Cyclophospholipids Enable a Protocellular Life Cycle

Toparlak, Ö. Duhan; Sebastianelli, Lorenzo; Egas Ortuno, Veronica; Karki, Megha; Xing, Yanfeng; Szostak, Jack W.; Krishnamurthy, Ramanarayanan; Mansy, Sheref S.

doi:10.1021/acsnano.3c07706

Cited by 11 publications

(6 citation statements)

References 79 publications

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“…The presence of Mg 2 + protects against the degradation of amino acids [26] and is critically important for the folding and function of nucleic acids. Since model protocells have recently been identified that can grow and divide in the presence of Mg 2 + , [27] and are stable over a broad range of pH, [28] it seems that we are beginning to gain insight into which environmental conditions allow for several parts of a protocell to coexist and function. What remains challenging to decipher is how regulatory control of a supporting (proto)metabolism emerged from such chemistry.…”

Section: Discussionmentioning

confidence: 99%

A Magnesium Binding Site And The Anomeric Effect Regulate The Abiotic Redox Chemistry Of Nicotinamide Nucleotides

Sebastianelli,

Kaur,

Chen

et al. 2024

Chemistry A European J

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Nicotinamide adenine dinucleotide (NAD+) is a redox active molecule that is universally found in biology. Despite the importance and simplicity of this molecule, few reports exist that investigate which molecular features are important for the activity of this ribodinucleotide. By exploiting the nonenzymatic reduction and oxidation of NAD+ by pyruvate and methylene blue, respectively, we were able to identify key molecular features necessary for the intrinsic activity of NAD+ through kinetic analysis. Such features may explain how NAD+ could have been selected early during the emergence of life. Simpler molecules, such as nicotinamide, that lack an anomeric carbon are incapable of accepting electrons from pyruvate. The phosphate moiety inhibits activity in the absence of metal ions but facilitates activity at physiological pH and model prebiotic conditions by recruiting catalytic Mg2+. Reduction proceeds through consecutive single electron transfer events. Of the derivatives tested, including nicotinamide mononucleotide, nicotinamide riboside, 3‐(aminocarbonyl)‐1‐(2,3‐dihydroxypropyl)pyridinium, 1‐methylnicotinamide, and nicotinamide, only NAD+ and nicotinamide mononucleotide would be capable of efficiently accepting and donating electrons from and to pyruvate within a nonenzymatic electron transport chain. The data are consistent with early metabolic chemistry exploiting NAD+ or nicotinamide mononucleotide and not simpler molecules.

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Section: Discussionmentioning

confidence: 99%

A Magnesium Binding Site And The Anomeric Effect Regulate The Abiotic Redox Chemistry Of Nicotinamide Nucleotides

Sebastianelli,

Kaur,

Chen

et al. 2024

Chemistry A European J

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“…This effect of Mg 2+ can be overcome either by chelating the Mg 2+ with citrate or, to a lesser extent, through the addition of membrane-stabilizing compounds . We have previously shown that this incompatibility may be overcome through chelation of Mg 2+ with citrate, suggesting that the catalytic Mg 2+ ion interacts with the reaction center through at most three coordination sites. − A better understanding of the coordination of the Mg 2+ ion with functional groups in the reaction center could potentially guide the search for more prebiotically plausible chelators that preserve or even enhance the rate of primer extension while retaining compatibility with fatty acid-based vesicles.…”

Section: Introductionmentioning

confidence: 99%

Catalytic Metal Ion–Substrate Coordination during Nonenzymatic RNA Primer Extension

Fang,

Pazienza,

Zhang

et al. 2024

J. Am. Chem. Soc.

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Nonenzymatic template-directed RNA copying requires catalysis by divalent metal ions. The primer extension reaction involves the attack of the primer 3′-hydroxyl on the adjacent phosphate of a 5′-5′-imidazolium-bridged dinucleotide substrate. However, the nature of the interaction of the catalytic metal ion with the reaction center remains unclear. To explore the coordination of the catalytic metal ion with the imidazoliumbridged dinucleotide substrate, we examined catalysis by oxophilic and thiophilic metal ions with both diastereomers of phosphorothioate-modified substrates. We show that Mg 2+ and Cd 2+ exhibit opposite preferences for the two phosphorothioate substrate diastereomers, indicating a stereospecific interaction of the divalent cation with one of the nonbridging phosphorus substituents. High-resolution X-ray crystal structures of the products of primer extension with phosphorothioate substrates reveal the absolute stereochemistry of this interaction and indicate that catalysis by Mg 2+ involves inner-sphere coordination with the nonbridging phosphate oxygen in the pro-S P position, while thiophilic cadmium ions interact with sulfur in the same position, as in one of the two phosphorothioate substrates. These results collectively suggest that during nonenzymatic RNA primer extension with a 5′-5′imidazolium-bridged dinucleotide substrate the interaction of the catalytic Mg 2+ ion with the pro-S P oxygen of the reactive phosphate plays a crucial role in the metal-catalyzed S N 2(P) reaction.

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“…Compared to diacyl phospholipids, which commonly compose the membranes of modern cells, fatty acid membranes provide greater permeability for relatively small molecules and display more rapid molecular dynamics. However, fatty acid vesicles, which are negatively charged overall, do show colloidal instability in the presence of divalent cations such as magnesium and calcium, which is problematic because ribozyme folding and catalysis often require divalent cations to interact with the negatively charged sugar–phosphate backbone of RNA. − Strategies to stabilize fatty acid vesicles include adding significant percentages of phospholipids or other lipids, including prebiotically plausible single-chain amphiphiles, or adding partial chelation agents. ,− Vesicles composed of simple lipids can already exhibit intriguing behaviors reminiscent of biological cells. For example, in addition to their ability to grow when fed, which derives from the thermodynamically downhill incorporation of lipids into the outer leaflet followed by rapid flip-flop of lipids to the inner leaflet, multilamellar vesicles can exhibit growth and division driven solely by compositional heterogeneity among individual vesicles .…”

Section: Introductionmentioning

confidence: 99%

Protocell Effects on RNA Folding, Function, and Evolution

Saha,

Choi,

Chen

2024

Acc. Chem. Res.

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Metrics & MoreArticle Recommendations CONSPECTUS: Creating a living system from nonliving matter is a great challenge in chemistry and biophysics. The early history of life can provide inspiration from the idea of the prebiotic "RNA World" established by ribozymes, in which all genetic and catalytic activities were executed by RNA. Such a system could be much simpler than the interdependent central dogma characterizing life today. At the same time, cooperative systems require a mechanism such as cellular compartmentalization in order to survive and evolve. Minimal cells might therefore consist of simple vesicles enclosing a prebiotic RNA metabolism.The internal volume of a vesicle is a distinctive environment due to its closed boundary, which alters diffusion and available volume for macromolecules and changes effective molecular concentrations, among other considerations. These physical effects are mechanistically distinct from chemical interactions, such as electrostatic repulsion, that might also occur between the membrane boundary and encapsulated contents. Both indirect and direct interactions between the membrane and RNA can give rise to nonintuitive, "emergent" behaviors in the model protocell system. We have been examining how encapsulation inside membrane vesicles would affect the folding and activity of entrapped RNA.Using biophysical techniques such as FRET, we characterized ribozyme folding and activity inside vesicles. Encapsulation inside model protocells generally promoted RNA folding, consistent with an excluded volume effect, independently of chemical interactions. This energetic stabilization translated into increased ribozyme activity in two different systems that were studied (hairpin ribozyme and self-aminoacylating RNAs). A particularly intriguing finding was that encapsulation could rescue the activity of mutant ribozymes, suggesting that encapsulation could affect not only folding and activity but also evolution. To study this further, we developed a high-throughput sequencing assay to measure the aminoacylation kinetics of many thousands of ribozyme variants in parallel. The results revealed an unexpected tendency for encapsulation to improve the better ribozyme variants more than worse variants. During evolution, this effect would create a tilted playing field, so to speak, that would give additional fitness gains to already-high-activity variants. According to Fisher's Fundamental Theorem of Natural Selection, the increased variance in fitness should manifest as faster evolutionary adaptation. This prediction was borne out experimentally during in vitro evolution, where we observed that the initially diverse ribozyme population converged more quickly to the most active sequences when they were encapsulated inside vesicles. The studies in this Account have expanded our understanding of emergent protocell behavior, by showing how simply entrapping an RNA inside a vesicle, which could occur spontaneously during vesicle formation, might profoundly affect the evolutionary landscape of the RN...

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Cyclophospholipids Enable a Protocellular Life Cycle

Cited by 11 publications

References 79 publications

A Magnesium Binding Site And The Anomeric Effect Regulate The Abiotic Redox Chemistry Of Nicotinamide Nucleotides

A Magnesium Binding Site And The Anomeric Effect Regulate The Abiotic Redox Chemistry Of Nicotinamide Nucleotides

Catalytic Metal Ion–Substrate Coordination during Nonenzymatic RNA Primer Extension

Protocell Effects on RNA Folding, Function, and Evolution

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