From experimental clues to theoretical modeling: Evolution associated with the membrane-takeover at an early stage of life

Abstract

Modern cell membranes are primarily composed of phospholipids, while primitive cell membranes in the beginning of life are believed to have formed from simpler lipids (such as fatty acids) synthesized in the prebiotic environment. An attractive experimental study suggested that the corresponding "membrane-takeover" (as an evolutionary process) is likely to have occurred very early (e.g., in the RNA world) due to some simple physical effects, and might have subsequently triggered some other evolutionary processes. Here, via computer modeling on a system of RNA-based protocells, we convinced the plausibility of such a scenario and elaborated on relevant mechanisms. It is shown that in protocells with a fatty-acid membrane, because of the benefit of phospholipid content (i.e., stabilizing the membrane), a ribozyme favoring the synthesis of phospholipids may emerge; subsequently, due to the reduced membrane permeability on account of the phospholipid content, two other functional RNA species could arise: a ribozyme exploiting more fundamental materials (thus more permeable) for nucleotide synthesis and a species favoring across-membrane transportation. This case exemplifies a combination of experimental and theoretical efforts regarding early evolution, which may shed light on that notoriously complicated problem: the origin of life.

Fig 1. Protocells would benefit from a ribozyme favoring the synthesis of phospholipids in the competition.

Legends: FA—fatty acid; PL—phospholipid (i.e., phosphatidic acid here); G—glycerophosphate; Gp—glycerophosphate precursor (e.g., glycerol); GR—glycerophosphate-synthetase ribozyme (here representing the ribozyme favoring the synthesis of phospholipids). The glycerophosphates produced through the catalysis of GR may reach the membrane and non-enzymatically react with fatty acids therein to form phosphatidic acids (the phospholipid molecules synthesized on the inner layer of the membrane may flip to the outer layer). The formation of phospholipids on the membrane would prevent fatty acids from leaving the membrane to a certain extent, which results in a net inflow of fatty acids in the lipid competition. With the growth of the membrane, the number of GR within the protocell may increase as a result of RNA replication.

Fig 2. The spread of the glycerophosphate-synthetase ribozyme (GR) and its co-spread with the nucleotide-synthetase ribozyme (NR) in RNA-based protocells.

For each subfigure, the upper panel shows the trend of protocells containing specific RNA species while the lower panel demonstrates the trend of the total molecule number of the relevant RNA species in the system. Legends: Cgr — protocells containing GR; Cnr — protocells containing NR; Cnrgr — protocells containing NR and GR; Cctl — protocells containing the control RNA species; gr — GR; nr — NR; ctl — the control RNA species (the legends apply to all the subfigures). For all the cases, an “empty” fatty-acid protocell is inoculated at step 1 × 10³. (a) The de novo spread of GR among protocells. Wherein, at step 1 × 10⁴, ten empty protocells are selected (arbitrarily, the same below), each inoculated with one GR molecule, and another ten empty protocells are selected, each inoculated with one control molecule. (b) The spread of GR in protocells containing NR. Wherein, at step 1 × 10⁴, ten empty protocells are selected, each inoculated with one NR, and another ten empty protocells are selected, each inoculated with one control; at step 3 × 10⁵, ten NR protocells are selected, each inoculated with one GR, and another ten NR protocells are selected, each inoculated with one control. (c) The spread of NR in protocells containing GR, Wherein, at step 1 × 10⁴, ten empty protocells are selected, each inoculated with one GR, and another ten empty protocells are selected, each inoculated with one control; at step 3 × 10⁵, ten GR protocells are selected, each inoculated with one NR, and another ten GR protocells are selected, each inoculated with one control. (d) An evolutionary case without inoculation of the RNA species – first, NR occurs naturally in empty protocells, and then GR occurs naturally in NR protocells. P_RL = 5 × 10^-6. The characteristic sequence of GR is “CCAUGUA” – only two nucleotides different from that of NR (default sequence: “GCACGUA”, see the footnotes of Table 1); the control species adopts a characteristic sequence of “UCAGGUA”, two nucleotides different from either of the two ribozymes.

Fig 3. The influence of several key parameters on the spread of the protocells containing GR.

For each subfigure, the upper panel shows the trend of GR protocells while the lower panel demonstrates the trend of the total number of GR molecules in the system. Legends: Cgr — GR protocells with all parameters adopting default values; Cgr-para-up — GR protocells with the relevant parameter increasing; Cgr-para-down — GR protocells with the relevant parameter decreasing; gr — GR with all parameters adopting default values; gr-para-up — GR with the relevant parameter increasing; gr-para-down — GR with the relevant parameter decreasing (the legends apply to all the subfigures). The red arrows indicate the critical steps where the parameter adjustments are conducted. For (P_GFR), the default value 0.9 is turned up to 0.95, 0.98 and 0.99 at these points of change, respectively, or turned down to 0.1, 0.05 and 0.02 at these points. For (F_PL), the default value 5 is turned up to 10, 20 and 50 at the first three points of change, respectively, or turned down to 2, 1 and 0 at these points; additionally, at the fourth change point of the turning-down case, P_FLM is changed from its default value 0.002 to 1 × 10^-4 (the legends Cgr* and gr* refer to this change). For (P_FLM), the default value 0.002 is turned up to 0.005, 0.01 and 0.02 at the first three points of change, respectively, or turned down to 5 × 10^-4, 2 × 10^-4 and 1 × 10^-4 at these points; additionally, at the fourth change point of the turning-down case, F_PL is changed from its default value 5 to 0 (the legends Cgr* and gr* refer to this change). For (F_PP), the default value 20 is turned down to 10, 5 and 2 at the first three change points, respectively, or turned up to 200, 2000 and 2 × 10⁴ at these points; additionally, at the fourth change point of the turning-up case, F_PPW is changed from its default value 3 to 3000 (the legends Cgr* and gr* refer to this change).

Fig 4. The snapshots on spatial distribution of a case exemplifying the natural spread of NR and GR among protocells.

The evolutionary dynamics of the case is shown in Fig 2d. The color-depth of yellow in the background represents the concentration of the raw materials for forming nucleotides in the system (i.e., precursors of nucleotide precursors). The grey squares denote the membranes of protocells, and the corresponding color-depth is in proportion to the phospholipid content in the membrane. The red dots denote NR, and the blue dots denote GR. An empty protocell is inoculated at step 1000 (the grey arrow), and then empty protocells spread in the system (in reality, the first empty protocell might have formed due to the inducing of mineral particles [69] or the concentration effect during dry-wet circles [61,62]). The red arrow indicates the first NR emerging naturally in an empty protocell. The blue arrow indicates the first GR emerging naturally in an NR protocell.

Fig 5. The alteration of membrane contents with the rising of a ribozyme favoring phospholipid-synthesis (i.e., GR).

For each of the two subfigures, the upper panel shows the trend of relevant protocells while the lower panel demonstrates the trend of RPM (the ratio of phospholipids in the membrane) for these protocells (averaged for each type of protocell). Legends: C — empty protocells; Cgr — protocells containing GR; Cnr — protocells containing NR; Cnrgr — protocells containing NR and GR. RPM for a protocell is calculated as 2 × p_num/(2 × p_num + f_num), where p_num and f_num denote the number of phospholipids and that of fatty acids on the membrane respectively (note that a phospholipid molecule has two non-polar tails whereas a fatty acid has one). Here the vertical axis represents the average RPM of the corresponding protocells, and it is set to 0 ad hoc at the points where that kind of protocells does not exist. (a) The change of membrane contents during the spread of GR in empty protocells (the case is the same as the one shown in Fig 2a, but the horizontal axis adopts a smaller scale). (b) The change of membrane contents during the spread of GR in NR protocells (the case is the same as the one shown in Fig 2b).

Fig 6. The decreased permeability caused by phospholipid content in the membrane could drive the emergence of other functions in the protocells.

For each of the two subfigures, the upper panel shows the trend of relevant protocells while the lower panel demonstrates the trend of relevant RNA species. The legends identical to those included in Fig 2 have the same meaning, and additional ones are as follows: Cnrgrnpr — protocells containing NR, GR and NPR; Cnrgrtr — protocells containing NR, GR and TR; npr — NPR; tr — TR. At step 1 × 10³, an empty fatty-acid protocell is inoculated. At step 1 × 10⁴, ten empty protocells are selected (arbitrarily, the same below), each of which is inoculated with one NR molecule, one GR molecule, and one control molecule. (a) NPR, i.e., a ribozyme using more fundamental raw materials, would not spread if the influence of phospholipid content on membrane permeability is not assumed (solid circles and solid lines; F_PP and F_PPW are set to 0 throughout the simulation), but would spread when this influence is considered (empty circles and dotted lines; at step 3 × 10⁵, F_PP and F_PPW are turned up to 30 and 3 respectively). In both cases, at step 6 × 10⁵, ten NR-GR protocells are selected, each of which is inoculated with one NPR molecule. (b) TR, an RNA species favoring the membrane transport, would not spread if the influence of phospholipid content on membrane permeability is not assumed (solid circles and solid lines; F_PP and F_PPW are set to 0 throughout the simulation), but would spread when this influence is considered (empty circles and dotted lines; at step 3 × 10⁵, F_PP and F_PPW are turned up to 30 and 3 respectively). In both cases, at step 6 × 10⁵, ten NR-GR protocells are selected, each of which is inoculated with one TR molecule. P_NP = 5 × 10^-6.

Fig 7. Events occurring in the model system and associated parameters.

Solid arrows denote chemical reactions and dashed arrows represent other events. Legends: Npp—nucleotide-precursor’s precursor; Np—nucleotide precursor; Nt—nucleotide; FA—fatty acid; Gp—glycerophosphate precursor; G—glycerophosphate; PL—phospholipid, i.e., phosphatidic acid here; NPR—nucleotide-precursor-synthetase ribozyme; NR—nucleotide-synthetase ribozyme; GR—glycerophosphate-synthetase ribozyme. The events occurring within a protocell are shown in (a), and the events concerning the behaviors of the protocells are depicted in (b), which adopts a smaller scale. For a naked room, there would be no membrane and associated events. Note that TR, i.e., the functional RNA species involved in the membrane transport, which functions in an abstract way in the model, is not depicted here; and there are a few parameters unsuitable or difficult to represent here (see text for detailed explanations).