1
|
Del Duca S, Vassallo A, Semenzato G, Fani R. Mimicking the last step of gene elongation: hints from the bacterial hisF gene. Gene 2023:147533. [PMID: 37279865 DOI: 10.1016/j.gene.2023.147533] [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: 02/23/2023] [Revised: 05/05/2023] [Accepted: 05/31/2023] [Indexed: 06/08/2023]
Abstract
Gene elongation consists in an in-tandem duplication of a gene and divergence and fusion of the two copies, resulting in a gene constituted by two divergent paralogous modules. Many present-day proteins show internal repeats of amino acid sequences, generated by gene elongation events; however, gene elongation is still a poorly studied evolutionary molecular mechanism. The most documented case is that of the histidine biosynthetic genes hisA and hisF, which derive from the gene elongation of an ancestral gene half the size of the extant ones. The aim of this work was to experimentally simulate the possible last step of the gene elongation event occurred during hisF gene evolution under selective pressure conditions. Azospirillum brasilense hisF gene, carrying a single nucleotide mutation that generates a stop codon between the two halves of the gene, was used to transform the histidine-auxotrophic Escherichia coli strain FB182 (hisF892). The transformed strain was subjected to selective pressure (i.e., low concentration/absence of histidine in the growth medium) and the obtained mutants were characterized. The restoration of prototrophy was strongly dependent on the time of incubation and on the strength of the selective pressure. The mutations involved the introduced stop codon with a single base substitution and none of the mutants restored the wild-type codon. Possible correlations between the different mutations and i) E. coli codon usage, ii) three-dimensional structures of the mutated HisF proteins, and iii) growth ability of the mutants were investigated. On the contrary, when the experiment was repeated by mutating a more conserved codon, only a synonymous substitution was obtained. Thus, experiments performed in this study allowed to mimic a possible gene elongation event occurred during the evolution of hisF gene, evidencing the ability of bacterial cells to modify their genome in short times under selective conditions.
Collapse
Affiliation(s)
- Sara Del Duca
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019, Sesto Fiorentino (FI), Italy; Research Centre for Agriculture and Environment, Council for Agricultural Research and Economics (CREA-AA), Via di Lanciola 12/A, 50125, Cascine del Riccio (FI), Italy
| | - Alberto Vassallo
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III Da Varano 1, 62032, Camerino (MC) Italy
| | - Giulia Semenzato
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019, Sesto Fiorentino (FI), Italy
| | - Renato Fani
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019, Sesto Fiorentino (FI), Italy.
| |
Collapse
|
2
|
Zhang Z, Jiang H, Ju P, Pan L, Rouillard J, Zhou G, Huang F, Hao J. Evaluating the abiotic synthesis potential and the stability of building blocks of life beneath an impact-induced steam atmosphere. Front Microbiol 2023; 14:1032073. [PMID: 37089554 PMCID: PMC10116804 DOI: 10.3389/fmicb.2023.1032073] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 03/21/2023] [Indexed: 04/05/2023] Open
Abstract
A prerequisite for prebiotic chemistry is the accumulation of critical building blocks of life. Some studies argue that more frequent impact events on the primitive Earth could have induced a more reducing steam atmosphere and thus favor widespread and more efficient synthesis of life building blocks. However, elevated temperature is also proposed to threaten the stability of organics and whether life building blocks could accumulate to appreciable levels in the reducing yet hot surface seawater beneath the steam atmosphere is still poorly examined. Here, we used a thermodynamic tool to examine the synthesis affinity of various life building blocks using inorganic gasses as reactants at elevated temperatures and corresponding steam pressures relevant with the steam-seawater interface. Our calculations show that although the synthesis affinity of all life building blocks decreases when temperature increases, many organics, including methane, methanol, and carboxylic acids, have positive synthesis affinity over a wide range of temperatures, implying that these species were favorable to form (>10-6 molal) in the surface seawater. However, cyanide and formaldehyde have overall negative affinities, suggesting that these critical compounds would tend to undergo hydrolysis in the surface seawaters. Most of the 18 investigated amino acids have positive affinities at temperature <220°C and their synthesis affinity increases under more alkaline conditions. Sugars, ribose, and nucleobases have overall negative synthesis affinities at the investigated range of temperatures. Synthesis affinities are shown to be sensitive to the hydrogen fugacity. Higher hydrogen fugacity (in equilibrium with FQI or IW) favors the synthesis and accumulation of nearly all the investigated compounds, except for HCN and its derivate products. In summary, our results suggest that reducing conditions induced by primitive impacts could indeed favor the synthesis/accumulation of some life building blocks, but some critical species, particularly HCN and nucleosides, were still unfavorable to accumulate to appreciable levels. Our results can provide helpful guidance for future efforts to search for or understand the stability of biomolecules on other planets like Mars and icy moons. We advocate examining craters formed by more reducing impactors to look for the preservation of prebiotic materials.
Collapse
Affiliation(s)
- Zongbin Zhang
- Deep Space Exploration Laboratory, University of Science and Technology of China, Hefei, China
- CAS Key Laboratory of Crust-Mantle Materials and Environments, School of Earth and Space Sciences, University of Science and Technology of China, Hefei, China
| | - Haofan Jiang
- CAS Key Laboratory of Crust-Mantle Materials and Environments, School of Earth and Space Sciences, University of Science and Technology of China, Hefei, China
| | - Pengcheng Ju
- State Key Laboratory of Continental Dynamics, Northwest University, Xi’an, China
- Shaanxi Key Laboratory of Early Life and Environment, Department of Geology, Northwest University, Xi’an, China
| | - Lu Pan
- Deep Space Exploration Laboratory, University of Science and Technology of China, Hefei, China
- Centre for Star and Planet Formation, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Joti Rouillard
- Deep Space Exploration Laboratory, University of Science and Technology of China, Hefei, China
- CAS Key Laboratory of Crust-Mantle Materials and Environments, School of Earth and Space Sciences, University of Science and Technology of China, Hefei, China
- CAS Center for Excellence in Comparative Planetology, University of Science and Technology of China (USTC), Hefei, Anhui, China
| | - Gentao Zhou
- Deep Space Exploration Laboratory, University of Science and Technology of China, Hefei, China
- CAS Key Laboratory of Crust-Mantle Materials and Environments, School of Earth and Space Sciences, University of Science and Technology of China, Hefei, China
| | - Fang Huang
- Deep Space Exploration Laboratory, University of Science and Technology of China, Hefei, China
| | - Jihua Hao
- Deep Space Exploration Laboratory, University of Science and Technology of China, Hefei, China
- CAS Key Laboratory of Crust-Mantle Materials and Environments, School of Earth and Space Sciences, University of Science and Technology of China, Hefei, China
- CAS Center for Excellence in Comparative Planetology, University of Science and Technology of China (USTC), Hefei, Anhui, China
| |
Collapse
|
3
|
Sallembien Q, Bouteiller L, Crassous J, Raynal M. Possible chemical and physical scenarios towards biological homochirality. Chem Soc Rev 2022; 51:3436-3476. [PMID: 35377372 DOI: 10.1039/d1cs01179k] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The single chirality of biological molecules in terrestrial biology raises more questions than certitudes about its origin. The emergence of biological homochirality (BH) and its connection with the appearance of life have elicited a large number of theories related to the generation, amplification and preservation of a chiral bias in molecules of life under prebiotically relevant conditions. However, a global scenario is still lacking. Here, the possibility of inducing a significant chiral bias "from scratch", i.e. in the absence of pre-existing enantiomerically-enriched chemical species, will be considered first. It includes phenomena that are inherent to the nature of matter itself, such as the infinitesimal energy difference between enantiomers as a result of violation of parity in certain fundamental interactions, and physicochemical processes related to interactions between chiral organic molecules and physical fields, polarized particles, polarized spins and chiral surfaces. The spontaneous emergence of chirality in the absence of detectable chiral physical and chemical sources has recently undergone significant advances thanks to the deracemization of conglomerates through Viedma ripening and asymmetric auto-catalysis with the Soai reaction. All these phenomena are commonly discussed as plausible sources of asymmetry under prebiotic conditions and are potentially accountable for the primeval chiral bias in molecules of life. Then, several scenarios will be discussed that are aimed to reflect the different debates about the emergence of BH: extra-terrestrial or terrestrial origin (where?), nature of the mechanisms leading to the propagation and enhancement of the primeval chiral bias (how?) and temporal sequence between chemical homochirality, BH and life emergence (when?). Intense and ongoing theories regarding the emergence of optically pure molecules at different moments of the evolution process towards life, i.e. at the levels of building blocks of Life, of the instructed or functional polymers, or even later at the stage of more elaborated chemical systems, will be critically discussed. The underlying principles and the experimental evidence will be commented for each scenario with particular attention on those leading to the induction and enhancement of enantiomeric excesses in proteinogenic amino acids, natural sugars, and their intermediates or derivatives. The aim of this review is to propose an updated and timely synopsis in order to stimulate new efforts in this interdisciplinary field.
Collapse
Affiliation(s)
- Quentin Sallembien
- Sorbonne Université, CNRS, Institut Parisien de Chimie Moléculaire, Equipe Chimie des Polymères, 4 Place Jussieu, 75005 Paris, France.
| | - Laurent Bouteiller
- Sorbonne Université, CNRS, Institut Parisien de Chimie Moléculaire, Equipe Chimie des Polymères, 4 Place Jussieu, 75005 Paris, France.
| | - Jeanne Crassous
- Univ Rennes, CNRS, Institut des Sciences Chimiques de Rennes, ISCR-UMR 6226, F-35000 Rennes, France.
| | - Matthieu Raynal
- Sorbonne Université, CNRS, Institut Parisien de Chimie Moléculaire, Equipe Chimie des Polymères, 4 Place Jussieu, 75005 Paris, France.
| |
Collapse
|
4
|
The Way forward for the Origin of Life: Prions and Prion-Like Molecules First Hypothesis. Life (Basel) 2021; 11:life11090872. [PMID: 34575021 PMCID: PMC8467930 DOI: 10.3390/life11090872] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/11/2021] [Accepted: 08/22/2021] [Indexed: 11/18/2022] Open
Abstract
In this paper the hypothesis that prions and prion-like molecules could have initiated the chemical evolutionary process which led to the eventual emergence of life is reappraised. The prions first hypothesis is a specific application of the protein-first hypothesis which asserts that protein-based chemical evolution preceded the evolution of genetic encoding processes. This genetics-first hypothesis asserts that an “RNA-world era” came before protein-based chemical evolution and rests on a singular premise that molecules such as RNA, acetyl-CoA, and NAD are relics of a long line of chemical evolutionary processes preceding the Last Universal Common Ancestor (LUCA). Nevertheless, we assert that prions and prion-like molecules may also be relics of chemical evolutionary processes preceding LUCA. To support this assertion is the observation that prions and prion-like molecules are involved in a plethora of activities in contemporary biology in both complex (eukaryotes) and primitive life forms. Furthermore, a literature survey reveals that small RNA virus genomes harbor information about prions (and amyloids). If, as has been presumed by proponents of the genetics-first hypotheses, small viruses were present during an RNA world era and were involved in some of the earliest evolutionary processes, this places prions and prion-like molecules potentially at the heart of the chemical evolutionary process whose eventual outcome was life. We deliberate on the case for prions and prion-like molecules as the frontier molecules at the dawn of evolution of living systems.
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Abstract
How did life begin on Earth? And is there life elsewhere in the Cosmos? Challenging questions, indeed. The series of conferences established by NoR CEL in 2013 addresses these very questions. This paper comprises a summary report of oral presentations that were delivered by NoR CEL’s network members during the 2018 Athens conference and, as such, disseminates the latest research which they have put forward. More in depth material can be found by consulting the contributors referenced papers. Overall, the outcome of this conspectus on the conference demonstrates a case for the existence of “probable chemistry” during the prebiotic epoch.
Collapse
|
7
|
Chioccioli S, Del Duca S, Vassallo A, Castronovo LM, Fani R. Exploring the role of the histidine biosynthetic hisF gene in cellular metabolism and in the evolution of (ancestral) genes: from LUCA to the extant (micro)organisms. Microbiol Res 2020; 240:126555. [PMID: 32673985 DOI: 10.1016/j.micres.2020.126555] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/29/2020] [Accepted: 07/06/2020] [Indexed: 01/14/2023]
Abstract
Histidine biosynthesis is an ancestral pathway that was assembled before the appearance of the Last Universal Common Ancestor; afterwards, it remained unaltered in all the extant histidine-synthesizing (micro)organisms. It is a metabolic cross-road interconnecting histidine biosynthesis to nitrogen metabolism and the de novo synthesis of purines. This interconnection is due to the reaction catalyzed by the products of hisH and hisF genes. The latter gene is an excellent model to study which trajectories have been followed by primordial cells to build the first metabolic routes, since its evolution is the result of different molecular rearrangement events, i.e. gene duplication, gene fusion, gene elongation, and domain shuffling. Additionally, this review summarizes data concerning the involvement of hisF and its product in other different cellular processes, revealing that HisF very likely plays a role also in cell division control and involvement in virulence and nodule development in different bacteria. From the metabolic viewpoint, these results suggest that HisF plays a central role in cellular metabolism, highlighting the interconnections of different metabolic pathways.
Collapse
Affiliation(s)
- Sofia Chioccioli
- Department of Biology, University of Florence, 50019, Sesto Fiorentino, Italy
| | - Sara Del Duca
- Department of Biology, University of Florence, 50019, Sesto Fiorentino, Italy
| | - Alberto Vassallo
- Department of Biology, University of Florence, 50019, Sesto Fiorentino, Italy
| | | | - Renato Fani
- Department of Biology, University of Florence, 50019, Sesto Fiorentino, Italy.
| |
Collapse
|
8
|
The Role of Gene Elongation in the Evolution of Histidine Biosynthetic Genes. Microorganisms 2020; 8:microorganisms8050732. [PMID: 32414216 PMCID: PMC7284861 DOI: 10.3390/microorganisms8050732] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/07/2020] [Accepted: 05/11/2020] [Indexed: 11/29/2022] Open
Abstract
Gene elongation is a molecular mechanism consisting of an in-tandem duplication of a gene and divergence and fusion of the two copies, resulting in a gene constituted by two divergent paralogous modules. The aim of this work was to evaluate the importance of gene elongation in the evolution of histidine biosynthetic genes and to propose a possible evolutionary model for some of them. Concerning the genes hisA and hisF, which code for two homologous (β/α)8-barrels, it has been proposed that the two extant genes could be the result of a cascade of gene elongation/domain shuffling events starting from an ancestor gene coding for just one (β/α) module. A gene elongation event has also been proposed for the evolution of hisB and hisD; structural analyses revealed the possibility of an early elongation event, resulting in the repetition of modules. Furthermore, it is quite possible that the gene elongations responsible for the evolution of the four proteins occurred before the earliest phylogenetic divergence. In conclusion, gene elongation events seem to have played a crucial role in the evolution of the histidine biosynthetic pathway, and they may have shaped the structures of many genes during the first steps of their evolution.
Collapse
|
9
|
Molecules to Microbes. SCI 2020. [DOI: 10.3390/sci2020020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
How did life begin on Earth? And is there life elsewhere in the Cosmos? Challenging questions, indeed. The series of conferences established by NoR CEL in 2013, addresses these very same questions. The basis for this paper is the summary report of oral presentations that were delivered by NoR CEL’s network members during the 2018 Athens conference and, as such, disseminates the latest research which they have put forward. More in depth material can be found by consulting the contributors referenced papers. Overall, the outcome of this conspectus on the conference demonstrates a case for the existence of “probable chemistry” during the prebiotic epoch.
Collapse
|
10
|
On the Habitable Lifetime of Terrestrial Worlds with High Radionuclide Abundances. ACTA ACUST UNITED AC 2020. [DOI: 10.3847/2041-8213/ab68e5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
11
|
Abstract
How did life begin on Earth? And is there life elsewhere in the Cosmos? Challenging questions, indeed. The series of conferences established by NoR CEL in 2013, addresses these very same questions. The basis for this paper is the summary report of oral presentations that were delivered by NoR CEL’s network members during the 2018 Athens conference and, as such, disseminates the latest research which they have put forward. More in depth material can be found by consulting the contributors referenced papers. Overall, the outcome of this conspectus on the conference demonstrates a case for the existence of “probable chemistry” during the prebiotic epoch.
Collapse
|
12
|
Limaye SS, Mogul R, Smith DJ, Ansari AH, Słowik GP, Vaishampayan P. Venus' Spectral Signatures and the Potential for Life in the Clouds. ASTROBIOLOGY 2018; 18:1181-1198. [PMID: 29600875 PMCID: PMC6150942 DOI: 10.1089/ast.2017.1783] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 02/11/2018] [Indexed: 05/17/2023]
Abstract
The lower cloud layer of Venus (47.5-50.5 km) is an exceptional target for exploration due to the favorable conditions for microbial life, including moderate temperatures and pressures (∼60°C and 1 atm), and the presence of micron-sized sulfuric acid aerosols. Nearly a century after the ultraviolet (UV) contrasts of Venus' cloud layer were discovered with Earth-based photographs, the substances and mechanisms responsible for the changes in Venus' contrasts and albedo are still unknown. While current models include sulfur dioxide and iron chloride as the UV absorbers, the temporal and spatial changes in contrasts, and albedo, between 330 and 500 nm, remain to be fully explained. Within this context, we present a discussion regarding the potential for microorganisms to survive in Venus' lower clouds and contribute to the observed bulk spectra. In this article, we provide an overview of relevant Venus observations, compare the spectral and physical properties of Venus' clouds to terrestrial biological materials, review the potential for an iron- and sulfur-centered metabolism in the clouds, discuss conceivable mechanisms of transport from the surface toward a more habitable zone in the clouds, and identify spectral and biological experiments that could measure the habitability of Venus' clouds and terrestrial analogues. Together, our lines of reasoning suggest that particles in Venus' lower clouds contain sufficient mass balance to harbor microorganisms, water, and solutes, and potentially sufficient biomass to be detected by optical methods. As such, the comparisons presented in this article warrant further investigations into the prospect of biosignatures in Venus' clouds.
Collapse
Affiliation(s)
- Sanjay S. Limaye
- Space Science and Engineering Center, University of Wisconsin, Madison, Wisconsin
| | - Rakesh Mogul
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, California
| | - David J. Smith
- Space Biosciences Research Branch, NASA Ames Research Center, Moffett Field, California
| | - Arif H. Ansari
- Precambrian Palaeobotany Laboratory, Birbal Sahni Institute of Palaeosciences, Lucknow, India
| | | | - Parag Vaishampayan
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California
| |
Collapse
|
13
|
Schulze-Makuch D, Crawford IA. Was There an Early Habitability Window for Earth's Moon? ASTROBIOLOGY 2018; 18:985-988. [PMID: 30035616 PMCID: PMC6225594 DOI: 10.1089/ast.2018.1844] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 06/20/2018] [Indexed: 06/08/2023]
Affiliation(s)
- Dirk Schulze-Makuch
- Center for Astronomy and Astrophysics, Technical University Berlin, Berlin, Germany
- School of the Environment, Washington State University, Pullman, Washington, USA
| | - Ian A. Crawford
- Department of Earth and Planetary Sciences, Birkbeck College, University of London, London, UK
| |
Collapse
|
14
|
The Abiotic Chemistry of Thiolated Acetate Derivatives and the Origin of Life. Sci Rep 2016; 6:29883. [PMID: 27443234 PMCID: PMC4956751 DOI: 10.1038/srep29883] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Accepted: 06/23/2016] [Indexed: 12/29/2022] Open
Abstract
Thioesters and thioacetic acid (TAA) have been invoked as key reagents for the origin of life as activated forms of acetate analogous to acetyl-CoA. These species could have served as high-energy group-transfer reagents and allowed carbon insertions to form higher molecular weight compounds such as pyruvate. The apparent antiquity of the Wood-Ljungdahl CO2 fixation pathway and its presence in organisms which inhabit hydrothermal (HT) environments has also led to suggestions that there may be a connection between the abiotic chemistry of compounds similar to TAA and the origins of metabolism. These compounds' apparent chemical simplicity has made their prebiotic availability assumed, however, although the kinetic behavior and thermochemical properties of TAA and analogous esters have been preliminarily explored in other contexts, the geochemical relevance of these compounds merits further evaluation. Therefore, the chemical behavior of the simplest thiolated acetic acid derivatives, TAA and methylthioacetate (MTA) were explored here. Using laboratory measurements, literature data, and thermochemical models, we examine the plausibility of the accumulation of these compounds in various geological settings. Due to the high free energy change of their hydrolysis and corresponding low equilibrium constants, it is unlikely that these species could have accumulated abiotically to any significant extant.
Collapse
|
15
|
Abstract
The requirements for life on Earth, its elemental composition, and its environmental limits provide a way to assess the habitability of exoplanets. Temperature is key both because of its influence on liquid water and because it can be directly estimated from orbital and climate models of exoplanetary systems. Life can grow and reproduce at temperatures as low as -15 °C, and as high as 122 °C. Studies of life in extreme deserts show that on a dry world, even a small amount of rain, fog, snow, and even atmospheric humidity can be adequate for photosynthetic production producing a small but detectable microbial community. Life is able to use light at levels less than 10(-5) of the solar flux at Earth. UV or ionizing radiation can be tolerated by many microorganisms at very high levels and is unlikely to be life limiting on an exoplanet. Biologically available nitrogen may limit habitability. Levels of O2 over a few percent on an exoplanet would be consistent with the presence of multicellular organisms and high levels of O2 on Earth-like worlds indicate oxygenic photosynthesis. Other factors such as pH and salinity are likely to vary and not limit life over an entire planet or moon.
Collapse
|
16
|
McKay CP, Anbar AD, Porco C, Tsou P. Follow the plume: the habitability of Enceladus. ASTROBIOLOGY 2014; 14:352-355. [PMID: 24684187 DOI: 10.1089/ast.2014.1158] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The astrobiological exploration of other worlds in our Solar System is moving from initial exploration to more focused astrobiology missions. In this context, we present the case that the plume of Enceladus currently represents the best astrobiology target in the Solar System. Analysis of the plume by the Cassini mission indicates that the steady plume derives from a subsurface liquid water reservoir that contains organic carbon, biologically available nitrogen, redox energy sources, and inorganic salts. Furthermore, samples from the plume jetting out into space are accessible to a low-cost flyby mission. No other world has such well-studied indications of habitable conditions. Thus, the science goals that would motivate an Enceladus mission are more advanced than for any other Solar System body. The goals of such a mission must go beyond further geophysical characterization, extending to the search for biomolecular evidence of life in the organic-rich plume. This will require improved in situ investigations and a sample return.
Collapse
|
17
|
Neupane A, Nepal MP, Piya S, Subramanian S, Rohila JS, Reese RN, Benson BV. Identification, nomenclature, and evolutionary relationships of mitogen-activated protein kinase (MAPK) genes in soybean. Evol Bioinform Online 2013; 9:363-86. [PMID: 24137047 PMCID: PMC3785387 DOI: 10.4137/ebo.s12526] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Mitogen-activated protein kinase (MAPK) genes in eukaryotes regulate various developmental and physiological processes including those associated with biotic and abiotic stresses. Although MAPKs in some plant species including Arabidopsis have been identified, they are yet to be identified in soybean. Major objectives of this study were to identify GmMAPKs, assess their evolutionary relationships, and analyze their functional divergence. We identified a total of 38 MAPKs, eleven MAPKKs, and 150 MAPKKKs in soybean. Within the GmMAPK family, we also identified a new clade of six genes: four genes with TEY and two genes with TQY motifs requiring further investigation into possible legume-specific functions. The results indicated the expansion of the GmMAPK families attributable to the ancestral polyploidy events followed by chromosomal rearrangements. The GmMAPK and GmMAPKKK families were substantially larger than those in other plant species. The duplicated GmMAPK members presented complex evolutionary relationships and functional divergence when compared to their counterparts in Arabidopsis. We also highlighted existing nomenclatural issues, stressing the need for nomenclatural consistency. GmMAPK identification is vital to soybean crop improvement, and novel insights into the evolutionary relationships will enhance our understanding about plant genome evolution.
Collapse
Affiliation(s)
- Achal Neupane
- Department of Biology and Microbiology, South Dakota State University, Brookings SD, USA
| | | | | | | | | | | | | |
Collapse
|
18
|
Prebiotic chemistry: geochemical context and reaction screening. Life (Basel) 2013; 3:331-45. [PMID: 25369745 PMCID: PMC4187135 DOI: 10.3390/life3020331] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 04/17/2013] [Accepted: 04/18/2013] [Indexed: 11/23/2022] Open
Abstract
The origin of life on Earth is widely believed to have required the reactions of organic compounds and their self- and/or environmental organization. What those compounds were remains open to debate, as do the environment in and process or processes by which they became organized. Prebiotic chemistry is the systematic organized study of these phenomena. It is difficult to study poorly defined phenomena, and research has focused on producing compounds and structures familiar to contemporary biochemistry, which may or may not have been crucial for the origin of life. Given our ignorance, it may be instructive to explore the extreme regions of known and future investigations of prebiotic chemistry, where reactions fail, that will relate them to or exclude them from plausible environments where they could occur. Come critical parameters which most deserve investigation are discussed.
Collapse
|
19
|
Shimada A, Ozaki H. Flexible enantioselectivity of tryptophanase attributable to benzene ring in heterocyclic moiety of d-tryptophan. Life (Basel) 2012; 2:215-28. [PMID: 25382167 PMCID: PMC4187121 DOI: 10.3390/life2020215] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Revised: 05/02/2012] [Accepted: 05/17/2012] [Indexed: 11/30/2022] Open
Abstract
The invariance principle of enzyme enantioselectivity must be absolute because it is absolutely essential to the homochiral biological world. Most enzymes are strictly enantioselective, and tryptophanase is one of the enzymes with extreme absolute enantioselectivity for L-tryptophan. Contrary to conventional knowledge about the principle, tryptophanase becomes flexible to catalyze D-tryptophan in the presence of diammonium hydrogenphosphate. Since D-amino acids are ordinarily inert or function as inhibitors even though they are bound to the active site, the inhibition behavior of D-tryptophan and several inhibitors involved in this process was examined in terms of kinetics to explain the reason for this flexible enantioselectivity in the presence of diammonium hydrogenphosphate. Diammonium hydrogenphosphate gave tryptophanase a small conformational change so that D-tryptophan could work as a substrate. As opposed to other D-amino acids, D-tryptophan is a very bulky amino acid with a benzene ring in its heterocyclic moiety, and so we suggest that this structural feature makes the catalysis of D-tryptophan degradation possible, consequently leading to the flexible enantioselectivity. The present results not only help to understand the mechanism of enzyme enantioselectivity, but also shed light on the origin of homochirality.
Collapse
Affiliation(s)
- Akihiko Shimada
- Sustainable Environmental Studies, Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan.
| | - Haruka Ozaki
- Sustainable Environmental Studies, Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan.
| |
Collapse
|
20
|
Huber C, Kraus F, Hanzlik M, Eisenreich W, Wächtershäuser G. Elements of metabolic evolution. Chemistry 2012; 18:2063-80. [PMID: 22241585 DOI: 10.1002/chem.201102914] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Indexed: 11/09/2022]
Abstract
Research into the origin of evolution is polarized between a genetics-first approach, with its focus on polymer replication, and a metabolism-first approach that takes aim at chemical reaction cycles. Taking the latter approach, we explored reductive carbon fixation in a volcanic hydrothermal setting, driven by the chemical potential of quenched volcanic fluids for converting volcanic C1 compounds into organic products by transition-metal catalysts. These catalysts are assumed to evolve by accepting ever-new organic products as ligands for enhancing their catalytic power, which in turn enhances the rates of synthetic pathways that give rise to ever-new organic products, with the overall effect of a self-expanding metabolism. We established HCN, CO, and CH(3)SH as carbon nutrients, CO and H(2) as reductants, and iron-group transition metals as catalysts. In one case, we employed the "cyano-system" [Ni(OH)(CN)] with [Ni(CN)(4)](2-) as the dominant nickel-cyano species. This reaction mainly produced α-amino acids and α-hydroxy acids as well as various intermediates and derivatives. An organo-metal-catalyzed mechanism is suggested that mainly builds carbon skeletons by repeated cyano insertions, with minor CO insertions in the presence of CO. The formation of elemental nickel (Ni(0)) points to an active reduced-nickel species. In another case, we employed the mercapto-carbonyl system [Co(2)(CO)(8)]/Ca(OH)(2)/CO for the double-carbonylation of mercaptans. In a "hybrid system", we combined benzyl mercaptan with the cyano system, in which [Ni(OH)(CN)] was the most productive for the double-carbon-fixation reaction. Finally, we demonstrated that the addition of products of the cyano system (Gly, Ala) to the hybrid system increased productivity. These results demonstrate the chemical possibility of metabolic evolution through rate-promotion of one synthetic reaction by the products of another.
Collapse
Affiliation(s)
- Claudia Huber
- Lehrstuhl für Biochemie, Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | | | | | | | | |
Collapse
|
21
|
Bayesian analysis of the astrobiological implications of life's early emergence on Earth. Proc Natl Acad Sci U S A 2011; 109:395-400. [PMID: 22198766 DOI: 10.1073/pnas.1111694108] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Life arose on Earth sometime in the first few hundred million years after the young planet had cooled to the point that it could support water-based organisms on its surface. The early emergence of life on Earth has been taken as evidence that the probability of abiogenesis is high, if starting from young Earth-like conditions. We revisit this argument quantitatively in a bayesian statistical framework. By constructing a simple model of the probability of abiogenesis, we calculate a bayesian estimate of its posterior probability, given the data that life emerged fairly early in Earth's history and that, billions of years later, curious creatures noted this fact and considered its implications. We find that, given only this very limited empirical information, the choice of bayesian prior for the abiogenesis probability parameter has a dominant influence on the computed posterior probability. Although terrestrial life's early emergence provides evidence that life might be abundant in the universe if early-Earth-like conditions are common, the evidence is inconclusive and indeed is consistent with an arbitrarily low intrinsic probability of abiogenesis for plausible uninformative priors. Finding a single case of life arising independently of our lineage (on Earth, elsewhere in the solar system, or on an extrasolar planet) would provide much stronger evidence that abiogenesis is not extremely rare in the universe.
Collapse
|
22
|
Cleaves HJ. The origin of the biologically coded amino acids. J Theor Biol 2010; 263:490-8. [PMID: 20034500 DOI: 10.1016/j.jtbi.2009.12.014] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2009] [Revised: 11/19/2009] [Accepted: 12/14/2009] [Indexed: 11/29/2022]
Affiliation(s)
- H James Cleaves
- Geophysical Laboratory, The Carnegie Institution for Science, 5251 Broad Branch Road NW, Washington, DC 20015, USA.
| |
Collapse
|
23
|
Tangen U. Enzyme-like replication de novo in a microcontroller environment. ARTIFICIAL LIFE 2010; 16:311-328. [PMID: 20712511 DOI: 10.1162/artl_a_00012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The desire to start evolution from scratch inside a computer memory is as old as computing. Here we demonstrate how viable computer programs can be established de novo in a Precambrian environment without supplying any specific instantiation, just starting with random bit sequences. These programs are not self-replicators, but act much more like catalysts. The microcontrollers used in the end are the result of a long series of simplifications. The objective of this simplification process was to produce universal machines with a human-readable interface, allowing software and/or hardware evolution to be studied. The power of the instruction set can be modified by introducing a secondary structure-folding mechanism, which is a state machine, allowing nontrivial replication to emerge with an instruction width of only a few bits. This state-machine approach not only attenuates the problems of brittleness and encoding functionality (too few bits available for coding, and too many instructions needed); it also enables the study of hardware evolution as such. Furthermore, the instruction set is sufficiently powerful to permit external signals to be processed. This information-theoretic approach forms one vertex of a triangle alongside artificial cell research and experimental research on the creation of life. Hopefully this work helps develop an understanding of how information—in a similar sense to the account of functional information described by Hazen et al.—is created by evolution and how this information interacts with or is embedded in its physico-chemical environment.
Collapse
|
24
|
Follmann H, Brownson C. Darwin’s warm little pond revisited: from molecules to the origin of life. Naturwissenschaften 2009; 96:1265-92. [PMID: 19760276 DOI: 10.1007/s00114-009-0602-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2009] [Revised: 08/05/2009] [Accepted: 08/10/2009] [Indexed: 11/26/2022]
Affiliation(s)
- Hartmut Follmann
- Institute of Biology, University of Kassel, 34109, Kassel, Germany.
| | | |
Collapse
|
25
|
Kalaitzis JA, Lauro FM, Neilan BA. Mining cyanobacterial genomes for genes encoding complex biosynthetic pathways. Nat Prod Rep 2009; 26:1447-65. [PMID: 19844640 DOI: 10.1039/b817074f] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- John A Kalaitzis
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
| | | | | |
Collapse
|
26
|
Simons MJP. The evolution of the cyanobacterial posttranslational clock from a primitive "phoscillator". J Biol Rhythms 2009; 24:175-82. [PMID: 19465694 DOI: 10.1177/0748730409333953] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Cyanobacteria were among the 1st organisms to evolve on earth. The molecular circadian clock proteins of cyanobacteria and their phylogenetics have recently been elucidated. This allows for a conjecture on the evolution of 1 of the 1st circadian clocks. A scenario has now been created by combining known in vitro and in vivo properties of the 3 clock proteins of cyanobacteria (KaiA, KaiB, and KaiC). This scenario describes the evolution of the cyanobacterial clock in gradual steps: evolving from a masking mechanism, toward an hourglass, into a clock.
Collapse
Affiliation(s)
- Mirre J P Simons
- Department of Chronobiology, University of Groningen, Haren, The Netherlands.
| |
Collapse
|
27
|
A possible mechanism for evading temperature quantum decoherence in living matter by feshbach resonance. Int J Mol Sci 2009; 10:2084-106. [PMID: 19564941 PMCID: PMC2695269 DOI: 10.3390/ijms10052084] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2009] [Revised: 04/29/2009] [Accepted: 05/11/2009] [Indexed: 12/02/2022] Open
Abstract
A new possible scenario for the origin of the molecular collective behaviour associated with the emergence of living matter is presented. We propose that the transition from a non-living to a living cell could be mapped to a quantum transition to a coherent entanglement of condensates, like in a multigap BCS superconductor. Here the decoherence-evading qualities at high temperature are based on the Feshbach resonance that has been recently proposed as the driving mechanism for high Tc superconductors. Finally we discuss how the proximity to a particular critical point is relevant to the emergence of coherence in the living cell.
Collapse
|
28
|
Fani R, Fondi M. Origin and evolution of metabolic pathways. Phys Life Rev 2009; 6:23-52. [PMID: 20416849 DOI: 10.1016/j.plrev.2008.12.003] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2008] [Revised: 11/27/2008] [Accepted: 12/01/2008] [Indexed: 10/21/2022]
Abstract
The emergence and evolution of metabolic pathways represented a crucial step in molecular and cellular evolution. In fact, the exhaustion of the prebiotic supply of amino acids and other compounds that were likely present in the ancestral environment, imposed an important selective pressure, favoring those primordial heterotrophic cells which became capable of synthesizing those molecules. Thus, the emergence of metabolic pathways allowed primitive organisms to become increasingly less-dependent on exogenous sources of organic compounds. Comparative analyses of genes and genomes from organisms belonging to Archaea, Bacteria and Eukarya revealed that, during evolution, different forces and molecular mechanisms might have driven the shaping of genomes and the arisal of new metabolic abilities. Among these gene elongations, gene and operon duplications undoubtedly played a major role since they can lead to the (immediate) appearance of new genetic material that, in turn, might undergo evolutionary divergence giving rise to new genes coding for new metabolic abilities. Gene duplication has been invoked in the different schemes proposed to explain why and how the extant metabolic pathways have arisen and shaped. Both the analysis of completely sequenced genomes and directed evolution experiments strongly support one of them, i.e. the patchwork hypothesis, according to which metabolic pathways have been assembled through the recruitment of primitive enzymes that could react with a wide range of chemically related substrates. However, the analysis of the structure and organization of genes belonging to ancient metabolic pathways, such as histidine biosynthesis and nitrogen fixation, suggested that other different hypothesis, i.e. the retrograde hypothesis or the semi-enzymatic theory, may account for the arisal of some metabolic routes.
Collapse
Affiliation(s)
- Renato Fani
- Laboratory of Microbial and Molecular Evolution, Department of Evolutionary Biology, Via Romana 17-19, University of Florence, Italy
| | | |
Collapse
|
29
|
McKay CP, Porco CC, Altheide T, Davis WL, Kral TA. The possible origin and persistence of life on Enceladus and detection of biomarkers in the plume. ASTROBIOLOGY 2008; 8:909-919. [PMID: 18950287 DOI: 10.1089/ast.2008.0265] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The jets of icy particles and water vapor issuing from the south pole of Enceladus are evidence for activity driven by some geophysical energy source. The vapor has also been shown to contain simple organic compounds, and the south polar terrain is bathed in excess heat coming from below. The source of the ice and vapor, and the mechanisms that accelerate the material into space, remain obscure. However, it is possible that a liquid water environment exists beneath the south polar cap, which may be conducive to life. Several theories for the origin of life on Earth would apply to Enceladus. These are (1) origin in an organic-rich mixture, (2) origin in the redox gradient of a submarine vent, and (3) panspermia. There are three microbial ecosystems on Earth that do not rely on sunlight, oxygen, or organics produced at the surface and, thus, provide analogues for possible ecologies on Enceladus. Two of these ecosystems are found deep in volcanic rock, and the primary productivity is based on the consumption by methanogens of hydrogen produced by rock reactions with water. The third ecosystem is found deep below the surface in South Africa and is based on sulfur-reducing bacteria consuming hydrogen and sulfate, both of which are ultimately produced by radioactive decay. Methane has been detected in the plume of Enceladus and may be biological in origin. An indicator of biological origin may be the ratio of non-methane hydrocarbons to methane, which is very low (0.001) for biological sources but is higher (0.1-0.01) for nonbiological sources. Thus, Cassini's instruments may detect plausible evidence for life by analysis of hydrocarbons in the plume during close encounters.
Collapse
Affiliation(s)
- Christopher P McKay
- Space Science Division, NASA Ames Research Center, Moffett Field, California 94035, USA.
| | | | | | | | | |
Collapse
|
30
|
Hengeveld R. Two approaches to the study of the origin of life. Acta Biotheor 2007; 55:97-131. [PMID: 17891504 DOI: 10.1007/s10441-007-9017-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2007] [Accepted: 05/07/2007] [Indexed: 10/22/2022]
Abstract
This paper compares two approaches that attempt to explain the origin of life, or biogenesis. The more established approach is one based on chemical principles, whereas a new, yet not widely known approach begins from a physical perspective. According to the first approach, life would have begun with--often organic--compounds. After having developed to a certain level of complexity and mutual dependence within a non-compartmentalised organic soup, they would have assembled into a functioning cell. In contrast, the second, physical type of approach has life developing within tiny compartments from the beginning. It emphasises the importance of redox reactions between inorganic elements and compounds found on two sides of a compartmental boundary. Without this boundary, "life" would not have begun, nor have been maintained; this boundary--and the complex cell membrane that evolved from it--forms the essence of life.
Collapse
Affiliation(s)
- R Hengeveld
- Institute of Ecological Science, Vrije Universiteit, De Boelelaan 1087, 1081 HV, Amsterdam, The Netherlands.
| |
Collapse
|
31
|
Costanzo G, Saladino R, Crestini C, Ciciriello F, Di Mauro E. Formamide as the main building block in the origin of nucleic acids. BMC Evol Biol 2007; 7 Suppl 2:S1. [PMID: 17767725 PMCID: PMC1963486 DOI: 10.1186/1471-2148-7-s2-s1] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The simplest molecules grouping the four most common elements of the universe H,C,O and N (with the exception of the biologically inert He) are isocyanate HNCO and formamide H2NCOH. Reasons for the availability of formamide on prebiotic Earth are presented. We review evidence showing that formamide in the presence of largely available catalysts and by moderate heating yields the complete set of nucleic bases necessary for the formation of nucleic acids. Formamide also favours the formation of acyclonucleosides and the phosphorylation and trans-phosphorylation of nucleosides, thus providing a plausible chemical frame for the passage from a simple one-carbon compound to nucleic polymers. Physico-chemical conditions exist in which formamide favours the stability of the phosphoester bonds in nucleic polymers relative to that of the same bonds in monomers. Starting from a formamide-laden environment subject only to the laws of chemistry, a hypothesis is outlined sketching the passage towards an aqueous world in which Darwinian rules apply.
Collapse
Affiliation(s)
- Giovanna Costanzo
- Istituto di Biologia e Patologia Molecolari, CNR, P.le Aldo Moro, 5, Rome 00185, Italy
| | - Raffaele Saladino
- Istituto di Biologia e Patologia Molecolari, CNR, P.le Aldo Moro, 5, Rome 00185, Italy
- Dipartimento A.B.A.C., Università della Tuscia, Via San Camillo De Lellis, Viterbo, Italy
| | - Claudia Crestini
- Marine Dipartimento di Scienze e Tecnologie Chimiche, Università "Tor Vergata", Rome 00133, Italy
| | - Fabiana Ciciriello
- Fondazione "Istituto Pasteur-Fondazione Cenci-Bolognetti" c/o Dipartimento di Genetica e Biologia Molecolare, Università "La Sapienza" di Roma, P.le Aldo Moro, 5, Rome 00185, Italy
| | - Ernesto Di Mauro
- Ernesto Di Mauro, Dipartimento di Genetica e Biologia Molecolare, Università "La Sapienza" di Roma, P.le Aldo Moro, 5, 00185 Rome, Italy
| |
Collapse
|
32
|
Rimola A, Sodupe M, Ugliengo P. Aluminosilicate surfaces as promoters for peptide bond formation: an assessment of Bernal's hypothesis by ab initio methods. J Am Chem Soc 2007; 129:8333-44. [PMID: 17552521 DOI: 10.1021/ja070451k] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The role in prebiotic chemistry that Brønsted and Lewis sites, both present at the surface of common aluminosilicates, may have played in favoring the peptide bond formation has been addressed by ab initio methods within a cluster approach. B3LYP/6-31+G(d,p) free energy potential energy surfaces have been fully characterized for the model reaction glycine + NH3 --> 2-NH2 acetamide (mimicking the true 2 Gly --> GlyGly one) occurring on (i) a Lewis site, (ii) a Brønsted site, and (iii) a combined action of Lewis/Brønsted sites. Compared to the gas-phase (gp) activation free energy of 50 kcal/mol, the Lewis site alone reduces the gp barrier to 41 kcal/mol, whereas the activation by the Brønsted site dramatically reduces the barrier to about 18 kcal/mol. Nevertheless, formation of the prereactant complex in this latter case will rarely occur, since water will easily displace the glycine molecule interacting with the Brønsted site. However, if a realistic feldspar surface with neighboring Brønsted and Lewis sites is considered, the proper prereactant complex is highly stabilized by a simultaneous interaction with the Lewis and the Brønsted sites, in such a way that the Lewis site strongly attaches the glycine molecule to the surface whereas the Brønsted site efficiently catalyzes the condensation reaction, showing that the interplay between Lewis/Brønsted sites is an important issue. The free energy barrier computed for the realistic feldspar surface model is 26 kcal/mol. The role of dispersive interactions on the free energy barrier and the stabilization of the final product, not accounted for by the B3LYP functional, have been estimated and shown to be substantial. Speculations about further elongation of the formed dipeptide have been put forward on the basis of the relatively strong interaction energy of the formed GlyGly dipeptide with the aluminosilicate surface.
Collapse
Affiliation(s)
- Albert Rimola
- Departament de Química, Universitat Autonoma de Barcelona, Bellaterra, Spain
| | | | | |
Collapse
|
33
|
Abstract
The First Cell arose in the previously pre-biotic world with the coming together of several entities that gave a single vesicle the unique chance to carry out three essential and quite different life processes. These were: (a) to copy informational macromolecules, (b) to carry out specific catalytic functions, and (c) to couple energy from the environment into usable chemical forms. These would foster subsequent cellular evolution and metabolism. Each of these three essential processes probably originated and was lost many times prior to The First Cell, but only when these three occurred together was life jump-started and Darwinian evolution of organisms began. The replication of informational molecules that made only occasional mistakes allowed evolution to form all the basic components of cellular life. Ribozymes, the first informational molecules, were also catalytic. Energy coupling required the formation of a closed lipid surface to generate and maintain an ion-motive gradient. The closed vesicle partitioned components and avoided dilution within the primordial sea. Closed membranes were essential for the first self-reproducing cell to arise and for its descendants to disperse. Subsequent cellular development after the origin of The First Cell led to the beginnings of intermediary metabolism and membrane transport processes. This long process, subject to strong evolutionary selection, developed the cellular biology that is now shared by all extant organisms.
Collapse
Affiliation(s)
- Arthur L Koch
- Biology Department, Indiana University, Bloomington, IN 47405-6801, USA
| | | |
Collapse
|
34
|
Delaye L, Becerra A, Lazcano A. The last common ancestor: what's in a name? ORIGINS LIFE EVOL B 2005; 35:537-54. [PMID: 16254691 DOI: 10.1007/s11084-005-5760-3] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2004] [Accepted: 04/09/2005] [Indexed: 11/28/2022]
Abstract
Twenty completely sequenced cellular genomes from the three major domains were analyzed using twice one-way BLAST searches in order to define the set of the most conserved protein-encoding sequences to characterize the gene complement of the last common ancestor of extant life. The resulting set is dominated by different putative ATPases, and by molecules involved in gene expression and RNA metabolism. DEAD-type RNA helicase and enolase genes, which are known to be part of the RNA degradosome, are as conserved as many transcription and translation genes. This suggests the early evolution of a control mechanism for gene expression at the RNA level, providing additional support to the hypothesis that during early cellular evolution RNA molecules played a more prominent role. Conserved sequences related to biosynthetic pathways include those encoding putative phosphoribosyl pyrophosphate synthase and thioredoxin, which participate in nucleotide metabolism. Although the information contained in the available databases corresponds only to a minor portion of biological diversity, the sequences reported here are likely to be part of an essential and highly conserved pool of proteins domains common to all organisms.
Collapse
Affiliation(s)
- Luis Delaye
- Facultad de Ciencias, UNAM Apdo., Postal 70-407, Cd. Universitaria, 04510, Mexico D.F., Mexico
| | | | | |
Collapse
|
35
|
Saladino R, Crestini C, Busiello V, Ciciriello F, Costanzo G, Di Mauro E. Origin of informational polymers. Differential stability of 3'- and 5'-phosphoester bonds in deoxy monomers and oligomers. J Biol Chem 2005; 280:35658-69. [PMID: 16036914 DOI: 10.1074/jbc.m504537200] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
To survive, an informational macromolecule must solve the major problem set by its very polymeric nature: instability. This is especially true in prebiotic terms because of the presumed initial absence of protective structures (proteins, lipids, etc.). We have analyzed the stability of the beta-glycosidic and of the 3'- and 5'-phosphoester bonds in both deoxy monomers and deoxy oligomers under a large set of conditions. The results show a strong dependence of the relative stability of these bonds on the physico-chemical environment. A set of conditions has been identified in which the stability of polymers becomes comparable with that of the precursor monomers. In certain instances the stability of the 5'-phosphoester bond is even higher in the polymer than in the mononucleotide.
Collapse
Affiliation(s)
- Raffaele Saladino
- Dipartimento AgroBiologia and AgroChimica, Università della Tuscia, Via San Camillo De Lellis, Viterbo 01100, Italy
| | | | | | | | | | | |
Collapse
|
36
|
Abstract
If life emerges readily under Earth-like conditions, the possibility arises of multiple terrestrial genesis events. We seek to quantify the probability of this scenario using estimates of the Archean bombardment rate and the fact that life established itself fairly rapidly on Earth once conditions became favorable. We find a significant likelihood that at least one more sample of life, referred to here as alien life, may have emerged on Earth, and could have coexisted with known life. Indeed, it is difficult to rule out the possibility of extant alien life. We offer some suggestions for how an alternative sample of life might be detected.
Collapse
Affiliation(s)
- P C W Davies
- Australian Centre for Astrobiology, Macquarie University, New South Wales, Australia
| | | |
Collapse
|
37
|
Schulze-Makuch D, Irwin LN, Lipps JH, LeMone D, Dohm JM, Fairén AG. Scenarios for the evolution of life on Mars. ACTA ACUST UNITED AC 2005. [DOI: 10.1029/2005je002430] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
38
|
Abstract
In recent years, Bacteria and Archaea have been discovered living in practically every conceivable terrestrial environment, including some previously thought to be too extreme for survival. Exploration of our solar system has revealed a number of extraterrestrial bodies that harbor environments analogous to many of the terrestrial environments in which extremophiles flourish. The recent discovery of more than 105 extrasolar planets suggests that planetary systems are quite common. These three findings have led some to speculate that life is therefore common in the universe, as life as we know it can seemingly survive almost anywhere there is liquid water. It is suggested here that while environments capable of supporting life may be common, this does not in itself support the notion that life is common in the universe. Given that interplanetary transfer of life may be unlikely, the actual origin of life may require specific environmental and geological conditions that may be much less common than the mere existence of liquid water.
Collapse
Affiliation(s)
- H James Cleaves
- Geosciences Research Divison, Scripps Institution of Oceanography, La Jolla, California 92093-0212, USA.
| | | |
Collapse
|
39
|
Mac Dónaill DA. Why nature chose A, C, G and U/T: an error-coding perspective of nucleotide alphabet composition. ORIGINS LIFE EVOL B 2003; 33:433-55. [PMID: 14604185 DOI: 10.1023/a:1025715209867] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The question of whether the size and make-up of the natural nucleotide alphabet is a consequence of selection pressure, or simply a frozen accident, is one of the fundamental questions of biology. Nucleotide replication is essentially an information transmission phenomenon, and so it seems reasonable to explore the issue from the perspective of theoretical computer science, and of error-coding theory in particular. In this analysis it is shown that the essential recognition features of nucleotides may be naturally expressed as 4-digit binary numbers, capturing the hydrogen acceptor/donor patterns (3-bits) and the purine/pyrimidine feature (1-bit). Optimal alphabets consist of nucleotides in which the purine/pyrimidine feature is related to the acceptor/donor pattern as a parity bit. Numerically interpreted, such alphabets correspond to parity check codes, simple but effective error-resistant structures. The natural alphabet appears to be an adaptation of one of two optimal solutions, constrained to its present size and composition by a combination of chemical and coding-theory factors.
Collapse
|
40
|
Abstract
DNA and RNA are nucleic acids that cells and viruses use to produce copies of themselves. However, there is an immense paucity of knowledge on how these nucleic acids originated and changed as early bacteria became capable of growth and cell division. One possibility is that parallel evolution of the genetic code and protein synthesis was required for assembly of the first cells capable of growth and division. It is also possible that DNA-RNA duplices were intermediate genetic material in the early assembly of the first cells. These ideas will be discussed as well as other aspects of the assembly of the first cells on the Earth.
Collapse
Affiliation(s)
- Jack Thomas Trevors
- Laboratory of Microbial Technology, Department of Environmental Biology University of Guelph, Guelph, Ontario, Canada, NIG 2Wl.
| |
Collapse
|
41
|
Ellery A, Wynn-Williams D. Why Raman spectroscopy on Mars?--a case of the right tool for the right job. ASTROBIOLOGY 2003; 3:565-579. [PMID: 14678665 DOI: 10.1089/153110703322610654] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We provide a scientific rationale for the astrobiological investigation of Mars. We suggest that, given practical constraints, the most promising locations for the search for former life on Mars are palaeolake craters and the evaporite deposits that may reside within them. We suggest that Raman spectroscopy offers a promising tool for the detection of evidence of former (or extant) biota on Mars. In particular, we highlight the detection of hopanoids as long-lived bacterial cell wall products and photosynthetic pigments as the most promising targets. We further suggest that Raman spectroscopy as a fibre optic-based instrument lends itself to flexible planetary deployment.
Collapse
Affiliation(s)
- Alex Ellery
- School of Engineering, Kingston University, London, United Kingdom.
| | | |
Collapse
|
42
|
Lineweaver CH, Davis TM. Does the rapid appearance of life on Earth suggest that life is common in the universe? ASTROBIOLOGY 2002; 2:293-304. [PMID: 12530239 DOI: 10.1089/153110702762027871] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
It is sometimes assumed that the rapidity of biogenesis on Earth suggests that life is common in the Universe. Here we critically examine the assumptions inherent in this if-life-evolved-rapidly-life-must-be-common argument. We use the observational constraints on the rapidity of biogenesis on Earth to infer the probability of biogenesis on terrestrial planets with the same unknown probability of biogenesis as the Earth. We find that on such planets, older than approximately 1 Gyr, the probability of biogenesis is > 13% at the 95% confidence level. This quantifies an important term in the Drake Equation but does not necessarily mean that life is common in the Universe.
Collapse
Affiliation(s)
- Charles H Lineweaver
- School of Physics, University of New South Wales, Australian Centre for Astrobiology, Macquarie University, Sydney, Australia.
| | | |
Collapse
|
43
|
Abstract
During the past decade, ancient gene duplications were recognized as one of the main forces in the generation of diverse gene families and the creation of new functional capabilities. New tools developed to search data banks for homologous sequences, and an increased availability of reliable three-dimensional structural information led to the recognition that proteins with diverse functions can belong to the same superfamily. Analyses of the evolution of these superfamilies promises to provide insights into early evolution but are complicated by several important evolutionary processes. Horizontal transfer of genes can lead to a vertical spread of innovations among organisms, therefore finding a certain property in some descendants of an ancestor does not guarantee that it was present in that ancestor. Complete or partial gene conversion between duplicated genes can yield phylogenetic trees with several, apparently independent gene duplications, suggesting an often surprising parallelism in the evolution of independent lineages. Additionally, the breakup of domains within a protein and the fusion of domains into multifunctional proteins makes the delineation of superfamilies a task that remains difficult to automate.
Collapse
Affiliation(s)
- J P Gogarten
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, 06269, USA.
| | | |
Collapse
|
44
|
Abstract
Comparative path lengths in amino acid biosynthesis and other molecular indicators of the timing of codon assignment were examined to reconstruct the main stages of code evolution. The codon tree obtained was rooted in the 4 N-fixing amino acids (Asp, Glu, Asn, Gln) and 16 triplets of the NAN set. This small, locally phased (commaless) code evidently arose from ambiguous translation on a poly(A) collector strand, in a surface reaction network. Copolymerisation of these amino acids yields polyanionic peptide chains, which could anchor uncharged amide residues to a positively charged mineral surface. From RNA virus structure and replication in vitro, the first genes seemed to be RNA segments spliced into tRNA. Expansion of the code reduced the risk of mutation to an unreadable codon. This step was conditional on initiation at the 5'-codon of a translated sequence. Incorporation of increasingly hydrophobic amino acids accompanied expansion. As codons of the NUN set were assigned most slowly, they received the most nonpolar amino acids. The origin of ferredoxin and Gln synthetase was traced to mid-expansion phase. Surface metabolism ceased by the end of code expansion, as cells bounded by a proteo-phospholipid membrane, with a protoATPase, had emerged. Incorporation of positively charged and aromatic amino acids followed. They entered the post-expansion code by codon capture. Synthesis of efficient enzymes with acid-base catalysis was then possible. Both types of aminoacyl-tRNA synthetases were attributed to this stage. tRNA sequence diversity and error rates in RNA replication indicate the code evolved within 20 million yr in the preIsuan era. These findings on the genetic code provide empirical evidence, from a contemporaneous source, that a surface reaction network, centred on C-fixing autocatalytic cycles, rapidly led to cellular life on Earth.
Collapse
Affiliation(s)
- B K Davis
- Research Foundation of Southern California Inc., La Jolla 92037, USA
| |
Collapse
|
45
|
Tessis AC, Penteado-Fava A, Pontes-Buarque M, De Amorim HS, Bonapace JA, De Souza-Barros F, Vieyra A. Pyrite suspended in artificial sea water catalyzes hydrolysis of adsorbed ATP: enhancing effect of acetate. ORIGINS LIFE EVOL B 1999; 29:361-74. [PMID: 10472626 DOI: 10.1023/a:1006535029107] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Minerals have been implicated in different catalytic processes during chemical evolution. It has been proposed that exergonic synthesis of pyrite (FeS2) could have served to promote the endergonic synthesis of biomonomers in early stages of life formation on Earth. The present study was aimed to investigate whether pyrite can adsorb nucleotides and oxo acids in the potentially mild prebiotic conditions found away from the hot hydrothermal vents. It is shown that pyrite strongly adsorbs adenosine 5'-triphosphate in an artificial medium that simulates primordial aqueous environments, and that adsorption is enhanced in the presence of acetate and in an oxygen-free atmosphere. Moreover, the mineral catalyzes the sequential hydrolysis of the gamma and beta phosphoanhydride bonds of the nucleotide.
Collapse
Affiliation(s)
- A C Tessis
- Department of Medical Biochemistry, Federal University of Rio de Janeiro, Brazil
| | | | | | | | | | | | | |
Collapse
|
46
|
Sleep NH, Zahnle K. Refugia from asteroid impacts on early Mars and the early Earth. ACTA ACUST UNITED AC 1998. [DOI: 10.1029/98je01809] [Citation(s) in RCA: 103] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
47
|
Abstract
The old question of a definition of minimal life is taken up again at the aim of providing a forum for an updated discussion. Briefly discussed are the reasons why such an attempt has previously encountered scepticism, and why such an attempt should be renewed at this stage of the inquiry on the origin of life. Then some of the definitions of life presently used are cited and briefly discussed, starting with the definition adopted by NASA as a general working definition. It is shown that this is too limited if one wishes to provide a broad encompassing definition, and some extensions of it are presented and discussed. Finally it is shown how the different definitions of life reflect the main schools of thought that presently dominate the field on the origin of life.
Collapse
Affiliation(s)
- P L Luisi
- Inst. für Polymere, ETH-Z, Zurich, Switzerland
| |
Collapse
|
48
|
Abstract
Competitive replication among RNA or DNA molecules at linear and non-linear rates of propagation has been reviewed from the perspective of a recent physicochemical model of molecular evolution and the findings are applied to pre-replication, prebiotic and biological evolution. A system of competitively replicating molecules was seen to follow a path of least action on both its thermodynamic and kinetic branch, in evolving toward steady state kinetics and equilibrium for the nucleotide condensation reaction. Stable and unstable states of coexistence, between competing molecular species, arise at nonlinear rates of propagation, and they derive from an equilibrium between kinetic forces. The de novo formation of self-replicating RNA molecules involves damping of these scalar forces, error tolerance and RNA driven strand separation. Increases in sequence complexity in the transition to self-replication does not exceed the free energy dissipated in RNA synthesis. Retrodiction of metabolic pathways and phylogenetic evidence point to the occurrence of three pre-replication metabolic systems, driven by autocatalytic C-fixation cycles. Thermodynamic and kinetic factors led to the replication take over. Biological evolution was found to involve resource capture, in addition to competition for a shared resource.
Collapse
Affiliation(s)
- B K Davis
- Research Foundation of Southern California Inc., La Jolla 92037, USA
| |
Collapse
|
49
|
Levy M, Miller SL. The stability of the RNA bases: implications for the origin of life. Proc Natl Acad Sci U S A 1998; 95:7933-8. [PMID: 9653118 PMCID: PMC20907 DOI: 10.1073/pnas.95.14.7933] [Citation(s) in RCA: 180] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
High-temperature origin-of-life theories require that the components of the first genetic material are stable. We therefore have measured the half-lives for the decomposition of the nucleobases. They have been found to be short on the geologic time scale. At 100 degreesC, the growth temperatures of the hyperthermophiles, the half-lives are too short to allow for the adequate accumulation of these compounds (t1/2 for A and G approximately 1 yr; U = 12 yr; C = 19 days). Therefore, unless the origin of life took place extremely rapidly (<100 yr), we conclude that a high-temperature origin of life may be possible, but it cannot involve adenine, uracil, guanine, or cytosine. The rates of hydrolysis at 100 degreesC also suggest that an ocean-boiling asteroid impact would reset the prebiotic clock, requiring prebiotic synthetic processes to begin again. At 0 degreesC, A, U, G, and T appear to be sufficiently stable (t1/2 >/= 10(6) yr) to be involved in a low-temperature origin of life. However, the lack of stability of cytosine at 0 degreesC (t1/2 = 17, 000 yr) raises the possibility that the GC base pair may not have been used in the first genetic material unless life arose quickly (<10(6) yr) after a sterilization event. A two-letter code or an alternative base pair may have been used instead.
Collapse
Affiliation(s)
- M Levy
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093-0506, USA
| | | |
Collapse
|
50
|
Abstract
We do not understand the steps leading from the abiotic early earth to the RNA world. Consequently, we cannot estimate the time required for the origins of life. Attempts to circumvent this essential difficulty are based on misunderstandings of the nature of the problem.
Collapse
Affiliation(s)
- L E Orgel
- The Salk Institute for Biological Studies, San Diego, CA 92186, USA
| |
Collapse
|