Current Opinion in Colloid & Interface Sciencehome.uchicago.edu/~jvieregg/pubs/COCIS.pdfaddition,...

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Polynucleotides in cellular mimics: Coacervates and lipid vesicles Jeffrey R Vieregg a , T-Y Dora Tang b, a Institute for Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637, USA b Max Planck Institute for Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany abstract article info Article history: Received 10 June 2016 Received in revised form 22 August 2016 Accepted 2 September 2016 Available online 28 September 2016 In this review, we examine the interaction of nucleic acids with cell-like structures based on liquidliquid phase separation of charged molecules (complex coacervation) and amphiphilic self-assembly (lipid vesicles). We discuss the mechanisms of their assembly and describe how they can be used as models for origin of life studies and for understanding two recently-described phenomena in modern cells: membrane-free organelles and exosomes. Hybrid cells with increased structural complexity are highlighted and we then briey explore how strategies based on electrostatic and hydrophobic assembly can be used for designing and synthesizing delivery agents for therapeutic nucleic acids. While the physical mechanisms of self-assembly vary, both strategies provide viable routes for generating minimal compartmentalized systems, modeling cellular pathways, and for rational design of new synthetic cells for technological applications. © 2016 Elsevier Ltd. All rights reserved. Keywords: Coacervate Lipid vesicle Self-assembly Protocells Nucleic acids Drug delivery Therapeutics Synthetic cells 1. Introduction Cells are the basic unit of self-replicating life on Earth. However, the complete mechanistic pathways that drive replication, homeostasis, information propagation and evolution, are still poorly understood. In addition, how biological life might have evolved from simple chemical processes remains an open, unanswered question. Therefore, synthesiz- ing abiotic cellular analogs, or protocells, is an important route for describing and understanding biological mechanisms and offers in- triguing models to describe evolutionary pathways in the pre-biotic world [1,2]. In order to synthesize suitable protocells it is important to connect molecular structure with self-assembly processes capable of supporting key features required for life, including concentration of functional molecules, creation of distinct chemical environments, and information propagation. Compartmentalization provides a mechanism for increasing local concentrations of enzymes and substrates sufciently to drive chemical reactions, and is a necessary feature for enriching functional molecules and their precursors. One plausible scenario for prebiotic compartmental- ization describes the spontaneous assembly and concomitant chemical enrichment of charged molecules to form membrane free droplets called coacervates [3 •• ]. An alternative route to chemical compartmentalization is via the formation of lipid membrane bound compartments, analogous to the membrane structure of modern cells [1,4,5]. Membranes also provide localization for heterogeneous reactions and are essential for the electrochemical gradients used for essential modern processes such as ATP synthesis, but can require complex protein machinery to create, maintain, and regulate ows of chemicals that cannot pass through them. Modern cellular biochemistry also provides clues with respect to information propagation in early life scenarios. Of the various biological molecules, only nucleic acids (RNA and DNA) have the capability to catalyze chemical reactions and template their own genetic propaga- tion. The RNA Worldhypothesis imagines a scenario on prebiotic earth where self-replicating RNA molecules were both enzymes and genes; today, these functionalities are primarily fullled by proteins and DNA. As there is no material evidence for the RNA Worldhypoth- esis it remains speculative [6], however the discovery that ribosomes are, at their core, ribozymes [7 ], strongly indicates that RNA preceded proteins in the chemical evolution of early life, thus highlighting the importance of considering polynucleotides in early life scenarios and in modern natural and synthetic self-assembled structures. In this review, we discuss the interaction of nucleic acids with two types of self-assembled systems that display cell-like properties: complex coacervates and hydrophobic assemblies such as micelles and vesicles. For each type, we briey discuss their mechanisms of formation and how these processes may be applied to early life scenarios, compartmen- talization phenomena in modern biology, and for therapeutics. All of these topics are exciting areas of research in their own right, and space does not permit a full exploration of any of them here. We instead attempt to highlight recent research results and interesting connections, while referring the reader to reviews for more comprehensive explana- tions of the underlying phenomena. Current Opinion in Colloid & Interface Science 26 (2016) 5057 Corresponding author. E-mail address: [email protected] (T.-Y.D. Tang). http://dx.doi.org/10.1016/j.cocis.2016.09.004 1359-0294/© 2016 Elsevier Ltd. All rights reserved. Contents lists available at ScienceDirect Current Opinion in Colloid & Interface Science journal homepage: www.elsevier.com/locate/cocis

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Current Opinion in Colloid & Interface Science 26 (2016) 50–57

Contents lists available at ScienceDirect

Current Opinion in Colloid & Interface Science

j ourna l homepage: www.e lsev ie r .com/ locate /coc is

Polynucleotides in cellular mimics: Coacervates and lipid vesicles

Jeffrey R Vieregg a, T-Y Dora Tang b,⁎a Institute for Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637, USAb Max Planck Institute for Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany

⁎ Corresponding author.E-mail address: [email protected] (T.-Y.D. Tang).

http://dx.doi.org/10.1016/j.cocis.2016.09.0041359-0294/© 2016 Elsevier Ltd. All rights reserved.

a b s t r a c t

a r t i c l e i n f o

Article history:Received 10 June 2016Received in revised form 22 August 2016Accepted 2 September 2016Available online 28 September 2016

In this review, we examine the interaction of nucleic acids with cell-like structures based on liquid–liquid phaseseparation of charged molecules (complex coacervation) and amphiphilic self-assembly (lipid vesicles). Wediscuss the mechanisms of their assembly and describe how they can be used as models for origin of life studiesand for understanding two recently-described phenomena in modern cells: membrane-free organelles andexosomes. Hybrid cells with increased structural complexity are highlighted and we then briefly explore howstrategies based on electrostatic and hydrophobic assembly can be used for designing and synthesizing deliveryagents for therapeutic nucleic acids. While the physical mechanisms of self-assembly vary, both strategiesprovide viable routes for generating minimal compartmentalized systems, modeling cellular pathways, and forrational design of new synthetic cells for technological applications.

© 2016 Elsevier Ltd. All rights reserved.

Keywords:CoacervateLipid vesicleSelf-assemblyProtocellsNucleic acidsDrug deliveryTherapeuticsSynthetic cells

1. Introduction

Cells are the basic unit of self-replicating life on Earth. However,the completemechanistic pathways that drive replication, homeostasis,information propagation and evolution, are still poorly understood. Inaddition, how biological life might have evolved from simple chemicalprocesses remains an open, unanswered question. Therefore, synthesiz-ing abiotic cellular analogs, or “protocells”, is an important route fordescribing and understanding biological mechanisms and offers in-triguing models to describe evolutionary pathways in the pre-bioticworld [1,2]. In order to synthesize suitable protocells it is importantto connect molecular structure with self-assembly processes capableof supporting key features required for life, including concentration offunctional molecules, creation of distinct chemical environments, andinformation propagation.

Compartmentalization provides a mechanism for increasing localconcentrations of enzymes and substrates sufficiently to drive chemicalreactions, and is a necessary feature for enriching functional moleculesand their precursors. Oneplausible scenario for prebiotic compartmental-ization describes the spontaneous assembly and concomitant chemicalenrichment of chargedmolecules to formmembrane free droplets calledcoacervates [3••]. An alternative route to chemical compartmentalizationis via the formation of lipid membrane bound compartments, analogousto the membrane structure of modern cells [1,4,5]. Membranes also

provide localization for heterogeneous reactions and are essential forthe electrochemical gradients used for essential modern processes suchas ATP synthesis, but can require complex protein machinery to create,maintain, and regulate flows of chemicals that cannot pass through them.

Modern cellular biochemistry also provides clues with respect toinformation propagation in early life scenarios. Of the various biologicalmolecules, only nucleic acids (RNA and DNA) have the capability tocatalyze chemical reactions and template their own genetic propaga-tion. The “RNA World” hypothesis imagines a scenario on prebioticearth where self-replicating RNA molecules were both enzymes andgenes; today, these functionalities are primarily fulfilled by proteinsand DNA. As there is nomaterial evidence for the “RNAWorld” hypoth-esis it remains speculative [6], however the discovery that ribosomesare, at their core, ribozymes [7•], strongly indicates that RNA precededproteins in the chemical evolution of early life, thus highlighting theimportance of considering polynucleotides in early life scenarios andin modern natural and synthetic self-assembled structures.

In this review, we discuss the interaction of nucleic acids with twotypes of self-assembled systems that display cell-like properties: complexcoacervates and hydrophobic assemblies such as micelles and vesicles.For each type, we briefly discuss their mechanisms of formation andhow these processesmay be applied to early life scenarios, compartmen-talization phenomena in modern biology, and for therapeutics. All ofthese topics are exciting areas of research in their own right, and spacedoes not permit a full exploration of any of them here. We insteadattempt to highlight recent research results and interesting connections,while referring the reader to reviews for more comprehensive explana-tions of the underlying phenomena.

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2. Electrostatic assembly: complex coacervate protocells

Interactions between oppositely charged molecules can lead tophase separation, forming either liquid droplets (complex coacervation)or solid precipitates depending on the length, charge density and typeof macromolecules. Complex coacervation refers to spontaneous forma-tion of a polymer-rich liquid phase in dynamic equilibrium with apolymer-poor phase [8,9••] via electrostatic interactions between oppo-sitely charged molecules in aqueous solution. This process was firstdescribed by Bungenberg de Jong in the 1920s in mixtures of gelatin(polycation) and gum arabic (polyanion) [10].While a complete quanti-tative model is still lacking, many aspects of complex coacervation arequalitatively understood for long polyelectrolytes. The formation ofmacroion pairs between oppositely charged molecules is driven by anincrease of entropy from the release of low valence counterions andwater rearrangement as they associate. Themacroion pairs then assem-ble into larger clusters, which leads to macroscopic phase separation(Fig. 1a) [9••,11]. Significantly, the dense phase, while highly enrichedin polymer, remains highly hydrated with a large concentration ofcounterions. The relative importance of ion pairing, hydration effects,and long-range electrostatics remains uncertain [12–14••] as do thefactors determining whether a particular macroion pair will form aliquid or a solid condensed complex [15]. As polyelectrolytes can bechemically diverse the process of complex coacervation is molecularlynon-specific. Indeed, since the 1920s complex coacervation has beenobserved between hundreds of different natural and synthetic polymers[8,16,17••]. Their properties including ease of formation, high viscosity,strong adhesion and high encapsulation efficiencies have led to arange of industrial applications including food additives [18] and elec-tronic ink [19], as well as therapeutic assemblies (see Section 5).

In 1924, Alexander Oparin put forward the idea that colloidalmicrodroplets formed via coacervation were the earliest metabolicunits in a reducing ‘prebiotic soup’ [20]. Over the next few decades,Oparin and co-workers demonstrated chemical enrichment within thedroplets, in-situ enzymatic reactions, and droplet growth and fissionreminiscent of cellular life [21••]. This ‘metabolism-first’ approach, how-ever, provided no clear connection to genetic evolution and informationpropagation via nucleic acids that would have been a key step at theonset of life. Their experiments also presumed the existence of largemacromolecules and polymers that are unlikely to have existed in aprebiotic environment.

In order for coacervates to be viable protocells, with the ability tosustain both chemical and genetic evolution, they must be able to

Fig. 1. Complex coacervation of chargedmolecules. (a) Oppositely-chargedmacromolecules for(b) Poly(lysine), (c) Adenosine triphosphate (ATP) and (d) deoxyribonucleic acid (DNA, sequewhile nucleotide polyphosphates have one negative charge per phosphate group.

form from small molecular weight molecules, particularly nucleotidesand their activated derivatives. This was first demonstrated in 2011 byKoga et al. [22••], who showed that coacervate microdroplets (Fig. 2a)could be formed from nucleoside triphosphates (ATP), diphosphates(ADP, FAD, NAD), and monophosphates (AMP) when mixed withshort (2–10 amino acid (aa)) lysine polypeptides (OLys) that mightplausibly be produced by prebiotic processes [23]. This study showedthat phase separation of small molecular weight ions has many similari-ties to complexation of larger polyelectrolytes. The dependence on elec-trostatic interactions, for example, is shown by the increase of the criticalconcentration required for coacervation (CCC) with decreasing negativecharge from ATP N ADP N AMP (Fig. 2b). In addition, they found thatincreasing the molecular weight of Poly(diallyldimethylammonium)(Poly(DADMAC)) from 150 to 275 kDa increased charge neutralization(with ATP) from 70 to 90%, These results suggest that increased hydro-phobicity, decreased solubility and increased orientational freedomfrom longer polymer chains all contribute to increasing charge neutrali-zation at the CCC.

Nucleotide coacervate droplets exhibit dynamic behaviors such ascoalescence and surface wetting (Fig. 2a) but remain stable over abroad pH and temperature range (between pH 2 and 10 and up to80 °C respectively). The coacervates also produce substantial chemicalenrichment of charged molecules, with OLys (2–10 aa)/ATP dropletsdisplaying a twenty-fold increase in ATP concentration relative to thedilute phase [22] and 15 kD poly(allylamine) droplets providing a300× increase of fluorescent solutes, as well as substantial enrichmentof Mg2+ and RNA oligonucleotides [24]. The dielectric constant of thedroplet interior is lower than that of the dilute phase, which providesa mechanism for sequestering low-charge molecules such as proteinenzymes. Sequestration provides a molecular route to accelerate bio-chemical reactions, primitive metabolism, and information processingby increasing the concentrations of substrates, as well as by crowding.This was demonstrated by Crosby et al. for the enzyme actinorhodinpolyketide synthase, which displayed an 18× rate increase whensequestered into ATP–PDDA coacervate droplets [25]. Significantly,mRNA transcription and sustained translation into protein have alsobeen demonstrated inside coacervates (Fig. 2c) [26•]. Taken together,these studies support the argument that coacervate microdropletsformed from nucleotide anions are viable platforms for protocell evolu-tion. Indeed, it has recently been shown that RNA within RNA–peptidecoacervates will elongate via temperature cycling. These results demon-strate a plausible scenario where compartmentalization is coupled withchemical evolution of polynucleotides [27].

m ion pairs that aggregate into membrane-free coacervate droplets. Molecular structure ofnce 5′-AGC-3′). At neutral pH, poly(lysine) and DNA each contain one charge per residue,

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Fig. 2.Membrane free artificial cells. (a) Mixing polycations (PDDA) and anions (ATP) leads to phase separation, as shown by turbidity and droplet formation (4:1molar ratio PDDAwithATP, 50mM, pH8). Brightfieldmicroscopy image (scale bar 20 μm) showswetting behavior ofmicrodroplets on a glass slide. (b) Critical coacervation concentration (CCC) vs anion chargefor nucleotide polyphosphates: AMP (1−), ADP (2−), ATP (3−), modified from [22••]. (c) Fluorescent protein (mCherry) expression in coacervate phase vs time [26•] published from theRoyal Society of Chemistry. (d) Fluorescence microscopy images of polylysine-RNA coacervate (scale bar 2 μm) with BODIPY FL C16 [69•]. (e) Fatty acid coated coacervate microdroplets.Heterogeneous distribution of lipophilic dye indicates fatty acid coating on the outer surface of the coacervate droplets (scale bar 2 μm) [69•].

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The coacervates discussed thus far are formed from ribonucleotidemonomers, but longer nucleic acids are also capable of forming com-plexes with polycations, as has been demonstrated with polyribonucle-otides and tRNA [28••,29]. Experience with synthetic polyelectrolytes,as well as theoretical considerations, suggests that polynucleotideswill experience stronger confinement than individual monomers, andthat their affinity for the coacervate phase will increase with theirlength [8,14]. This may overcome one challenge for coacervates asfunctional protocells, namely that the lack of a membrane leads to lowconfinement times [30], while coupling the chemical evolution of poly-nucleotides to more efficient compartmentalization.

2.1. Membrane-free organelles: intracellular phase separation

The facilemechanisms of synthetic droplet formation via electrostaticself-assembly have also been observed in present day biological systems.For example, DNA is condensed to near crystalline density by basicproteins and small polyamines in the nucleoid of bacteria, spermatozoaheads, and viral capsids by the same electrostatic interactions thatdrive coacervate formation [31]. Over the last decade, it has been pro-posed that liquid–liquid phase separation is the mechanism drivingthe formation of RNA granules, processing (P) bodies, Cajal bodies, andthe nucleolus and other membrane-free compartments, in eukaryoticcells (Fig. 3) [32–37 (34••,35•)]. Like the synthetic coacervates thesemembrane-free organelles are dynamic but appear to have significantinvolvement in essential cellular processes such as replication, signaling,stress response, and disease.

The mechanisms of phase separation are not fully understoodbut it appears that intrinsically disordered proteins (IDPs) with low-complexity sequence domains and charged residues are intimatelyinvolved in the formation of these membrane-free organelles [34,38].In addition, many of these compartments either contain large fractionsof RNA or require it for assembly, as in the case of stress granules(SGs). The presence of these charged molecules suggests that electro-statics play an important role in liquid droplet formation. Moreover,studies have shown that increasing the negative charge of liquidforming protein domains by serine phosphorylation inhibits SG

formation [32]. In vitro results support this hypothesis, as exemplifiedby the Ddx4 protein, which forms nuage bodies in humans and P gran-ules inworms [39]. Liquid droplets formed by the N-terminal domain ofDdx4 are destabilized to a similar extent by increased salt concentrationand by neutralization (via methylation) of multiple positively chargedarginine residues, although cation–pi interactions also appear to playa role in phase separation. Interestingly, membrane-free Ddx4 liquiddroplets also exhibited differential chemical environments as single-stranded DNA was concentrated within the droplets while double-stranded DNA was largely excluded. Measurements with the RNA-binding proteins LAF-1 [40••], hnRNPA1 [41], and Whi3 [42] also pointto electrostatics as a key driving force for droplet formation, as well asthe crucial role of RNA. For example in-vitro experiments with liquiddroplets formed from Whi3 showed a phase transition to gels andsolidfibers under certain conditions. Similar phenomenawere observedwith a prion-like protein FUS [43–45•] (Fig. 3d), where ALS-associatedmutations accelerated the solidification process. These results indicatethat in some instances intracellular phase transitions may also be asso-ciated with disease when proteins or RNA concentrations are mis-regulated.

3. Hydrophobic assembly: vesicles

Modern cells are physically defined by semi-permeable lipid bilayerscomposed primarily of phospholipid amphiphiles (two hydrocarbonchains linkedby a phosphate head group, Fig. 4ai) and sterols (e.g. choles-terol, Fig. 4aii), along with numerous proteins. As this structural elementis ubiquitous across all kingdoms it is likely that a similar lipidmembranewas present in the last common ancestor. Self-assembly of lipid amphi-philes into membrane-delineated compartments for protocell modelsand therapeutic assemblies has therefore attracted strong interest overthe last half a century. Above a critical concentration, amphiphilic lipidmonomers will self-assemble in water, driven by the hydrophobic effect,to form micelles (Fig. 4bi) or vesicles (Fig. 4bii) with bilayer membranesand an aqueous interior. The latter strongly resembles the basic structureof modern cells and organelles, and a large number of studies haveexamined vesicular behaviors such as budding and fission [46], as well

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Fig. 3. Liquid-phase separations in vivo. (a) Freely-diffusing RNA and protein form phase-separated liquid droplets (ii) that can mature into ordered solids (iii). Modified from [39].(b) RNA–protein liquid droplets (P granules) in a dividing Caenorhabditis elegans germ cell [37]. Droplets are actively transported to the posterior (P) end of the single-cell embryoover ~10 min prior to division into a germ and a somatic cell. Green: GFP-tagged PGL-1 protein; Red: DIC image. (c) Temperature-concentration phase diagram of Ddx4 proteinin vitro [39]. Methylation of multiple arginine residues (red line) destabilizes droplets to a similar extent as doubling the NaCl concentration, consistent with a primarily electrostaticinteraction. (d) In vitro, GFP-tagged FUS protein forms small liquid droplets (left, t = 0) that coalesce (middle, t = 4 h) and mature into fibrous solids (right, t = 8 h) [45].

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as encapsulation of complex biochemical reactions such as proteinexpression [47–49••] as a proxy to model cellular processes. Moreover,studies that have coupled RNA encapsulation and RNA interactionswith cell membranes give new insights into origins of life, as well as pro-viding tools for therapeutic delivery of nucleic acids.

3.1. Vesicle protocells in early life

While essential for modern life, phospholipid membranes haveseveral characteristics thatmake themproblematic for early-life scenarios[1,4]. The bilayer formed by phospholipids is highly impermeable tocharged compounds, which enables high electrochemical potentials

Fig. 4.Hydrophobic protocells. (a) Examples of lipidmembrane building blocks (i) Phospholipidacid), (iv) cationic lipid N-[1-(2,3-Dioleoyloxy)propyl]-N,N,N-trimethylammonium methy(i) micelles or (ii) vesicles with bilayer membranes depending on their structure and concentrswells vesicles, causing them to grow at the expense of empty vesicles. In the presence of excto mechanical stress or changing environment. The vesicles containing self-replicating RNA gro

for energy harvesting and signaling in modern cells but also preventsimportation of activated nucleosides and essential ions. Phospholipidbilayers are also very stable, making growth and division difficultwithoutthe aid of modern enzymes such as flippases and permeases. By contrast,single-chain fatty acids (Fig. 4aiii) form dynamic bilayers with leafletexchange times on the order of seconds and residence times on theorder of minutes, enabling growth/decay dynamics and selective perme-ability via transient defect formation [50]. Fatty acids are also relativelyeasy to synthesize abiotically, being detected inmeteorites at abundances20 times that of amino acids [4]. At certain concentrations fatty acidswill form micelles or vesicles depending on the pKa of the acid and thepH of the solution. The chemistry and dynamics of fatty acid assemblies

, palmitoyl-oleoyl-sn-phosphatidylcholine (POPC), (ii) cholesterol, (iii) fatty acid (gadoleicl-sulfate (DOTAP). (b) In aqueous solution, amphiphiles can self-assemble into eitheration. (c) A plausible scenario for coupled protocell growth and division. RNA elongationess amphiphile and micelles, vesicles grow and become unstable, leading to splitting duew, thus spiraling toward increased functionality.

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are amply reviewed elsewhere; here we focus on a few key ques-tions related to their interactions with polynucleotides or origin oflife studies.

The first of these relates to activated ribonucleosides and chainelongation. Protein nucleic acid polymerases use basic residues to stabi-lize the high negative charge transition state containing a nucleosidetriphosphate (NTP) and nucleic acid in close proximity. Lacking thisability, ribozyme polymerases rely on divalent cations such as Mg2+

at concentrations up to hundreds of mM [51], which causes precip-itation of fatty acids, membrane destruction [5] and polynucleotidehydrolysis. Non-enzymatic template elongation reactions also requirehigh Mg2+ concentrations, making it difficult to reconcile NTP poly-merization with the physical requirements of fatty acid self-assembly.One way around this problem is to use nucleotides with alternateleaving groups such as imidazole, 2-methylimidazole (2MeIm), and1-hydroxy-7-azabenzotriazole, which carry a lower charge (1− vs 3−

for NTPs) and react more readily than NTPs. If citrate is includedas a chelating agent, 2MeIm-activated nucleotides polymerize non-enzymatically on a single-stranded template at a rate of 0.67 h−1 insolution and copy short templates overnight in oleic acid vesicles[52••]. This does not solve the problem for ribozymes, however, and nei-ther citrate nor the alternate activated nucleosides have been producedby plausible abiotic reactions. It may be that more efficient ribozymepolymerases can be found; ribozyme ligases have been identified thatfunction with Mg2+ concentrations as low as 2 mM in the presenceof fatty acid vesicles and low-concentration EDTA as a chelator [53].Another attractive possibility is charge reduction through complexationof either the NTP or polynucleotides by basic peptides, analogous to(or even composed of) the coacervates discussed above [27].

A second problem involves coupling vesicle growth to replication ofthe interior contents, a key requirement for effective chemical evolu-tion. In this case, polynucleotides can provide a solution, via osmoticpressure. Due to their higher charge density, polynucleotides complexmore counterions compared to monomers, particularly if they arefolded. It has been proposed that RNA elongation generates a decreasein osmotic pressure that drives vesicle growth at the expense of lessactive vesicles [54] successfully coupling polymerase evolution to com-petition at the protocellular scale (Fig. 4c). Larger vesicles are alsomorelikely to be split by external shear stress and, if they are multilamellar,are subject to “pearling” instabilities, both of which provide plausiblepathways for division [1].

A final problem relates to the eventual transition from simple fattyacid vesicles to more stable membranes required for evolution ofmore sophisticated reactions. As mentioned above, phospholipid bilay-ers are impermeable to charged molecules. Modern cells solve thisproblem by using protein pores and channels to selectively regulateflows into and out of the cell, sustaining concentration differencesrequired for metabolism. Several results indicate that RNA is also capa-ble of forming pores in phospholipid bilayers. Vlassov et al. showed thatmultimeric RNA sequences are capable of permeabilizing liposomesand membranes via interaction with the phosphate head groups [55],and subsequent work demonstrated selective transport of tryptophanamino acids, thus demonstrating that the RNAworld can support mem-brane transport [50].

3.2. Exosomes: protocells in the modern world?

Exosomes are small (30–120 nm diameter) lipid vesicles thatlack internal organelles and circulate independently in the extracellularenvironment; as such, they sharemany of the physico-chemical charac-teristics of lipid membrane based protocells despite very differentbiogenesis and functions. Originally thought to be cellular waste prod-ucts, they are now known to function in intercellular communicationand have become the subject of intense interest due to their abilityto alter the phenotype of distant cells via transport of proteins andmicroRNAs (miRNAs) [56,57].

Exosomes are found in diverse body fluids, and are producedby many types of cells. In contrast to microvesicles [58], exosomesare derived from late endosomes, also known as multi-vesicularbodies, and released into the environment via SNARE-mediatedfusion within the plasma membrane. This process is initiated byvarying signaling pathways in different cell types, and is regulatedby RAB and ESCRT proteins [57]. Compared to the plasma mem-brane, exosome membranes are enriched in raft-type lipids suchas cholesterol and sphingomyelin [58] and possess generic andcell-type specific membrane protein and glycosylation signatures[59]. The latter can provide a “delivery address” for tissue-specifictargeting. A key discovery showed that exosomes contained mRNAand miRNA that were both active in target cells [60–63••]. Further-more, exosomal RNA populations differ from those of the parentcell, a characteristic of functional signaling [64]. Much remains tobe discovered about the content of exosomal messages, but theyhave been implicated in pathological processes such as tumor metas-tasis, viral infection, drug resistance, and immune response, as wellas embryonic development [57,64]. A deeper understanding of therole and functions of exosomes in biology should help unlock theirpotential for therapeutics and non-invasive diagnostics. As an exam-ple, researchers have attempted to deliver therapeutic RNAs withexosomes, either by loading purified exosomes and injecting theminto the body or by transfecting host cells with therapeutic RNAsto be packaged and exported [65•]. Currently, exosome-mediated de-livery lags behind engineered vesicle systems (Section 5) [66,67],but the intense interest in the field suggests that progress may berapid in this area.

4. Hybrid systems: electrostatic and hydrophobic assembly together

Combining electrostatic and hydrophobic assembly allows forcreation of more complex systems with enhanced capabilities. Lipidswith cationic head groups are commonly used to co-assemble lipidvesicles with nucleic acid polyanions (Section 5), and electrostatically-assembled nanoparticles can be further stabilized by functionalizing theanionic RNA component with cholesterol [68•]. Hybrid electrostatic–hydrophobic assembly is also interesting for early-life protocellstudies, as coacervates and lipid vesicles are in many ways comple-mentary in terms of capabilities required for self-replication. Coac-ervation readily concentrates charged molecules such as nucleicacids and activated nucleotides, but does not allow for internalstructure or heterogeneous catalysis and has limited capability tosustain electrochemical gradients at the boundary. Lipid vesiclesprovide powerful models for compartmentalization, but lack amechanism for enriching their interiors with ions and hydrophilicbiomolecules. Co-assembly of coacervates and vesicles is a promis-ing route to more complete cellularity, as is encapsulation of pre-formed coacervates. The latter was recently demonstrated by addingsodium oleate to positively-charged coacervates formed from RNAor ATP and polylysine or poly(DADMAC) [69•]. In the absence ofoleic acid, a lipophilic dye (BODIPY FL C16) partitioned homoge-neously within the coacervate droplets due to the lower dielectricconstant of the interior compared to the dilute exterior phase. Afterthe addition of the fatty acid, fluorescence was observed at the drop-let boundary only, indicating the formation of a lipid membrane.Small angle X-ray scattering measurements showed Bragg peaksconsistent with the formation of a multilamellar membrane, anddye uptake measurements showed differential permeability basedon charge and molecular weight. Increasing the exterior ionicstrength resulted in droplet disassembly and growth, reminiscentof the encapsulated PEG/dextran systems discussed earlier. Whilemuch work remains, this study shows that very simple chemical andphysical processes are capable of transforming various membrane-freecoacervate droplets, including OLys/RNA, into membrane-encapsulatedprotocells.

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5. Electrostatic assemblies and engineering lipid vesicles fortherapeutics

Therapeutic nucleic acids come in several forms, including DNA(gene therapy), RNA duplexes (siRNA), and oligonucleotides formicroRNA and antisense pathways, but they face common challengesas drugs. To be effective, within the target tissue, the nucleic acidsmust evade clearance by the liver and kidney, cross the hydrophobiccell membrane, and avoid degradation by nuclease enzymes bothoutside and inside the cell [70]. The same electrostatic and hydrophobicinteractions that give rise to protocells can also be harnessed to produceself-assembling delivery systems that offer solutions to several of theseproblems. A detailed description of these systems is beyond the scopeof this review, instead, we mention the basic chemical and physicalstrategies and provide references for the interested reader.

Encapsulation by coacervate and solid polyelectrolyte complexesformed from nucleic acids and cationic polymers (polyplexes) hasbeen extensively studied as non-viral transfection vectors both in vitroand in vivo [65•,71–73]. One strategy to prevent aggregation, reduceunwanted interactions with serum proteins, and promote longer circu-lation time is based on functionalizing the polycations with neutralhydrophilic polymers such as polyethylene glycol (PEG). In the case ofpolyplexes this leads to the formation of nanoparticleswith a coacervateor solid complex core surrounded by a PEG corona and typical diametersbetween 20 and 200 nm [74]. Layer-by-layer electrostatic assemblycan also be used to produce nanoparticles and functionalize surfacesof implanted devices [75,76].

Hydrophobically-assembled micelles, or liposomes, have alsobeen extensively engineered to be effective delivery platforms fornucleic acids [65•]. Cationic and ionizable lipids enable efficient load-ing of anionic polynucleotides and release upon endocytosis, thoughin vivo potency and toxicity remain challenging [77,78]. As withpolyplexes, PEG-functionalized liposomes (stable nucleic acid lipidparticles, or SNALPS) display improved circulation time, reducedtoxicity and immunogenicity and have been used in multiple clinicaltrials [70,79•]. Other strategies for modifying and tuning the deliveryvehicles include incorporation of targeting moieties and/or labilelinkages for intracellular disassembly [80]. Nucleic acids can also bemade amphiphilic by conjugating them with hydrophobic groups,enabling interesting new types of self-assembled nanostructures[81••,82].

6. Conclusion

In this review, we have discussed how cellular mimics can beproduced by self-assembly of charged biomolecules (complexcoacervation) and lipid amphiphiles (vesicles) and discussed theirutility for prebiotic pathways, biological organization and (briefly)therapeutic applications. Both mechanisms incorporate essentialfeatures of modern cells, and their spontaneous assembly propertiessuggest that they might have been viable routes for cellular evolutionon early earth and these possibilities are still under investigation. Addi-tionally, the incorporation of synthetic biology and high-throughputapproaches [83–85 (84••)] provide a valuable complement to the morephysico-chemical approaches described here, raising hopes for under-standing the basic principles governing how cells evolved, and howwe can use cellular mimics in the modern world.

• Of special interest.•• Of outstanding interest.

Acknowledgments

T-Y T's work was supported by the MaxSynBio, MPG(M.IF.A.MOZGDT80). We would like to acknowledge F. Friedrichat MTO (Media Technologies and Outreach) group at MPI-CBGfor assistance with the graphical abstract.

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