Biology subjects

Meyer, M. O.

Publications and source records attributed to Meyer, M. O..

5 recordsLinked to original sources

bioRxiv2025

Primitive Molecular Buffering by Low-Multivalency Coacervates

Coacervate droplets formed by liquid-liquid phase separation serve as models for intracellular biomolecular condensates and as potential protocellular compartments during the emergence of life. Changes in availability of molecular components can be anticipated for intracellular and prebiotic milieu, and protocells may have also faced fluctuations in salinity and pH. Compartments able to maintain their molecular composition, i.e. homeostasis, under such conditions would be better able to preserve internal functions. Phase separation could in principle provide resistance to local changes in molecular composition. To evaluate this possibility, we investigated the impact of non-stoichiometric charge ratios of coacervate molecules on coacervate formation and RNA compartmentalization in oligoarginine (R10)/ATP coacervates across salinity and pH conditions relatable to plausible prebiotic environments. These R10/ATP coacervate systems resisted changes in oligoarginine concentration in both phases under freshwater and ocean-relevant salt conditions, providing a primitive molecular buffering function. Moreover, RNA accumulation was observed in the coacervates over a range of pH, salinity, and R10/ATP stoichiometry. We also observed salt-dependent differences in molecular buffering and compartmentalization that can be understood in terms of how salinity impacts the relative strengths of intermolecular binding modes that drive coacervation and RNA uptake. By varying relative phase volumes and altering which intermolecular binding modes dominate, LLPS provides general mechanisms for resisting changes in molecular availability and environmental conditions, even without the active homeostasis of living cells. Such primitive molecular buffering could have aided the emergence of life and may find utility in biotechnological or commercial applications based on molecular compartmentalization.

biophysics↗

bioRxiv2024

Direct testing of natural twister ribozymes from over a thousand organisms reveals a broad tolerance for structural imperfections

Twister ribozymes are an extensively studied class of nucleolytic RNAs. Thousands of natural twisters have been proposed using sequence homology and structural descriptors. Yet, most of these candidates have not been validated experimentally. To address this gap, we developed CHiTA (Cleavage High-Throughput Assay), a high-throughput pipeline utilizing massively parallel oligonucleotide synthesis and next-generation sequencing to test putative ribozymes en masse in a scarless fashion. As proof of principle, we applied CHiTA to a small set of known active and mutant ribozymes. We then used CHiTA to test two large sets of naturally occurring twister ribozymes: over 1, 600 previously reported putative twisters and [~]1, 000 new candidate twisters. The new candidates were identified computationally in [~]1, 000 organisms, representing a massive increase in the number of ribozyme-harboring organisms. Approximately 94% of the twisters we tested were active and cleaved site-specifically. Analysis of their structural features revealed that many substitutions and helical imperfections can be tolerated. We repeated our computational search with structural descriptors updated from this analysis, whereupon we identified and confirmed the first intrinsically active twister ribozyme in mammals. CHiTA broadly expands the number of active twister ribozymes found in nature and provides a powerful method for functional analyses of other RNAs. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=64 SRC="FIGDIR/small/603121v1_ufig1.gif" ALT="Figure 1"> View larger version (17K): org.highwire.dtl.DTLVardef@a9cc05org.highwire.dtl.DTLVardef@1917d6dorg.highwire.dtl.DTLVardef@c1a5ddorg.highwire.dtl.DTLVardef@1706f54_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2023

The Functional RNA Identification (FRID) Pipeline: Identification of Potential Pseudoknot-Containing RNA Elements as Therapeutic Targets for SARS-CoV-2

The COVID-19 pandemic persists despite the development of effective vaccines. As such, it remains crucial to identify new targets for antiviral therapies. The causative virus of COVID-19, SARS-CoV-2, is a positive-sense RNA virus with RNA structures that could serve as therapeutic targets. One such RNA with established function is the frameshift stimulatory element (FSE), which promotes programmed ribosomal frameshifting. To accelerate identification of additional functional RNA elements, we introduce a novel computational approach termed the Functional RNA Identification (FRID) pipeline. The guiding principle of our pipeline, which uses established component programs as well as customized component programs, is that functional RNA elements have conserved secondary and pseudoknot structures that facilitate function. To assess the presence and conservation of putative functional RNA elements in SARS-CoV-2, we compared over 6,000 SARS-CoV-2 genomic isolates. We identified 22 functional RNA elements from the SARS-CoV-2 genome, 14 of which have conserved pseudoknots and serve as potential targets for small molecule or antisense oligonucleotide therapeutics. The FRID pipeline is general and can be applied to identify pseudoknotted RNAs for targeted therapeutics in genomes or transcriptomes from any virus or organism.

bioinformatics↗

bioRxiv2023

RNA folding studies inside peptide-rich droplets reveal roles of modified nucleosides at the origin of life

Compartmentalization of RNA in biopolymer-rich membraneless organelles is now understood to be pervasive and critical for the function of extant biology and has been proposed as a prebiotically-plausible way to accumulate RNA. However, compartment-RNA interactions that drive encapsulation have the potential to influence RNA structure and function in compartment- and RNA sequence-dependent ways. Herein, we detail Next-Generation Sequencing (NGS) experiments performed for the first time in membraneless compartments called complex coacervates to characterize the fold of many different transfer RNAs (tRNAs) simultaneously under the potentially denaturing conditions of these compartments. Strikingly, we find that natural modifications favor the native fold of tRNAs in these compartments. This suggests that covalent RNA modifications could have played a critical role in metabolic processes at the origin of life. One Sentence SummaryWe demonstrate that RNA folds into native secondary and tertiary structures in protocell models and that this is favored by covalent modifications, which is critical for the origins of life.

biochemistry↗

bioRxiv2020

Prebiotically-relevant low polyion multivalency can improve functionality of membraneless compartments

Multivalent polyions can undergo complex coacervation, producing membraneless compartments that accumulate ribozymes and enhance catalysis, and offering a mechanism for functional prebiotic compartmentalization in the origins of life. Here, we evaluated the impact of low, prebiotically-relevant polyion multivalency in coacervate performance as functional compartments. As model polyions, we used positively and negatively charged homopeptides with one to 100 residues, and adenosine mono-, di-, and triphosphate nucleotides. Polycation/polyanion pairs were tested for coacervation, and resulting membraneless compartments were analyzed for salt resistance, ability to provide a distinct internal microenvironment (apparent local pH, RNA partitioning), and effect on RNA structure formation. We find that coacervates formed by phase separation of the relatively shorter polyions more effectively generated distinct pH microenvironments, accumulated RNA, and preserved duplexes. Hence, reduced multivalency polyions are not only viable as functional compartments for prebiotic chemistries, but they can offer advantages over higher molecular weight analogues.

biophysics↗