The Origin of Life and the Origin of Enzymes

Ai, Oparin

doi:10.1002/9780470122723.ch7

Cited by 41 publications

(35 citation statements)

References 69 publications

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“…It is widely accepted that prebiotic chemistry happened in a reducing environment (Oparin, 1924;Haldane, 1929); moreover, life on Earth evolved in the absence of atmospheric oxygen for at least 1 Gyr (e.g., Anbar et al, 2007;Schopf et al, 2007). Early organisms relied on the free energy available in redox reactions involving a variety of hydrogen compounds; on an O 2 -rich planet, organisms would have to compete with the oxygen for this free energy.…”

Section: Implications For Habitabilitymentioning

confidence: 99%

Extreme Water Loss and Abiotic O₂Buildup on Planets Throughout the Habitable Zones of M Dwarfs

2015

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We show that terrestrial planets in the habitable zones of M dwarfs older than *1 Gyr could have been in runaway greenhouses for several hundred million years following their formation due to the star's extended premain sequence phase, provided they form with abundant surface water. Such prolonged runaway greenhouses can lead to planetary evolution divergent from that of Earth. During this early runaway phase, photolysis of water vapor and hydrogen/oxygen escape to space can lead to the loss of several Earth oceans of water from planets throughout the habitable zone, regardless of whether the escape is energy-limited or diffusion-limited. We find that the amount of water lost scales with the planet mass, since the diffusion-limited hydrogen escape flux is proportional to the planet surface gravity. In addition to undergoing potential desiccation, planets with inefficient oxygen sinks at the surface may build up hundreds to thousands of bar of abiotically produced O 2 , resulting in potential false positives for life. The amount of O 2 that builds up also scales with the planet mass; we find that O 2 builds up at a constant rate that is controlled by diffusion: *5 bar/Myr on Earth-mass planets and up to *25 bar/Myr on super-Earths. As a result, some recently discovered super-Earths in the habitable zone such as GJ 667Cc could have built up as many as 2000 bar of O 2 due to the loss of up to 10 Earth oceans of water. The fate of a given planet strongly depends on the extreme ultraviolet flux, the duration of the runaway regime, the initial water content, and the rate at which oxygen is absorbed by the surface. In general, we find that the initial phase of high luminosity may compromise the habitability of many terrestrial planets orbiting low-mass stars.

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Section: Implications For Habitabilitymentioning

confidence: 99%

Extreme Water Loss and Abiotic O₂Buildup on Planets Throughout the Habitable Zones of M Dwarfs

2015

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“…Because the aggregates with efficient EJ capacity are selective in the intermolecular mode of EJ and are readily accessible to external ATP molecules, the internal structure must be fluid and must be an open system. Thus, we argue that this organization of nucleoproteins on linear DNA qualifies as coacervation, which has been implicated in the mechanism for the condensed process of prebiotic charged polymers and has been established as a condition interactive with the external environment during their continuous synthesis and breakdown [23, and references therein].…”

Section: Resultsmentioning

confidence: 99%

“…The increasing amounts of extracts quantitatively precipitated the DNA, ending up with saturation at a full extent (lanes 7 and 14). Considering the biological significance of the aggregation, we expected that the aggregates would be structurally fluid and anisotropic like the polyamine-induced DNA aggregation and so would possess the feature of coacervate [22], defined as a dynamic phase which appears by self-assembly of colloidal biopolymers in dilute solutions [23].…”

Section: Aberrant Types Of Dna Coaggregate With Nucleoproteinsmentioning

confidence: 99%

Aggregative organization enhances the DNA end‐joining process that is mediated by DNA‐dependent protein kinase

Takahagi

Tatsumi

2006

The FEBS Journal

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DNA double-strand breaks (DSBs) are a serious threat to the genetic integrity of organisms, causing cell death if not repaired. The repair mechanism for DSBs resides not only in catalytic processes but also in the association with chromatin structures [1,2], although the details in the higher-order context remain obscure. Some evidence has implicated structural alterations in the vicinity of DSB sites. DSBs can form nuclear foci linked to phosphorylated histone H2AX (c-H2AX) [3], which is responsible for the redistribution of repair factors to DSB sites [4], although it is dispensable for initial damage recognition [5]. Approximately 2000 c-H2AX molecules accumulate per focus in a normal human cell, suggesting reorganization of chromosomal DNA over a region of Mbp order [6]. c-H2AX-associated foci are morphologically dynamic; the DSB-containing chromosome domains can be mobile, and in a subpopulation of damaged cells, they can juxtapose via an adhesion process irrespective of DNA repair processes [7].In addition to these large-scale responses to DSBs, real-time analysis of the temporo-spatial distribution of DNA repair factors in situ in living cells has been providing us with striking information. For instance, even following exposure to ionizing radiation (IR), the DNA end-binding factor Ku moves rapidly throughout the nucleus but associates transiently with filamentous nuclear substrates [8]. A checkpoint regulator NBS1, the product of the Nijmegen breakage syndrome gene, shuttles rapidly between DSB sites and the flanking chromatin [9]. These findings indicate that the action of DSB-interactive proteins within the nuclear microenvironment must be coupled with the mobile state of those proteins. The occurrence of DNA double-strand breaks in the nucleus provokes in its structural organization a large-scale alteration whose molecular basis is still mostly unclear. Here, we show that double-strand breaks trigger preferential assembly of nucleoproteins in human cellular fractions and that they mediate the separation of large protein-DNA aggregates from aqueous solution. The interaction among the aggregative nucleoproteins presents a dynamic condition that allows the effective interaction of nucleoproteins with external molecules like free ATP and facilitates intrinsic DNA end-joining activity. This aggregative organization is functionally coacervate-like. The key component is DNA-dependent protein kinase (DNA-PK), which can be characterized as a DNA-specific aggregation factor as well as a nuclear scaffold ⁄ matrix-interactive factor. In the context of aggregation, the kinase activity of DNA-PK is essential for efficient DNA end-joining. The massive and functional concentration of nucleoproteins on DNA in vitro may represent a possible status of nuclear dynamics in vivo, which probably includes the DNA-PK-dependent response to multiple double-strand breaks.

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“…It is reasonable to assume that precursor structures of the first cell(s), so-called "progenotes" (Woese, 1998;Doolittle and Brown, 1994) or "protocells" (Morowitz et al, 1988), "protobionts" (Oparin, 1965) or "probionts" (Oparin and Gladilin, 1980), were a bit simpler than the first cells. They may have been composed of simple membranes (as boundaries of the structures), an internal set of catalysts (possibly simple oligopeptides/proteins and/or metal ion complexes), sequence-encoded information-carrying molecules (simple RNA/DNA), and a polypeptide/protein synthesis apparatus (possibly a mixture of RNAs and proteins; or just RNAs (Moore and Steitz, 2002)).…”

Section: Some Of the Origin-of-life-related Questions And Their Relatmentioning

confidence: 99%

Surfactant Assemblies and their Various Possible Roles for the Origin(S) of Life

Walde

2006

Orig Life Evol Biosph

139

110

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A large number of surfactants (surface active molecules) are chemically simple compounds that can be obtained by simple chemical reactions, in some cases even under presumably prebiotic conditions. Surfactant assemblies are self-organized polymolecular aggregates of surfactants, in the simplest case micelles, vesicles, hexagonal and cubic phases. It may be that these different types of surfactant assemblies have played various, so-far underestimated important roles in the processes that led to the formation of the first living systems. Although nucleic acids are key players in the formation of cells as we know them today (RNA world hypothesis), it is still unclear how RNA could have been formed under prebiotic conditions. Surfactants with their self-organizing properties may have assisted, controlled and compartimentalized some of the chemical reactions that eventually led to the formation of molecules like RNA. Therefore, surfactants were possibly very important in prebiotic times in the sense that they may have been involved in different physical and chemical processes that finally led to a transformation of non-living matter to the first cellular form(s) of life. This hypothesis is based on four main experimental observations: (i) Surfactant aggregation can lead to cell-like compartimentation (vesicles). (ii) Surfactant assemblies can provide local reaction conditions that are very different from the bulk medium, which may lead to a dramatic change in the rate of chemical reactions and to a change in reaction product distributions. (iii) The surface properties of surfactant assemblies that may be liquid- or solid-like, charged or neutral, and the elasticity and packing density of surfactant assemblies depend on the chemical structure of the surfactants, on the presence of other molecules, and on the overall environmental conditions (e. g. temperature). This wide range of surface characteristics of surfactant assemblies may allow a control of surface-bound chemical reactions not only by the charge or hydrophobicity of the surface but also by its "softness". (iv) Chiral polymolecular assemblies (helices) may form from chiral surfactants. There are many examples that illustrate the different roles and potential roles of surfactant assemblies in different research areas outside of the field of the origin(s) of life, most importantly in investigations of contemporary living systems, in nanotechnology applications, and in the development of drug delivery systems. Concepts and ideas behind many of these applications may have relevance also in connection to the different unsolved problems in understanding the origin(s) of life.

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The Origin of Life and the Origin of Enzymes

Cited by 41 publications

References 69 publications

Extreme Water Loss and Abiotic O₂Buildup on Planets Throughout the Habitable Zones of M Dwarfs

Extreme Water Loss and Abiotic O₂Buildup on Planets Throughout the Habitable Zones of M Dwarfs

Aggregative organization enhances the DNA end‐joining process that is mediated by DNA‐dependent protein kinase

Surfactant Assemblies and their Various Possible Roles for the Origin(S) of Life

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The Origin of Life and the Origin of Enzymes

Cited by 41 publications

References 69 publications

Extreme Water Loss and Abiotic O2Buildup on Planets Throughout the Habitable Zones of M Dwarfs

Extreme Water Loss and Abiotic O2Buildup on Planets Throughout the Habitable Zones of M Dwarfs

Aggregative organization enhances the DNA end‐joining process that is mediated by DNA‐dependent protein kinase

Surfactant Assemblies and their Various Possible Roles for the Origin(S) of Life

Contact Info

Product

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Extreme Water Loss and Abiotic O₂Buildup on Planets Throughout the Habitable Zones of M Dwarfs

Extreme Water Loss and Abiotic O₂Buildup on Planets Throughout the Habitable Zones of M Dwarfs