Diffusion of LLPS Droplets Consisting of Poly(PR) Dipeptide Repeats and RNA on Chemically Modified Glass Surface

Primitive homochiral polyester formation driven by tartaric acid and calcium availability

α-hydroxy acids (αHAs), simple and prebiotically plausible organic monomers, were likely present in various environments on and off Earth and could have played a role in directing the emergence of the first homochiral living systems. Some αHAs, which could have been of varying chirality, can undergo dehydration polymerization into polyesters, which could assemble into membraneless microdroplets upon rehydration; understanding these processes is critical for unraveling how simple prebiotic molecules transitioned into more complex systems capable of supporting selective chemical reactions, a key step toward the origin of life. Here, we focused on tartaric acid (TA), a prebiotically relevant αHA with multiple chiral forms, to probe plausible mechanisms by which primitive αHA and polyester-based systems could have participated in selective homochiral polymer synthesis. Enantiopure solutions of d-TA or l-TA polymerize efficiently via dehydration, while racemic dl-TA polymerization is inhibited due to stereochemical incompatibility. We found that Ca2+ ions influence this process in two significant ways: 1) regulating TA monomer availability through selective crystallization, removing equal amounts of both enantiomers in racemic proportion and thereby enriching the enantiomeric excess of the remaining nonracemic TA solution; and 2) modulating polymerization by suppressing enantiopure TA polymerization while enabling dl-TA polymerization. These findings suggest that the differential availability of simple inorganic ions, such as Ca2+, could have indirectly mediated the selection of simple organic chiral monomers and the emergence of homochirality in primitive protocell-forming polymers, offering a pathway from nonliving to living matter in early Earth environments.

Graphene Biosensor Differentiating Sensitive Interactions between Ribonucleic Acid and Dipeptide Repeats in Liquid-Liquid Phase Separation

Liquid-Liquid Phase Separation (LLPS) plays a crucial role in cell biology and is closely associated with neurodegenerative diseases like Amyotrophic Lateral Sclerosis (ALS) and Frontotemporal Dementia (FTD). Recent studies connect mutations in the C9ORF72 gene to the production of arginine-rich dipeptide repeat proteins (R-DPRs), such as poly(PR) and poly(GR). These R-DPRs disrupt LLPS in membrane-less organelles (MLOs) and contribute to disease pathology. While traditional analysis techniques like nuclear magnetic resonance (NMR), fluorescence recovery after photobleaching (FRAP), and Förster resonance energy transfer (FRET) provide insights into LLPS's role in these diseases, their ability is limited in detecting weak intermolecular interactions within LLPS droplets. This study employs graphene field-effect transistors (GFETs) for their superior sensitivity in detecting these molecular interactions. We immobilized RNA (poly-A) on GFETs and measured the electrical conductivity of GFETs to characterize shifts in the voltage of the charge neutral point in GFETs, allowing for the detection of dipeptide repeat peptides, such as (PR)12, (GR)12, and R12. Our results show that interactions between peptides and RNA require a specific peptide concentration threshold and vary between peptide types. Notably, the minimal conductivity shift suggests that peptides containing proline residues exhibit a nonuniform spatial distribution during interactions with RNA on graphene surfaces. This finding indicates that peptide rigidity induced by prolines plays a vital role in these molecular interactions and their multivalent contacts with RNA, which agrees with findings reported in other recent works. The capability of GFETs to detect these interactions at nanomolar concentrations marks a significant advancement in sensitivity over existing methods. This research sheds light on the mechanisms of LLPS involving R-DPRs and opens avenues for further understanding of related neurodegenerative diseases.

Interfacial and intrinsic molecular effects on the phase separation/transition of heteroprotein condensates

Liquid-liquid phase separation (LLPS) and droplet formation by LLPS are key concepts used to explain compartmentalization in living cells. Protein contact to a membrane surface is considered an important process for protein organization in a liquid phase or during transition to a solid or liquid dispersion state. The direct experimental comprehensive investigation is; however, not performed on the surface-droplet interaction and phase transition. In the present study, we constructed simple and reproducible experiments to analyze the structural transition of aggregates and droplets in an ovalbumin (OVA) and lysozyme (LYZ) complex on glass slides with various coatings. The difference in droplet-surface interaction may only be important in the boundary region between aggregates and droplets of a protein mixture, as shown in the phase diagram. Co-aggregates of OVA-LYZ changed to droplet-like circular forms during incubation. In contrast, free l-lysine resulted in the uniform droplet-to-solid phase separation at lower concentrations and dissolved any structures at higher concentrations. These results represent the first phase-diagram-based analysis of the phase transition of droplets in a protein mixture and a comparison of surface-surface and small molecular-droplet structure interactions.

Spectroscopic and Biophysical Methods to Determine Differential Salt-Uptake by Primitive Membraneless Polyester Microdroplets

α-Hydroxy acids are prebiotic monomers that undergo dehydration synthesis to form polyester gels, which assemble into membraneless microdroplets upon aqueous rehydration. These microdroplets are proposed as protocells that can segregate and compartmentalize primitive molecules/reactions. Different primitive aqueous environments with a variety of salts could have hosted chemistries that formed polyester microdroplets. These salts could be essential cofactors of compartmentalized prebiotic reactions or even directly affect protocell structure. However, fully understanding polyester-salt interactions remains elusive, partially due to technical challenges of quantitative measurements in condensed phases. Here, spectroscopic and biophysical methods are applied to analyze salt uptake by polyester microdroplets. Inductively coupled plasma mass spectrometry is applied to measure the cation concentration within polyester microdroplets after addition of chloride salts. Combined with methods to determine the effects of salt uptake on droplet turbidity, size, surface potential and internal water distribution, it was observed that polyester microdroplets can selectively partition salt cations, leading to differential microdroplet coalescence due to ionic screening effects reducing electrostatic repulsion forces between microdroplets. Through applying existing techniques to novel analyses related to primitive compartment chemistry and biophysics, this study suggests that even minor differences in analyte uptake can lead to significant protocellular structural change.

Micro-Raman spectroscopic analysis of liquid-liquid phase separation

Liquid-liquid phase separation (LLPS) plays a significant role in various biological processes, including the formation of membraneless organelles and pathological protein aggregation. Although many studies have found various factors that modulate the LLPS process or the liquid-to-solid phase transition (LSPT) using microscopy or fluorescence-based methods, the molecular mechanistic details underlying LLPS and protein aggregation within liquid droplets remain uncharacterized. Therefore, structural information on proteins inside liquid droplets is required to understand the mechanistic link to amyloid formation. In the present study, we monitored droplet formation related to protein fibrillation using micro-Raman spectroscopy in combination with differential interference contrast (DIC) microscopy to study the conformational change in proteins and the hydrogen-bonding (H-bonding) structure of water during LLPS. Interestingly, we found that the O-D stretching band for water (HOD in H₂O) inside the droplets exhibited a distinct Raman spectrum from that of the bulk water, suggesting that the time-dependent change in the hydration environment in the protein droplets during the process of LLPS can be studied. These results demonstrate that the superior spatial resolution of micro-Raman spectroscopy offers significant advantages in investigating the molecular mechanisms of LLPS and following LSPT processes.

A fish herpesvirus highlights functional diversities among Zα domains related to phase separation induction and A-to-Z conversion

Zalpha (Zα) domains bind to left-handed Z-DNA and Z-RNA. The Zα domain protein family includes cellular (ADAR1, ZBP1 and PKZ) and viral (vaccinia virus E3 and cyprinid herpesvirus 3 (CyHV-3) ORF112) proteins. We studied CyHV-3 ORF112, which contains an intrinsically disordered region and a Zα domain. Genome editing of CyHV-3 indicated that the expression of only the Zα domain of ORF112 was sufficient for normal viral replication in cell culture and virulence in carp. In contrast, its deletion was lethal for the virus. These observations revealed the potential of the CyHV-3 model as a unique platform to compare the exchangeability of Zα domains expressed alone in living cells. Attempts to rescue the ORF112 deletion by a broad spectrum of cellular, viral, and artificial Zα domains showed that only those expressing Z-binding activity, the capacity to induce liquid-liquid phase separation (LLPS), and A-to-Z conversion, could rescue viral replication. For the first time, this study reports the ability of some Zα domains to induce LLPS and supports the biological relevance of dsRNA A-to-Z conversion mediated by Zα domains. This study expands the functional diversity of Zα domains and stimulates new hypotheses concerning the mechanisms of action of proteins containing Zα domains.

Effect of Multivalency on Phase-Separated Droplets Consisting of Poly(PR) Dipeptide Repeats and RNA at the Solid/Liquid Interface

Dipeptide repeat proteins (DRPs) are considered a significant cause of amyotrophic lateral sclerosis (ALS), and their liquid-liquid phase separation (LLPS) formation with other biological molecules has been studied both in vitro and in vivo. The immobilization and wetting of the LLPS droplets on glass surfaces are technically crucial for the measurement with optical microscopy. In this work, we characterized the surface diffusion of LLPS droplets of the DRPs with different lengths to investigate the multivalent effect on the interactions of their LLPS droplets with the glass surface. Using fluorescence microscopy and the single-particle tracking method, we observed that the large multivalency drastically changed the surface behavior of the droplets. The coalescence and wetting of the droplets were accelerated by increasing the multivalency of peptides in the LLPS system. Our findings on the effect of multivalency on interactions between droplets and glass surfaces could provide a new insight to enhance the understanding of LLPS formation and biophysical properties related to the solid/liquid interface.

A material-based panspermia hypothesis: The potential of polymer gels and membraneless droplets

The Panspermia hypothesis posits that either life's building blocks (molecular Panspermia) or life itself (organism-based Panspermia) may have been interplanetarily transferred to facilitate the origins of life (OoL) on a given planet, complementing several current OoL frameworks. Although many spaceflight experiments were performed in the past to test for potential terrestrial organisms as Panspermia seeds, it is uncertain whether such organisms will likely "seed" a new planet even if they are able to survive spaceflight. Therefore, rather than using organisms, using abiotic chemicals as seeds has been proposed as part of the molecular Panspermia hypothesis. Here, as an extension of this hypothesis, we introduce and review the plausibility of a polymeric material-based Panspermia seed (M-BPS) as a theoretical concept, where the type of polymeric material that can function as a M-BPS must be able to: (1) survive spaceflight and (2) "function", i.e., contingently drive chemical evolution toward some form of abiogenesis once arriving on a foreign planet. We use polymeric gels as a model example of a potential M-BPS. Polymeric gels that can be prebiotically synthesized on one planet (such as polyester gels) could be transferred to another planet via meteoritic transfer, where upon landing on a liquid bearing planet, can assemble into structures containing cellular-like characteristics and functionalities. Such features presupposed that these gels can assemble into compartments through phase separation to accomplish relevant functions such as encapsulation of primitive metabolic, genetic and catalytic materials, exchange of these materials, motion, coalescence, and evolution. All of these functions can result in the gels' capability to alter local geochemical niches on other planets, thereby allowing chemical evolution to lead to OoL events.