Abiotic RNA Formation in Natural Nanoconfinements of Water: Overcoming the Water Paradox via a Nanofluidic Bridge Between Geochemistry and Biochemistry

<p class="western">The "water paradox" is an obstinate problem in the research on the chemical evolution towards the emergence of life. It states that although aqueous environments are essential for life, they hamper key condensation reactions such as nucleotide polymerisation. To overcome this paradox several hypotheses have been proposed, including scenarios based on alternative solvents like formamide, condensing agents like cyanamide, high temperatures of over 150 °C or wet/dry cycles in surface ponds. However, when appraising the prebiotic plausibility of such scenarios some general weaknesses appear. Besides the fact that all known life manages the water paradox without needing such proposed conditions, the principle that evolution builds on existing pathways indicates that the same physicochemical effects were probably involved in the abiotic origin of biopolymers as now being tapped by life via complex enzymes.</p> <p class="western">Here we show that abiotic temporal nanoconfinements of water can act as natural reactions vessels for prebiotic RNA formation. We present evidence for spontaneous, abiotic polymerisation of nucleotides in water. According to our results the reaction is enabled by the rise of anomalous properties of water when being temporarily confined between nanoscale separated particles of geological ubiquity within aqueous suspensions. These findings can solve the water paradox in such a way that nanofluidic effects in aqueous particle suspensions open up an abiotic route to biopolymerisation and polymer stabilisation under chemical and thermodynamic conditions which also exist within the intracellular environment of living cells. The fact that polymerase enzymes also form temporal nanoconfined water clusters inside their active site implies that the same physico-chemical effects are tapped for nucleotide condensation in water both by biochemical pathways and the reported abiotic route. This indicates that our model is consistent with evolutionary conservatism stretching back to the era of prebiotic chemical evolution. The consistency is further supported by the fact that water is not trapped by nanoconfinements within the polymerase core but can exchange with the surrounding intracellular fluid – a situation which is also prevalent in nanofluidic environments within aqueous particle suspensions. Our experimental finding that under the reported conditions an amino acid catalyses the abiotic polymerisation of nucleotides may give a hint to a nanofluidic origin of cooperation between amino acids and nucleotides evolving to the interdependent synthesis of proteins and nucleic acids in living cells.</p> <p class="western">The effect of abiotic RNA polymerisation in temporal nanoconfined water does not depend on highly specific mineral species and geological environments as watery suspensions of micro- and nanoparticles are virtually ubiquitous – they exist, for example, in the form of sediments with pore water, hydrothermal vent fluids containing precipitated inorganic and polyaromatic particles or dispersed aggregates inside water-filled cracks in the crust of the earth and possibly of icy moons in the outer solar system.</p> <p class="western"><strong>References</strong></p> <p class="western">Greiner de Herrera, A., Markert, T. & Trixler, F. Temporal nanofluidic confinements induce prebiotic condensation in water. Preprint, DOI: 10.21203/rs.3.rs-163645/v3</p>

To “Z” or not to “Z”: Z-RNA, self-recognition, and the MDA5 helicase

Double-stranded RNA (dsRNA) is produced both by virus and host. Its recognition by the melanoma differentiation–associated gene 5 (MDA5) initiates type I interferon responses. How can a host distinguish self-transcripts from nonself to ensure that responses are targeted correctly? Here, I discuss a role for MDA5 helicase in inducing Z-RNA formation by Alu inverted repeat (AIR) elements. These retroelements have highly conserved sequences that favor Z-formation, creating a site for the dsRNA-specific deaminase enzyme ADAR1 to dock. The subsequent editing destabilizes the dsRNA, ending further interaction with MDA5 and terminating innate immune responses directed against self. By enabling self-recognition, Alu retrotransposons, once invaders, now are genetic elements that keep immune responses in check. I also discuss the possible but less characterized roles of the other helicases in modulating innate immune responses, focusing on DExH-box helicase 9 (DHX9) and Mov10 RISC complex RNA helicase (MOV10). DHX9 and MOV10 function differently from MDA5, but still use nucleic acid structure, rather than nucleotide sequence, to define self. Those genetic elements encoding the alternative conformations involved, referred to as flipons, enable helicases to dynamically shape a cell’s repertoire of responses. In the case of MDA5, Alu flipons switch off the dsRNA-dependent responses against self. I suggest a number of genetic systems in which to study interactions between flipons and helicases further.

Prebiotic Pathway from Ribose to RNA Formation

At the focus of abiotic chemical reactions is the synthesis of ribose. No satisfactory explanation was provided as to the missing link between the prebiotic synthesis of ribose and prebiotic RNA (preRNA). Hydrogen cyanide (HCN) is assumed to have been the principal precursor in the prebiotic formation of aldopentoses in the formose reaction and in the synthesis of ribose. Ribose as the best fitting aldopentose became the exclusive sugar component of RNA. The elevated yield of ribose synthesis at higher temperatures and its protection from decomposition could have driven the polymerization of the ribose-phosphate backbone and the coupling of nucleobases to the backbone. RNA could have come into being without the involvement of nucleotide precursors. The first nucleoside monophosphate is likely to have appeared upon the hydrolysis of preRNA contributed by the presence of reactive 2′-OH moieties in the preRNA chain. As a result of phosphorylation, nucleoside monophosphates became nucleoside triphosphates, substrates for the selective synthesis of genRNA.

Temporal nanofluidic confinements induce prebiotic condensation in water

A long-standing, crucial problem in the research on the chemical evolution towards the origin of life is the so-called ‘water paradox’. It states that although water is essential to life, key chemical reactions such as the synthesis of RNA are inhibited by it. Current hypotheses addressing this paradox have low prebiotic plausibility when taking the conservative nature of evolution into account. Here, we report spontaneous abiotic RNA formation in aqueous environments. The synthesis is driven by nanofluidic phenomena that alter critical properties of water. Our findings provide a solution to the paradox in a multifaceted way: abiotic, temporal nanofluidic confinements allow prebiotic condensation reaction pathways in water under stable, moderate conditions, emerge in aqueous particle suspensions as a geologically ubiquitous and thus prebiotic highly plausible environment and are consistent with the principle that evolution builds on existing pathways, as living cells also work with temporal nanoconfined water.

Temporal nanofluidic confinements induce prebiotic condensation in water

A long-standing, crucial problem in the research on the chemical evolution towards the origin of life is the so-called ‘water paradox’. It states that although water is essential to life, key chemical reactions such as the synthesis of RNA are inhibited by it. Current hypotheses addressing this paradox have low prebiotic plausibility when taking the conservative nature of evolution into account. Here, we report spontaneous abiotic RNA formation in aqueous environments. The synthesis is driven by nanofluidic phenomena that alter critical properties of water. Our findings provide a solution to the paradox in a multifaceted way: abiotic, temporal nanofluidic confinements allow prebiotic condensation reaction pathways in water under stable, moderate conditions, emerge in aqueous particle suspensions as a geologically ubiquitous and thus prebiotic highly plausible environment and are consistent with the principle that evolution builds on existing pathways, as living cells also work with temporal nanoconfined water.

Recognition of non-CpG repeats in Alu and ribosomal RNAs by the Z-RNA binding domain of ADAR1 induces A-Z junctions

Adenosine-to-inosine (A-to-I) editing of eukaryotic cellular RNAs is essential for protection against auto-immune disorders. Editing is carried out by ADAR1, whose innate immune response-specific cytoplasmic isoform possesses a Z-DNA binding domain (Zα) of unknown function. Zα also binds to CpG repeats in RNA, which are a hallmark of Z-RNA formation. Unexpectedly, Zα has been predicted — and in some cases even shown — to bind to specific regions within mRNA and rRNA devoid of such repeats. Here, we use NMR, circular dichroism, and other biophysical approaches to demonstrate and characterize the binding of Zα to mRNA and rRNA fragments. Our results reveal a broad range of RNA sequences that bind to Zα and adopt Z-RNA conformations. Binding is accompanied by destabilization of neighboring A-form regions which is similar in character to what has been observed for B-Z-DNA junctions. The binding of Zα to non-CpG sequences is specific, cooperative and occurs with an affinity in the low micromolar range. This work allows us to propose a model for how Zα could influence the RNA binding specificity of ADAR1.

Mirror Symmetry Breaking in Liquids and Their Impact on the Development of Homochirality in Abiogenesis: Emerging Proto-RNA as Source of Biochirality?

Recent progress in mirror symmetry breaking and chirality amplification in isotropic liquids and liquid crystalline cubic phases of achiral molecule is reviewed and discussed with respect to its implications for the hypothesis of emergence of biological chirality. It is shown that mirror symmetry breaking takes place in fluid systems where homochiral interactions are preferred over heterochiral and a dynamic network structure leads to chirality synchronization if the enantiomerization barrier is sufficiently low, i.e., that racemization drives the development of uniform chirality. Local mirror symmetry breaking leads to conglomerate formation. Total mirror symmetry breaking requires either a proper phase transitions kinetics or minor chiral fields, leading to stochastic and deterministic homochirality, respectively, associated with an extreme chirality amplification power close to the bifurcation point. These mirror symmetry broken liquids are thermodynamically stable states and considered as possible systems in which uniform biochirality could have emerged. A model is hypothesized, which assumes the emergence of uniform chirality by chirality synchronization in dynamic “helical network fluids” followed by polymerization, fixing the chirality and leading to proto-RNA formation in a single process.

Dengue virus strain 2 capsid protein switches the annealing pathway and reduces the intrinsic dynamics of the conserved 5’ untranslated region

ABSTRACTThe capsid protein of Dengue Virus strain 2 (DENV2C) is a structural protein with RNA chaperone activity that promotes multiple nucleic acid structural rearrangements, critical for transcription of the single-stranded positive-sense DENV2 genomic RNA. Annealing of the conserved 5’ untranslated region (5’UTR) to either its complementary sequence or to the 3’ untranslated region (3’UTR) occurs during (+)/(−) ds-RNA formation and (+) RNA circularization, respectively, both essential steps during DENV RNA replication. We investigated the effect of DENV2C on the annealing mechanism of two hairpin structures from the 5’UTR region (21-nt upstream AUG region (5’UAR) and 23-nt capsid-coding hairpin (5’cHP)) to their complementary sequences during (+)/(−) ds-RNA formation and (+) RNA circularization. Using fluorescence spectroscopy, DENV2C was found to switch annealing reactions nucleated mainly through kissing-loop intermediates to stem-stem interactions during (+)/(−) ds-RNA formation while it promotes annealing mainly through kissing-loop interactions during the (+) RNA circularization. Using FRET-FCS and trFRET, we determined that DENV2C exerts RNA chaperone activities by modulating intrinsic dynamics and by reducing the kinetically trapped unfavorable conformations of the 5’UTR sequence. Thus, DENV2C is likely to facilitate genome folding into functional conformations required for replication, playing a role in modulating (+)/(−) ds-RNA formation and (+) RNA circularization.