RNA catalysis through compartmentalization

Abstract

RNA performs important cellular functions in contemporary life forms. Its ability to act both as a catalyst and a storage mechanism for genetic information is also an important part of the RNA world hypothesis. Compartmentalization within modern cells allows the local concentration of RNA to be controlled and it has been suggested that this was also important in early life forms. Here, we mimic intracellular compartmentalization and macromolecular crowding by partitioning RNA in an aqueous two-phase system (ATPS). We show that the concentration of RNA is enriched by up to 3,000-fold in the dextran-rich phase of a polyethylene glycol/dextran ATPS and demonstrate that this can lead to approximately 70-fold increase in the rate of ribozyme cleavage. This rate enhancement can be tuned by the relative volumes of the two phases in the ATPS. Our observations support the importance of compartmentalization in the attainment of function in an RNA World as well as in modern biology.

Bioreactor droplets from liposome-stabilized all-aqueous emulsions

“…Crowding can considerably alter kinetics and thermodynamics for many biochemical reactions 17 , for example PEG and dextran polymers favour reactivity of the CPEB3 ribozyme 18 . In the PEG/dextran system, RNA partitions strongly to the dextran-rich phase 10,12 . This effect, which is length-dependent, has been used to increase ribozyme reaction rates up to nearly 70-fold by localization in the dextran-rich phase 10 .…”

“…Aqueous two-phase systems (ATPS), such as the well-known PEG/dextran system 12 , are attractive as biomimetic media because they offer coexisting macromolecularly crowded aqueous compartments with different chemical and physical properties separated by a low-energy boundary, across which solutes such as proteins or nucleic acids can equilibrate without denaturation 10,13,14 . This is similar to biological fluids such as the cytoplasm and nucleoplasm, which contain 17-40 wt% biomacromolecules 15,16 .…”

“…At its most basic, a microreactor consists of a semipermeable shell through which reactants and products can pass and an interior environment where reactions can occur. Notable examples of compartments that have been used as microreactors include liposomes 1 , polymer capsules 2,3 , colloidosomes 4,5 , hydrogels and liquid-liquid emulsions (oil/water 6,7 , aqueous/aqueous [8][9][10] ), in which individual droplets can be considered as microreactors 11 . Interior reactivity can be facilitated by catalysts that are either physically trapped in the interior (for example, by a membrane), or concentrated there on the basis of preferential solubility (for example, in a water/oil biphasic system) 6 .…”

Enhanced transcription rates in membrane-free protocells formed by coacervation of cell lysate

“…Compartmentalization is but one characteristic, as protocells ideally also mimic the highly crowded interior of living cells, which have total macromolecule concentrations in excess of 300 g/L (7). Examples in which compartmentalization and high local concentrations are obtained concurrently, include DNA brushes (8), aqueous two-phase systems (9), and liquid coacervates (10). Phase separation or coacervation occurs in a wide range of polymer and protein solutions, often triggered by changes in temperature or salt concentration, or by the addition of coacervating agents (11).…”

Are Proposed Early Genetic Codes Capable of Encoding Viable Proteins?

“…For the origin of the genetic code and the first proteins, a number of scenarios have been put forward and probably even more are possible (see e.g. Szathmáry 1993;Koonin 2009;Strulson 2012). These scenarios differ in the aspect whether proteins emerged with or without closely linked to RNA and whether template-based synthesis evolved after the first proteins emerged or that a primitive form of translation was a prerequisite for the birth of the first functional proteins.…”