Hydrophobic-cationic peptides enhance RNA polymerase ribozyme activity by accretion
Preprint posted on 23 February 2021 https://www.biorxiv.org/content/10.1101/2021.02.22.432394v1
Article now published in Nature Communications at http://dx.doi.org/10.1038/s41467-022-30590-3
Written by: Julia van den Boogert, Isabel van Rongen, Emile van Weert & Olivier Zadelhoff
The origin of life is thought to have arisen from an RNA world in which ribozymes catalysed biochemical reactions and RNA stored genetic information. However, the emergence of RNA-based life required compartmentalization, or otherwise RNA replication systems would be overrun and genetic selection could not have occurred. Compartmentalization may have been achieved by accretion of peptides and RNA. The term accretion implies that biopolymers gradually accumulate into macromolecular aggregates stabilized by intermolecular forces. Accretion of peptides and RNA could lead to an increased local concentration and a basic form of compartmentalization, which may have played a role in the origin of life. However, the impact of accretion on ribozymes is largely unknown.
Examining the accretion hypothesis, Li et al. discover the RNA binding peptide P43 (AKKVWIIMGGS), which is able to accrete multiple ribozyme species and regulate their activity.
The authors obtain P43 by performing a randomized peptide phage display, selecting for peptides that bind and regulate RNA polymerase ribozyme (RPR). P43 is a cationic-hydrophobic peptide which forms insoluble aggregates that can accrete RNA and ribozymes on its surface. The phage display reveals that P43 inhibits RPR activity. By assessing the inhibiting potential of truncated P43 variants, the authors find that not only hydrophobic but also cationic residues are crucial in forming P43 aggregates and in accretion, indicating a role for electrostatic interactions between cationic residues and anionic RNA. This differs from a previously studied, purely cationic, non-aggregating (Lys)10 prebiotic peptide (Tagami et al., 2017).
P43 shows preferential binding for longer RNA strands, hence acting as a suitable platform for the formation of longer biopolymers. By showing that the shorter and simpler peptide (Lys2)(Val)6 is also able to inhibit RPR activity, the authors prove that the P43 inhibitory efficacy is a general feature of cationic-hydrophobic peptides. This simplification is a proof of concept, making the accretion model even more plausible in evolutionary terms.
The prebiotic hypothesis posits that salt concentrations frequently fluctuated. Because of this, the authors are curious about the influence of salt concentration on the P43-RPR interaction. Low salt allows P43 aggregates to inhibit RPR, likely because the electrostatic interactions with RNA are so tight that they distort the ribozyme structure. At high salt concentrations, loosened interactions between accreted RNA and P43 enhance RPR activity. Next, the authors demonstrate that P43 captures inactive ribozymes at low salt, and reactivates them by subsequent resuspension in high salt concentrations.
These findings suggest a potential role for freeze/thaw cycles in the prebiotic world. Diurnal cycling of wet and dry periods brought about the occurrence of three conditions: dry, wet and condensed. The dry phases would have favored biopolymer formation due to dehydration; subsequent wet conditions the accretion of biomaterials through the influx of water. Entering condensed conditions through evaporation of water, the enhancement of ribozyme activity by peptide aggregates would have occurred, as salt concentrations increased (Figure 6). In short, it is likely that freeze/thaw cycles in combination with cationic/hydrophobic peptides like P43 enabled RNA polymerization without the use of complicated biochemical pathways.
The authors of this preprint advocate the importance of accretion in the formation of prebiotic peptides. As accretion leads to a gradual increase in RNA and peptide concentration, it might have preceded the formation of liquid-like compartments. Ultimately, compartmentalization through accretion protects from environmental stress factors, thereby enabling the retainment of novel functions. Consequently, bulk P43-like peptide synthesis would pose evolutionary advantages even before the emergence of cell-like life.
What we like about this preprint
Compartmentalization is crucial for the origin of life, however there is no consensus as to how this was attained. It is interesting to see how the authors describe and demonstrate that compartmentalization can be achieved through accretion. We like the simplicity of the accretion model as one of the first steps towards the immensely complex emergence of life. We believe that this paper is an extension to our knowledge on the origin of life and can perhaps grant insights in other fields of biochemical research.
- Attwater, J., Wochner, A., & Holliger, P. (2013). In-ice evolution of RNA polymerase ribozyme activity. Nature chemistry, 5(12), 1011–1018.
- Tagami, S., Attwater, J., & Holliger, P. (2017). Simple peptides derived from the ribosomal core potentiate RNA polymerase ribozyme function. Nature chemistry, 9(4), 325–332.2
Posted on: 23 April 2021
doi: PendingRead preprint
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