Tag mechanism as a strategy for the RNA replicase to resist parasites in the RNA world

Abstract

The idea that life may have started with an "RNA world" is attractive. Wherein, a crucial event (perhaps at the very beginning of the scenario) should have been the emergence of a ribozyme that catalyzes its own replication, i.e., an RNA replicase. Although now there is experimental evidence supporting the chemical feasibility of such a ribozyme, the evolutionary dynamics of how the replicase could overcome the "parasite" problem (because other RNAs may also exploit this ribozyme) and thrive, as described in the scenario, remains unclear. It has been suggested that spatial limitation may have been important for the replicase to confront parasites. However, more studies showed that such a mechanism is not sufficient when this ribozyme's altruistic trait is taken into full consideration. "Tag mechanism", which means labeling the replicase with a short subsequence for recognition in replication, may be a further mechanism supporting the thriving of the replicase. However, because parasites may also "equip" themselves with the tag, it is far from clear whether the tag mechanism could take effect. Here, we conducted a computer simulation using a Monte-Carlo model to study the evolutionary dynamics surrounding the development of a tag-driven (polymerase-type) RNA replicase in the RNA world. We concluded that (1) with the tag mechanism the replicase could resist the parasites and become prosperous, (2) the main underlying reason should be that the parasitic molecules, especially those strong parasites, are more difficult to appear in the tag-driven system, and (3) the tag mechanism has a synergic effect with the spatial limitation mechanism-while the former provides "time" for the replicase to escape from parasites, the latter provides "space" for the replicase to escape. Notably, tags may readily serve as "control handles", and once the tag mechanism was exploited, the evolution towards complex life may have been much easier.

Fig 1. Events occurring in the system and their associated probabilities.

The diagram shows these events in a background of one grid room in the N × N grid. L-shapes represent nucleotides, dots represent raw materials (nucleotide precursors) and crescent-shapes represent the replicase. Dashed lines outline a complete turn of the template-directed copying catalyzed by the polymerase-type replicase. Note that nucleotides and RNAs may also move into or out of the room, with a probability in relation to P_MV (see the text for details).

Fig 2. The tag mechanism is important for the polymerase-type RNA replicase to resist parasites and spread in the system.

(A) The system in which the tag mechanism works. See Table 1 (the last column) for the parameter values adopted in this case. Characteristic domains of the polymerase: CGACGUCAG; 3’-tag: AUG; and 5’-reverse-tag: CAU. At step 1×10⁴, four grid rooms, chosen randomly, were each inoculated with five molecules of the following RNA species: a double-tagged polymerase (AUGCGACGUCAGCAU), the complement of the double-tagged polymerase, a double-tagged control (AUGCAGUCGUACCAU) and the complement of the double-tagged control. Circles represent the double-tagged polymerase plus its complement. Triangles represent the RNA species (longer than the polymerase’s cover-length) that contain a 3’-tag but not a characteristic domain of the polymerase (or its complement). Squares represent the double-tagged control plus its complement. (B) The system in which the tag mechanism does not work. The situation is the same as that in the case shown in A, except that P_RB is set to be equal to P_RBT (0.9). (C) The system in which the tag mechanism does not work and also, no tag sequences are introduced. The situation is the same as that in the case shown in B, except that the polymerase and its complement (circles), as well as the control and its complement (squares), do not contain the two tags. Triangles represent the RNA species (longer than the polymerase’s cover-length) that do not contain the characteristic domain of the polymerase (or its complement). (D) The same case as that shown in A, but P_RB is turn up to be equal to P_RBT (0.9) at step 3×10⁶.

Fig 3. Influence of the tag mechanism on the two routes of the parasites’ de novo appearance.

(A) Naturally appearing through random ligation. The data are from different cases with different P_RL values, and they were sampled at step 5 × 10⁵ in these cases, which has the same parameter settings (except P_RL) as the case shown in Fig 2A but without the initial inoculation of the replicase (and the control). All of the RNA molecules (longer than the cover-length of the polymerase) that are not the replicase or its complement were counted. Because of the limitation of raw materials, the molecules would not increase with the enlargement of P_RL continuously. White bars denote the molecules without the tag, gray bars denote the 3’-tagged molecules, and black bars denote the double-tagged molecules. The lower half is an amplified version of the upper half, to show those extremely rare double-tagged parasites (black bars) clearly. (B) Derived from the ribozyme (here only degradation is considered, while partial replication is another important route–see the text). The data are from one case but recorded at different time steps. 10⁴ double-tagged replicase molecules were inoculated into the system at step 1 × 10⁴, and only the event of RNA degradation is allowed (P_BB = 2×10⁻⁵) in the model. The bars are interpreted the same way as in A, and the lower half is an amplified version of the upper half.

Fig 4. Parasites’ statistics during the spread of the replicase in the tag-ruled system.

The case is the one shown in Fig 2A. (A) The RNA molecules other than the replicase and its complement (longer than the polymerase’s cover-length). White bars denote the molecules without the 3’-tag, gray bars denote the 3’-tagged molecules (thus, pseudo-parasites), and black bars denote the double-tagged molecules (thus, true-parasites). (B) The chain-length distribution of the double-tagged parasites. The longer the chain, the upper its corresponding bar is placed in the stack. The super-parasites (6nt), which have a sequence that consists of merely a 3’-tag and a 5’-retag, are denoted in purple, and the double-tagged parasites longer than the length of the double-tagged replicase (i.e., “16~”nt), are denoted in white. Others are denoted in different tones from dark red to light yellow, according to their chain-length (the longer, the lighter)–those as long as the double-tagged replicase (15nt) are in the lightest yellow. Note that those “16~” parasites are rare (e.g., see step 1.4×10⁶ and 2.5×10⁶), and this is not surprising because they are difficult to form (though not impossible, for example, by the chain breaking of two double-tagged replicases and re-ligation of the longer remains), and even if they could appear, they are at a disadvantage in the “proliferation” competition owing to their length.

Fig 5. Influence of spatial limitation on the tag-ruled system.

The denotations in the upper panel of the subfigures are the same as those in Fig 2A, and the denotations in the lower panel of the subfigures are the same as those in Fig 4B. (A) The case is that shown in Fig 2A, except that the value of P_MV is changed from 0.001 to 0.002. The super-parasite appears at about step 3.2 × 10⁵ and spreads in the system, thus impairing the thriving of the replicase. (B) When the value of P_MV is returned to 0.001 at step 6 × 10⁵, the super-parasite disappears and the replicase increases again.

Fig 6. Spatial distributions of the replicase and parasites in the dynamic process.

Green dots represent the double-tagged replicase (or its complement); orange dots represent the pseudo-parasites; and red dots represent the true-parasites. The length of the RNA species is represented as the diameter of the dots. For a grid room, the depth of the background yellow represents the quantity of free nucleotides therein (the deeper the color, the greater the quantity). (A) The case shown in Fig 2A, step 1 × 10⁶. (B) The case shown in Fig 5A, step 9.07 × 10⁶. (C) The case shown in Fig 5A, step 9.33 × 10⁶. (D) The case shown in Fig 2B, step 4 × 10⁴.

Fig 7. Tracking the molecular evolution in a single grid room.

The denotations are the same as those in Fig 6, except that the quantity of nucleotides is not shown here (as the background yellow). The upper row shows the development of a room in a tag-ruled system. It is a room picked from a 5 × 5 grid, having the same parameter values as those used in Fig 2A, except that P_MV is set to 0 here. The lower row shows the development of a room in a tag-free system. It is a room picked from a 5 × 5 grid, having the same parameter values as those used in Fig 2, except that P_MV is set to 0 here. In each case, two molecules of the double-tagged replicase were inoculated into the room at step 1 × 10⁴, and then its development was monitored.