin. One of the most distinctive characteristics of Darwinian evolution in comparison with all other processes is the establishment of a fundamentally new level of matter capable of evolving and adapting. Therefore, the initiation of Darwinian evolution is the "point of no return" after which life begins. In summary: a definition and a mechanism for Darwinian evolution are provided together with a critical analysis of some of the hypotheses for the origin of life.
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Affiliation(s)
- Dimiter Kunnev
- Department of Oral Biology, University at Buffalo, Buffalo, NY 14263, USA
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26
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Cell Communications among Microorganisms, Plants, and Animals: Origin, Evolution, and Interplays. Int J Mol Sci 2020; 21:ijms21218052. [PMID: 33126770 PMCID: PMC7663094 DOI: 10.3390/ijms21218052] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/17/2020] [Accepted: 10/27/2020] [Indexed: 02/06/2023] Open
Abstract
Cellular communications play pivotal roles in multi-cellular species, but they do so also in uni-cellular species. Moreover, cells communicate with each other not only within the same individual, but also with cells in other individuals belonging to the same or other species. These communications occur between two unicellular species, two multicellular species, or between unicellular and multicellular species. The molecular mechanisms involved exhibit diversity and specificity, but they share common basic features, which allow common pathways of communication between different species, often phylogenetically very distant. These interactions are possible by the high degree of conservation of the basic molecular mechanisms of interaction of many ligand-receptor pairs in evolutionary remote species. These inter-species cellular communications played crucial roles during Evolution and must have been positively selected, particularly when collectively beneficial in hostile environments. It is likely that communications between cells did not arise after their emergence, but were part of the very nature of the first cells. Synchronization of populations of non-living protocells through chemical communications may have been a mandatory step towards their emergence as populations of living cells and explain the large commonality of cell communication mechanisms among microorganisms, plants, and animals.
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Gefaell J, Prieto T, Abdelaziz M, Álvarez I, Antón J, Arroyo J, Bella JL, Botella M, Bugallo A, Claramonte V, Gijón J, Lizarte E, Maroto RM, Megías M, Milá B, Ramón C, Vila M, Rolán-Alvarez E. Acceptance and knowledge of evolutionary theory among third-year university students in Spain. PLoS One 2020; 15:e0238345. [PMID: 32881957 PMCID: PMC7470367 DOI: 10.1371/journal.pone.0238345] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 08/04/2020] [Indexed: 11/18/2022] Open
Abstract
The theory of evolution is one of the greatest scientific achievements in the intellectual history of humankind, yet it is still contentious within certain social groups. Despite being as robust and evidence-based as any other notable scientific theory, some people show a strong reluctance to accept it. In this study, we used the Measure of Acceptance of the Theory of Evolution (MATE) and Knowledge of Evolution Exam (KEE) questionnaires with university students from four academic degree programs (Chemistry, English, History, and Biology) of ten universities from Spain to measure, respectively, acceptance and knowledge of evolutionary theory among third-year undergraduate students (nMATE = 978; nKEE = 981). Results show that acceptance of evolution is relatively high (87.2%), whereas knowledge of the theory is moderate (5.4 out of 10) although there are differences across degrees (Biology>Chemistry>History>English), and even among various universities (ranging from 4.71 to 5.81). Statistical analysis reveals that knowledge of evolutionary theory among Biology students is partially explained by the relative weight of evolutionary themes within the curriculum, suggesting that an increase in the number of hours dedicated to this topic could have a direct influence on students' knowledge of it. We also found that religion may have a significant-although relatively small-negative influence on evolutionary theory acceptance. The moderate knowledge of evolution in our undergraduate students, together with the potential problem of acceptance in certain groups, suggests the need for a revision of the evolutionary concepts in the teaching curricula of our students since primary school.
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Affiliation(s)
- Juan Gefaell
- Facultade de Bioloxía, Universidade de Vigo, Campus de Vigo, Vigo, Spain
| | - Tamara Prieto
- Centro de Investigacións Biomédicas (CINBIO), Universidade de Vigo, Campus de Vigo, Vigo, Spain
| | - Mohamed Abdelaziz
- Departamento de Genética, Universidad de Granada, Avda Fuentenueva, Granada, Spain
| | - Inés Álvarez
- Real Jardín Botánico, Consejo Superior de Investigaciones Científicas (CSIC), Pza. de Murillo, Madrid, Spain
| | - Josefa Antón
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Apdo., Alicante, Spain
| | - Juan Arroyo
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Sevilla, Spain
| | - Jose L. Bella
- Departamento de Biología (Genética), Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Miguel Botella
- Departamento de Medicina Legal, Toxicología y Antropología Física, Universidad de Granada, Parque Tecnológico de la Salud, Av. de la Investigación, Granada, Spain
| | - Anxela Bugallo
- Departamento de Pedagogía y Didáctica, Universidade da Coruña, Campus de Elviña, A Coruña, Spain
| | - Vicente Claramonte
- Unidad Docente de Lógica y Filosofía de la Ciencia, Departamento de Filosofía, Facultad de Filosofía y Ciencias de la Educación, Universitat de València, Valencia, Spain
| | - José Gijón
- Departamento de Didáctica y Organización Escolar, Universidad de Granada, Campus de Cartuja, Granada, Spain
| | - Emilio Lizarte
- Departamento de Didáctica y Organización Escolar, Universidad de Granada, Campus de Cartuja, Granada, Spain
| | - Rosa M. Maroto
- Departamento de Medicina Legal, Toxicología y Antropología Física, Universidad de Granada, Parque Tecnológico de la Salud, Av. de la Investigación, Granada, Spain
| | - Manuel Megías
- Facultade de Bioloxía, Universidade de Vigo, Campus de Vigo, Vigo, Spain
| | - Borja Milá
- Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Cori Ramón
- Departament de Biología, Universitat de les Illes Balears, Palma de Mallorca, Carretera de Valldemossa, Illes Balears, Spain
| | - Marta Vila
- Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, Campus da Zapateira, A Coruña, Spain
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Estimating survival probability using the terrestrial extinction history for the search for extraterrestrial life. Sci Rep 2020; 10:12795. [PMID: 32733049 PMCID: PMC7392900 DOI: 10.1038/s41598-020-69724-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 07/20/2020] [Indexed: 12/28/2022] Open
Abstract
Several exoplanets have been discovered to date, and the next step is the search for extraterrestrial life. However, it is difficult to estimate the number of life-bearing exoplanets because our only template is based on life on Earth. In this paper, a new approach is introduced to estimate the probability that life on Earth has survived from birth to the present based on its terrestrial extinction history. A histogram of the extinction intensity during the Phanerozoic Eon is modeled effectively with a log-normal function, supporting the idea that terrestrial extinction is a random multiplicative process. Assuming that the fitted function is a probability density function of extinction intensity per unit time, the estimated survival probability of life on Earth is \documentclass[12pt]{minimal}
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\begin{document}$$\sim0.15$$\end{document}∼0.15 from the beginning of life to the present. This value can be a constraint on \documentclass[12pt]{minimal}
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\begin{document}$$f_i$$\end{document}fi in the Drake equation, which contributes to estimating the number of life-bearing exoplanets.
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Sauterey B, Charnay B, Affholder A, Mazevet S, Ferrière R. Co-evolution of primitive methane-cycling ecosystems and early Earth's atmosphere and climate. Nat Commun 2020; 11:2705. [PMID: 32483130 PMCID: PMC7264298 DOI: 10.1038/s41467-020-16374-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 04/28/2020] [Indexed: 01/24/2023] Open
Abstract
The history of the Earth has been marked by major ecological transitions, driven by metabolic innovation, that radically reshaped the composition of the oceans and atmosphere. The nature and magnitude of the earliest transitions, hundreds of million years before photosynthesis evolved, remain poorly understood. Using a novel ecosystem-planetary model, we find that pre-photosynthetic methane-cycling microbial ecosystems are much less productive than previously thought. In spite of their low productivity, the evolution of methanogenic metabolisms strongly modifies the atmospheric composition, leading to a warmer but less resilient climate. As the abiotic carbon cycle responds, further metabolic evolution (anaerobic methanotrophy) may feed back to the atmosphere and destabilize the climate, triggering a transient global glaciation. Although early metabolic evolution may cause strong climatic instability, a low CO:CH4 atmospheric ratio emerges as a robust signature of simple methane-cycling ecosystems on a globally reduced planet such as the late Hadean/early Archean Earth.
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Affiliation(s)
- Boris Sauterey
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Université Paris Sciences et Lettres, CNRS, INSERM, 75005, Paris, France.
- International Center for Interdisciplinary Global Environmental Studies (iGLOBES), CNRS, ENS-PSL University, University of Arizona, Tucson, AZ, 85721, USA.
- Institut de Mécanique Céleste et de Calcul des Ephémérides (IMCCE), Observatoire de Paris, Université PSL, CNRS, Sorbonne Université, Univ. Lille, F-75014, Paris, France.
| | - Benjamin Charnay
- LESIA, Observatoire de Paris, Université PSL, CNRS, Sorbonne Université, Université de Paris, 5 place Jules Janssen, 92195, Meudon, France
| | - Antonin Affholder
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Université Paris Sciences et Lettres, CNRS, INSERM, 75005, Paris, France
- International Center for Interdisciplinary Global Environmental Studies (iGLOBES), CNRS, ENS-PSL University, University of Arizona, Tucson, AZ, 85721, USA
- Institut de Mécanique Céleste et de Calcul des Ephémérides (IMCCE), Observatoire de Paris, Université PSL, CNRS, Sorbonne Université, Univ. Lille, F-75014, Paris, France
| | - Stéphane Mazevet
- Institut de Mécanique Céleste et de Calcul des Ephémérides (IMCCE), Observatoire de Paris, Université PSL, CNRS, Sorbonne Université, Univ. Lille, F-75014, Paris, France
| | - Régis Ferrière
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Université Paris Sciences et Lettres, CNRS, INSERM, 75005, Paris, France
- International Center for Interdisciplinary Global Environmental Studies (iGLOBES), CNRS, ENS-PSL University, University of Arizona, Tucson, AZ, 85721, USA
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
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Longo A, Damer B. Factoring Origin of Life Hypotheses into the Search for Life in the Solar System and Beyond. Life (Basel) 2020; 10:E52. [PMID: 32349245 PMCID: PMC7281141 DOI: 10.3390/life10050052] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 04/14/2020] [Accepted: 04/22/2020] [Indexed: 01/13/2023] Open
Abstract
Two widely-cited alternative hypotheses propose geological localities and biochemical mechanisms for life's origins. The first states that chemical energy available in submarine hydrothermal vents supported the formation of organic compounds and initiated primitive metabolic pathways which became incorporated in the earliest cells; the second proposes that protocells self-assembled from exogenous and geothermally-delivered monomers in freshwater hot springs. These alternative hypotheses are relevant to the fossil record of early life on Earth, and can be factored into the search for life elsewhere in the Solar System. This review summarizes the evidence supporting and challenging these hypotheses, and considers their implications for the search for life on various habitable worlds. It will discuss the relative probability that life could have emerged in environments on early Mars, on the icy moons of Jupiter and Saturn, and also the degree to which prebiotic chemistry could have advanced on Titan. These environments will be compared to ancient and modern terrestrial analogs to assess their habitability and biopreservation potential. Origins of life approaches can guide the biosignature detection strategies of the next generation of planetary science missions, which could in turn advance one or both of the leading alternative abiogenesis hypotheses.
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Affiliation(s)
- Alex Longo
- National Aeronautics and Space Administration Headquarters, Washington, DC 20546, USA
- Department of Geology, The University of North Carolina, Chapel Hill, NC 27599, USA
| | - Bruce Damer
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA or
- Digital Space Research, Boulder Creek, CA 95006, USA
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31
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Damer B, Deamer D. The Hot Spring Hypothesis for an Origin of Life. ASTROBIOLOGY 2020; 20:429-452. [PMID: 31841362 PMCID: PMC7133448 DOI: 10.1089/ast.2019.2045] [Citation(s) in RCA: 164] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 10/23/2019] [Indexed: 05/05/2023]
Abstract
We present a testable hypothesis related to an origin of life on land in which fluctuating volcanic hot spring pools play a central role. The hypothesis is based on experimental evidence that lipid-encapsulated polymers can be synthesized by cycles of hydration and dehydration to form protocells. Drawing on metaphors from the bootstrapping of a simple computer operating system, we show how protocells cycling through wet, dry, and moist phases will subject polymers to combinatorial selection and draw structural and catalytic functions out of initially random sequences, including structural stabilization, pore formation, and primitive metabolic activity. We propose that protocells aggregating into a hydrogel in the intermediate moist phase of wet-dry cycles represent a primitive progenote system. Progenote populations can undergo selection and distribution, construct niches in new environments, and enable a sharing network effect that can collectively evolve them into the first microbial communities. Laboratory and field experiments testing the first steps of the scenario are summarized. The scenario is then placed in a geological setting on the early Earth to suggest a plausible pathway from life's origin in chemically optimal freshwater hot spring pools to the emergence of microbial communities tolerant to more extreme conditions in dilute lakes and salty conditions in marine environments. A continuity is observed for biogenesis beginning with simple protocell aggregates, through the transitional form of the progenote, to robust microbial mats that leave the fossil imprints of stromatolites so representative in the rock record. A roadmap to future testing of the hypothesis is presented. We compare the oceanic vent with land-based pool scenarios for an origin of life and explore their implications for subsequent evolution to multicellular life such as plants. We conclude by utilizing the hypothesis to posit where life might also have emerged in habitats such as Mars or Saturn's icy moon Enceladus. "To postulate one fortuitously catalyzed reaction, perhaps catalyzed by a metal ion, might be reasonable, but to postulate a suite of them is to appeal to magic." -Leslie Orgel.
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Affiliation(s)
- Bruce Damer
- Department of Biomolecular Engineering, University of California, Santa Cruz, California
| | - David Deamer
- Department of Biomolecular Engineering, University of California, Santa Cruz, California
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Abstract
Abiotic emergence of ordered information stored in the form of RNA is an important unresolved problem concerning the origin of life. A polymer longer than 40–100 nucleotides is necessary to expect a self-replicating activity, but the formation of such a long polymer having a correct nucleotide sequence by random reactions seems statistically unlikely. However, our universe, created by a single inflation event, likely includes more than 10100 Sun-like stars. If life can emerge at least once in such a large volume, it is not in contradiction with our observations of life on Earth, even if the expected number of abiogenesis events is negligibly small within the observable universe that contains only 1022 stars. Here, a quantitative relation is derived between the minimum RNA length lmin required to be the first biological polymer, and the universe size necessary to expect the formation of such a long and active RNA by randomly adding monomers. It is then shown that an active RNA can indeed be produced somewhere in an inflationary universe, giving a solution to the abiotic polymerization problem. On the other hand, lmin must be shorter than ~20 nucleotides for the abiogenesis probability close to unity on a terrestrial planet, but a self-replicating activity is not expected for such a short RNA. Therefore, if extraterrestrial organisms of a different origin from those on Earth are discovered in the future, it would imply an unknown mechanism at work to polymerize nucleotides much faster than random statistical processes.
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33
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Haqq-Misra J. Does the Evolution of Complex Life Depend on the Stellar Spectral Energy Distribution? ASTROBIOLOGY 2019; 19:1292-1299. [PMID: 31429585 DOI: 10.1089/ast.2018.1946] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
This article presents the proportional evolutionary time (PET) hypothesis, which posits that the mean time required for the evolution of complex life is a function of stellar mass. The "biological available window" is defined as the region of a stellar spectrum between 200 and 1200 nm that generates free energy for life. Over the ∼4 Gyr history of Earth, the total energy incident at the top of the atmosphere and within the biological available window is ∼1034 J. The hypothesis assumes that the rate of evolution from the origin of life to complex life is proportional to this total energy, which would suggest that planets orbiting other stars should not show signs of complex life if the total energy incident on the planet is below this energy threshold. The PET hypothesis predicts that late K- and M-dwarf stars (M < 0.7 [Formula: see text]) are too young to host any complex life at the present age of the Universe. F-, G-, and early K-dwarf stars (M > 0.7 [Formula: see text]) represent the best targets for the next generation of space telescopes to search for spectroscopic biosignatures indicative of complex life.
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Cleaves HJ, Butch C, Burger PB, Goodwin J, Meringer M. One Among Millions: The Chemical Space of Nucleic Acid-Like Molecules. J Chem Inf Model 2019; 59:4266-4277. [PMID: 31498614 DOI: 10.1021/acs.jcim.9b00632] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Biology encodes hereditary information in DNA and RNA, which are finely tuned to their biological functions and modes of biological production. The central role of nucleic acids in biological information flow makes them key targets of pharmaceutical research. Indeed, other nucleic acid-like polymers can play similar roles to natural nucleic acids both in vivo and in vitro; yet despite remarkable advances over the last few decades, much remains unknown regarding which structures are compatible with molecular information storage. Chemical space describes the structures and properties of molecules that could exist within a given molecular formula or other classification system. Using structure generation methods, we explore nucleic acid analogues within the formula ranges BC3-7H5-15O2-4 and BC3-6H5-15N1-2O0-4, where B is a recognition element (e.g., a nucleobase). Other restrictions included two obligatory points of attachment for inclusion into a linear polymer and substructures predicting chemical stability. These sets contain 86,007 (CHO) and 75,309 (CHNO) compositionally isomeric structures, representing 706,568 CHO and 454,422 CHNO stereoisomers, that diversely and densely occupy this space. These libraries point toward there being large spaces of unexplored chemistry relevant to pharmacology and biochemistry and efforts to understand the origins of life.
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Affiliation(s)
- Henderson James Cleaves
- Earth-Life Science Institute , Tokyo Institute of Technology , 2-12-IE-1 Ookayama , Meguro-ku , Tokyo 152-8551 , Japan.,Institute for Advanced Study , Princeton , New Jersey 08540 , United States.,Blue Marble Space Institute for Science , 1515 Gallatin St. NW , Washington , DC 20011 , United States
| | - Christopher Butch
- Earth-Life Science Institute , Tokyo Institute of Technology , 2-12-IE-1 Ookayama , Meguro-ku , Tokyo 152-8551 , Japan.,Blue Marble Space Institute for Science , 1515 Gallatin St. NW , Washington , DC 20011 , United States.,Department of Chemistry , Emory University , 1515 Dickey Dr. , Atlanta , Georgia 30322 , United States
| | - Pieter Buys Burger
- Department of Chemistry , Emory University , 1515 Dickey Dr. , Atlanta , Georgia 30322 , United States
| | - Jay Goodwin
- Department of Chemistry , Emory University , 1515 Dickey Dr. , Atlanta , Georgia 30322 , United States
| | - Markus Meringer
- German Aerospace Center (DLR) , Earth Observation Center (EOC) , Münchner Straße 20 , 82234 Oberpfaffenhofen-Wessling , Germany
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Ślesak I, Kula M, Ślesak H, Miszalski Z, Strzałka K. How to define obligatory anaerobiosis? An evolutionary view on the antioxidant response system and the early stages of the evolution of life on Earth. Free Radic Biol Med 2019; 140:61-73. [PMID: 30862543 DOI: 10.1016/j.freeradbiomed.2019.03.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 03/01/2019] [Accepted: 03/05/2019] [Indexed: 10/27/2022]
Abstract
One of the former definitions of "obligate anaerobiosis" was based on three main criteria: 1) it occurs in organisms, so-called obligate anaerobes, which live in environments without oxygen (O2), 2) O2-dependent (aerobic) respiration, and 3) antioxidant enzymes are absent in obligate anaerobes. In contrast, aerobes need O2 in order to grow and develop properly. Obligate (or strict) anaerobes belong to prokaryotic microorganisms from two domains, Bacteria and Archaea. A closer look at anaerobiosis covers a wide range of microorganisms that permanently or in a time-dependent manner tolerate different concentrations of O2 in their habitats. On this basis they can be classified as obligate/facultative anaerobes, microaerophiles and nanaerobes. Paradoxically, O2 tolerance in strict anaerobes is usually, as in aerobes, associated with the activity of the antioxidant response system, which involves different antioxidant enzymes responsible for removing excess reactive oxygen species (ROS). In our opinion, the traditional definition of "obligate anaerobiosis" loses its original sense. Strict anaerobiosis should only be restricted to the occurrence of O2-independent pathways involved in energy generation. For that reason, a term better than "obligate anaerobes" would be O2/ROS tolerant anaerobes, where the role of the O2/ROS detoxification system is separated from O2-independent metabolic pathways that supply energy. Ubiquitous key antioxidant enzymes like superoxide dismutase (SOD) and superoxide reductase (SOR) in contemporary obligate anaerobes might suggest that their origin is ancient, maybe even the beginning of the evolution of life on Earth. It cannot be ruled out that c. 3.5 Gyr ago, local microquantities of O2/ROS played a role in the evolution of the last universal common ancestor (LUCA) of all modern organisms. On the basis of data in the literature, the hypothesis that LUCA could be an O2/ROS tolerant anaerobe is discussed together with the question of the abiotic sources of O2/ROS and/or the early evolution of cyanobacteria that perform oxygenic photosynthesis.
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Affiliation(s)
- Ireneusz Ślesak
- The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek 21, 30-239, Krakow, Poland.
| | - Monika Kula
- The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek 21, 30-239, Krakow, Poland.
| | - Halina Ślesak
- Institute of Botany, Jagiellonian University, Gronostajowa 9, 30-387, Krakow, Poland.
| | - Zbigniew Miszalski
- The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek 21, 30-239, Krakow, Poland.
| | - Kazimierz Strzałka
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Krakow, Poland; Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland.
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36
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Kunnev D, Gospodinov A. Possible Emergence of Sequence Specific RNA Aminoacylation via Peptide Intermediary to Initiate Darwinian Evolution and Code Through Origin of Life. Life (Basel) 2018; 8:E44. [PMID: 30279401 PMCID: PMC6316189 DOI: 10.3390/life8040044] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 09/30/2018] [Accepted: 09/30/2018] [Indexed: 12/12/2022] Open
Abstract
One of the most intriguing questions in biological science is how life originated on Earth. A large number of hypotheses have been proposed to explain it, each putting an emphasis on different events leading to functional translation and self-sustained system. Here, we propose a set of interactions that could have taken place in the prebiotic environment. According to our hypothesis, hybridization-induced proximity of short aminoacylated RNAs led to the synthesis of peptides of random sequence. We postulate that among these emerged a type of peptide(s) capable of stimulating the interaction between specific RNAs and specific amino acids, which we call "bridge peptide" (BP). We conclude that translation should have emerged at the same time when the standard genetic code begun to evolve due to the stabilizing effect on RNA-peptide complexes with the help of BPs. Ribosomes, ribozymes, and the enzyme-directed RNA replication could co-evolve within the same period, as logical outcome of RNA-peptide world without the need of RNA only self-sustained step.
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Affiliation(s)
- Dimiter Kunnev
- Roswell Park Cancer Institute, Department of Molecular & Cellular Biology, Buffalo, NY 14263, USA.
| | - Anastas Gospodinov
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. 21, Sofia 1113, Bulgaria.
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