Vesicle encapsulation stabilizes intermolecular association and structure formation of functional RNA and DNA

Peng, Huan; Lelievre, Amandine; Landenfeld, Katharina; Müller, Sabine; Chen, Irene

doi:10.1016/j.cub.2021.10.047

Cited by 21 publications

(12 citation statements)

References 74 publications

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“…Compartmentalisation can also support the formation of crowded environments, which have long been known to enhance folding and catalysis of catalytic nucleic acids 41 – 44 . Furthermore, the encapsulation of functional RNA has been shown to preserve activity at high lipid concentrations that would otherwise inhibit unencapsulated RNA 45 . Although we do see signs and possible effects of potentially beneficial RNA-membrane interactions (Supplementary Figs.…”

Section: Discussionmentioning

confidence: 99%

Periodic temperature changes drive the proliferation of self-replicating RNAs in vesicle populations

et al. 2023

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Growth and division of biological cells are based on the complex orchestration of spatiotemporally controlled reactions driven by highly evolved proteins. In contrast, it remains unknown how their primordial predecessors could achieve a stable inheritance of cytosolic components before the advent of translation. An attractive scenario assumes that periodic changes of environmental conditions acted as pacemakers for the proliferation of early protocells. Using catalytic RNA (ribozymes) as models for primitive biocatalytic molecules, we demonstrate that the repeated freezing and thawing of aqueous solutions enables the assembly of active ribozymes from inactive precursors encapsulated in separate lipid vesicle populations. Furthermore, we show that encapsulated ribozyme replicators can overcome freezing-induced content loss and successive dilution by freeze-thaw driven propagation in feedstock vesicles. Thus, cyclic freezing and melting of aqueous solvents – a plausible physicochemical driver likely present on early Earth – provides a simple scenario that uncouples compartment growth and division from RNA self-replication, while maintaining the propagation of these replicators inside new vesicle populations.

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Section: Discussionmentioning

confidence: 99%

Periodic temperature changes drive the proliferation of self-replicating RNAs in vesicle populations

et al. 2023

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“…Such conditions are expected to alter many properties of ctRSD circuits. For example, ion availability and molecular crowding influence transcription, − RNA folding and ribozyme catalysis, − and strand displacement. ,, Further, encapsulation and localization of RNA can influence RNA folding and ribozyme catalysis, , and strand displacement reactions . Strand displacement reactions are also influenced by the presence of non-target nucleic acids, and the presence of RNases will introduce sequence and structure specific degradation rates .…”

Section: Discussionmentioning

confidence: 99%

Design Approaches to Expand the Toolkit for Building Cotranscriptionally Encoded RNA Strand Displacement Circuits

et al. 2023

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Cotranscriptionally encoded RNA strand displacement (ctRSD) circuits are an emerging tool for programmable molecular computation, with potential applications spanning in vitro diagnostics to continuous computation inside living cells. In ctRSD circuits, RNA strand displacement components are continuously produced together via transcription. These RNA components can be rationally programmed through base pairing interactions to execute logic and signaling cascades. However, the small number of ctRSD components characterized to date limits circuit size and capabilities. Here, we characterize over 200 ctRSD gate sequences, exploring different input, output, and toehold sequences and changes to other design parameters, including domain lengths, ribozyme sequences, and the order in which gate strands are transcribed. This characterization provides a library of sequence domains for engineering ctRSD components, i.e., a toolkit, enabling circuits with up to 4-fold more inputs than previously possible. We also identify specific failure modes and systematically develop design approaches that reduce the likelihood of failure across different gate sequences. Lastly, we show the ctRSD gate design is robust to changes in transcriptional encoding, opening a broad design space for applications in more complex environments. Together, these results deliver an expanded toolkit and design approaches for building ctRSD circuits that will dramatically extend capabilities and potential applications.

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“…Branched actin nucleation by WAS proteins and the Arp2/3 complex near the membrane can generate the force necessary to deform membrane and the underlying cytoskeleton in many cellular processes, including endocytosis and the formation of cellular protrusions, whereas actin bundling acts to assemble and organize/scaffold proteins within a cell (Rotty et al, 2013; Siton-Mendelson and Bernheim-Groswasser, 2017; Svitkina, 2018; Swaney and Li, 2016). Interestingly, the encapsulation or confinement of RNAs or proteins within vesicles has been shown to promote RNA-RNA and RNA-protein associations, organization, stability, and functions (Cheng et al, 2018; Peng et al, 2021; Ross et al, 2020). Our previous study suggests that actin organization is indispensable for the formation of NE buds.…”

Section: Discussionmentioning

confidence: 99%

The Centralspindlin proteins Pavarotti and Tumbleweed work with WASH to regulate Nuclear Envelope budding

Davidson

Nakamura

Verboon

et al. 2022

Preprint

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Nuclear envelope (NE) budding is a nuclear pore independent nuclear export pathway, analogous to the egress of herpesviruses, and required for protein quality control, synapse development and mitochondrial integrity. The physical formation of NE buds is dependent on the Wiskott-Aldrich Syndrome protein Wash, its regulatory complex (SHRC), and Arp2/3, and requires Wash actin nucleation activity. However, the machinery governing cargo recruitment and organization within the NE bud remains unknown. Here, we identify Pavarotti (Pav) and Tumbleweed (Tum) as new molecular components of NE budding. Pav and Tum interact directly with Wash and define a second nuclear Wash-containing complex required for NE budding. Interestingly, we find that the actin bundling activities of Wash and Pav are required, suggesting a structural role in the physical and/or organizational aspects of NE buds. Thus, Pav and Tum are providing exciting new entry points into the physical machineries of this alternative nuclear export pathway for large cargos during cell differentiation and development.

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Vesicle encapsulation stabilizes intermolecular association and structure formation of functional RNA and DNA

Cited by 21 publications

References 74 publications

Periodic temperature changes drive the proliferation of self-replicating RNAs in vesicle populations

Periodic temperature changes drive the proliferation of self-replicating RNAs in vesicle populations

Design Approaches to Expand the Toolkit for Building Cotranscriptionally Encoded RNA Strand Displacement Circuits

The Centralspindlin proteins Pavarotti and Tumbleweed work with WASH to regulate Nuclear Envelope budding

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