Compartmentalisation and metabolism are two universal features observed among all living organisms. Their emergence and harmonious functioning are considered critical for the emergence of life. In an attempt to understand the chemical processes that may have resulted in the emergence of life, origin(s)-of-life researchers have investigated 1. possible mechanisms of prebiotic compartmentalisation and 2. plausible protometabolic reactions as precursors to metabolic chemistry. Historically, these two aspects of origin(s)-of-life research have been investigated in isolation. However, there is a growing consensus regarding the necessity of investigating prebiotic compartmentalisation and protometabolic reactions in tandem.
Prebiotic compartmentalisation via formation of lipid vesicles have long been regarded as a general route for protocell formation. However, modern views on protocell formation suggest that such structures might be insufficient, in the absence of specialised transport proteins, to efficiently create suitable environments for sustaining out-of-equilibrium reactions, necessary for the emergence of life. This, coupled with the discovery of membrane-less organelles, formed through liquid-liquid phase separation (LLPS) in modern cells, and their ever increasingly identified roles in biology, has sparked renewed interest among origin(s)-of-life researchers in the synergy between prebiotic reactions and Oparin’s hypothesis of prebiotic compartmentalisation via coacervation. To date, most of the work, investigating the effect of coacervation on chemical reactions, have focused on biochemical reactions catalysed by complex biomolecules such as proteinaceous enzymes and ribozymes. Moreover, historically, the phenomenon of complex coacervation has primarily been associated with long-chain polymers. However, recent demonstrations of complex coacervation among several prebiotically relevant metabolites necessitates the need for developing experimental strategies that can comprehensively investigate complex coacervation, in terms of phase diagrams, involving such prebiotically relevant metabolites. Such understanding is essential to enhance the design of experiments that aim to combine protometabolic reactions and complex coacervation.
To this end, the research presented in this thesis, at first, demonstrates a highthroughput screening methodology for complex coacervate formation, in chapter 2, using automated liquid handling strategies and random forest classifier machine learning algorithm based classification of bright-field microscopy images. This methodology has then been utilised to obtain the conditions in which oxidised and reduced nicotineamide adenine dinucleotide (NAD+ and NADH) form coacervate with 50-mer poly-lysine and poly-arginine. Further, the precipitation properties of 50-mer poly-arginine in sodium bicarbonate solution have been investigated.
In chapter 3, incorporation of complex coacervation in three different protometabolic reactions in three different ways have been exhibited. In “Protometabolic NAD+ reduction using pyruvate”, NADH, which is the product of the reaction, participates in coacervation with 50-mer poly-arginine. In “Coenzyme A catalysed peptide ligation”, the catalyst of the reaction, coenzyme A contributes to coacervation with 10-mer polyarginine.
In “Heme catalysed oxidation of Amplex Red”, the coacervate is formed form polymers, such as carboxymethyl dextran and poly-diallyldimethylammonium, that are not reactants, products or catalyst of the studied reaction. It has been further shown that the incorporation of coacervation, to “Protometabolic NAD+ reduction using pyruvate”, results in the enhancement of NADH formation by 2.5 times in comparison to the amount of NADH produced in the absence of any poly-cations. Preliminary results also suggest that the presence of coacervation resulted in the suppression of both “Coenzyme A catalysed peptide ligation” and “Heme catalysed oxidation of Amplex Red”.
This study elucidates an unprecedented methodology for screening of coacervate formation as well as highlighting the various ways in which coacervation of prebiotically relevant metabolites can be embedded into protometabolic reactions. Further, this study also sheds light on the influence of coacervation on protometabolic reactions, revealing patterns that were previously primarily observed in biochemical reactions catalysed by enzymes (or ribozymes).
| Identifer | oai:union.ndltd.org:DRESDEN/oai:qucosa:de:qucosa:91935 |
| Date | 17 June 2024 |
| Creators | Bose, Rudrarup |
| Contributors | Hyman, Anthony A., Tang, Tsing-Young Dora, Mansy, Sheref, Technische Universität Dresden, Max Planck Institute of Molecular Cell Biology |
| Source Sets | Hochschulschriftenserver (HSSS) der SLUB Dresden |
| Language | English |
| Detected Language | English |
| Type | info:eu-repo/semantics/publishedVersion, doc-type:doctoralThesis, info:eu-repo/semantics/doctoralThesis, doc-type:Text |
| Rights | info:eu-repo/semantics/openAccess |
| Relation | info:eu-repo/grantAgreement/European Commission/Horizon2020/813873//PROTOMETABOLIC PATHWAYS: EXPLORING THE CHEMICAL ROOTS OF SYSTEMS BIOLOGY/ProtoMet |
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