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Darwinian evolution in a translation-coupled RNA replication system within a cell-like compartment

Darwinian evolution in a translation-coupled RNA replication system within a cell-like compartment ARTICLE Received 28 Mar 2013 | Accepted 22 Aug 2013 | Published 3 Oct 2013 DOI: 10.1038/ncomms3494 Darwinian evolution in a translation-coupled RNA replication system within a cell-like compartment 1,2 1 1 1,2 1,2,3 Norikazu Ichihashi , Kimihito Usui , Yasuaki Kazuta , Takeshi Sunami , Tomoaki Matsuura 1,2,4 & Tetsuya Yomo The ability to evolve is a key characteristic that distinguishes living things from non-living chemical compounds. The construction of an evolvable cell-like system entirely from non-living molecules has been a major challenge. Here we construct an evolvable artificial cell model from an assembly of biochemical molecules. The artificial cell model contains artificial genomic RNA that replicates through the translation of its encoded RNA replicase. We perform a long-term (600-generation) replication experiment using this system, in which mutations are spontaneously introduced into the RNA by replication error, and highly replicable mutants dominate the population according to Darwinian principles. During evolution, the genomic RNA gradually reinforces its interaction with the translated replicase, thereby acquiring competitiveness against selfish (parasitic) RNAs. This study provides the first experimental evidence that replicating systems can be developed through Darwinian evolution in a cell-like compartment, even in the presence of parasitic replicators. 1 2 Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Osaka University, Suita, Osaka 565-0871, Japan. Graduate School of Information Science and Technology, Osaka University, Suita, Osaka 565-0871, Japan. Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan. Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan. Correspondence and requests for materials should be addressed to T.Y. (email: yomo@ist.osaka-u.ac.jp). NATURE COMMUNICATIONS | 4:2494 | DOI: 10.1038/ncomms3494 | www.nature.com/naturecommunications 1 & 2013 Macmillan Publishers Limited. All rights reserved. UP: Single-strand ratio UP: Genome UP: Affinity of genomic of genome replication replication rate minus RNA with replicase ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/ncomms3494 he construction of an artificial cell or model protocell Genomic RNA replication Parasitic RNA is hypothesized to provide important insights into replication Translation Tthe emergence of life from an assembly of non-living 1,2 molecules , the basic principles that underlie biological 3–5 6,7 functions and the production of new technology . To date, Parasitic Plus-strand RNA several cellular functions have been reconstructed using simple Replicase compounds, such as fatty acids, that may have existed during 8–12 the prebiotic era . Using other approaches, including the 13 13 Minus-strand semi-synthetic approach and the supramolecular approach , various cellular functions have been reconstituted from purified Double- stranded RNA biological polymers, such as proteins and RNA, in either lipid vesicles or water-in-oil emulsions to determine the conditions b Round 0 14–18 sufficient for achieving the target biological functions . However, the creation of an artificial cell that harbours the same level of evolutionary ability as natural organisms remains a major challenge. 55 The evolution of living organisms is a result of the error-prone replication processes of genetic material, either DNA or RNA, by the replication enzyme translated from its own information. To date, several replication systems have been constructed Round 32 19,20 either from various sets of RNA and proteins or from RNA 21,22 ribozymes only , although these replication systems lack the process by which the genetic information is translated into 0.37 proteins. To construct an artificial system that replicates in the 260 0.37 same manner as natural organisms, through the translation of a replication enzyme, we combined an artificial genomic RNA that encodes an RNA-dependent RNA polymerase, the Qb replicase, 23,24 with a reconstituted translation system . In this translation- Round 80 coupled RNA replication (TcRR) system, the genomic plus-strand RNA (2,125 nucleotides) replicates using an RNA replicase translated from its own sequence via the synthesis of the comple- 0.044 mentary minus-strand (Genomic RNA replication, Fig. 1a). The 0.044 TcRR requires a cell-like compartment to ensure interaction between the translated replicase and the original genomic RNA. In this study, we encapsulated the TcRR system into a microscale 25,26 1–6 mm cell-like compartment, a water-in-oil emulsion . Round 128 Translation coupling increases the complexity of the replica- 140 tion scheme; therefore, the TcRR system becomes vulnerable to selfish or parasitic RNAs, which are continuously generated from 0.0005 genomic RNA by the deletion of the internal replicase-encoding 0.0005 region, while retaining the terminal region for replicase recogni- tion. These small RNAs are selfish and parasitic in that they do not produce replicase but replicate rapidly because of their small size (typically 222 nucleotides), utilizing the already existing replicase, until genome replication is competitively inhibited 27 Figure 1 | A reaction network in a TcRR system. (a) Reaction scheme. The (parasitic RNA replication in Fig. 1a) . The genomic RNA must TcRR system is composed of genomic plus-strand RNA (2,125 nucleotides) overcome the parasitic RNA to recursively replicate in the TcRR encoding the catalytic b-subunit of Qb RNA replicase and a purified system. translation system. The translated replicase replicates the original plus- In the present study, we perform a long-term TcRR experiment strand RNA via complementary minus-strand RNA synthesis, during which in the manual fusion-division cycle of a cell-like compartment the double-stranded RNA is produced via hybridization between the and find that genomic RNA can spontaneously evolve according template and the newly synthesized strand. A parasitic RNA replicates and to Darwinian principles and overcome the parasitic RNA through competes with the genomic RNA for the replicase. (b) The transition of evolution. reaction flow through evolution. The amount of reaction flow was simulated using the parameters shown in Table 1 (initially, 100 nM plus-strand and 10 fM parasitic RNA). The intensity of the colour of the arrows and Results molecules roughly represents the quantities in the reaction. The absolute Long-term TcRR experiment increases replication ability.We values are shown next to the arrows (nM h ). Processes that were first performed a long-term TcRR experiment under conditions governed by the significantly changed parameters are highlighted in orange. in which the RNA amplification was assisted by reverse trans- cription and PCR (RT-PCR) because of the inefficient replication during the initial stage (Fig. 2a). The plus-strand RNA (0.1 nM) was encapsulated with the purified translation system in a amplified the minus-strand RNA by RT-PCR and converted the water-in-oil emulsion with a droplet diameter of 1–6 mm complementary DNA into plus-strand RNA via in vitro trans- (Supplementary Fig. S1);B1 in 10 water droplets was expected to cription (IVT). The plus-strand was then re-encapsulated into the contain a single plus-strand RNA molecule. After incubation at emulsion for the next round of replication cycle. This process was 37 C for 2 h to allow for RNA replication, we recovered and repeated 32 times, and mutations occurred via replication errors 2 NATURE COMMUNICATIONS | 4:2494 | DOI: 10.1038/ncomms3494 | www.nature.com/naturecommunications & 2013 Macmillan Publishers Limited. All rights reserved. Evolution NATURE COMMUNICATIONS | DOI: 10.1038/ncomms3494 ARTICLE (v) Encapsulation ab Compartment (iv) Division Plus-strand Bulk 1.0 (iv) IVT (i) RNA Bulk (i) RNA (iii) Fusion replication replication 0.1 (iii) RT-PCR Fresh 0.01 (ii) Transfer translation Minus-strand (ii) RNA recovery subfraction system c 100 0.001 010 20 30 40 Round Figure 3 | No increase in the replication ability in the control TcRR cycles without compartmentalization. Two independent serial TcRR cycles were performed using the method represented in Fig. 2a, without 2 h reaction 1 h reaction compartmentalization (Bulk); in these cycles, the initial plus-strand 0.1 concentration was 1 nM, corresponding to the effective plus-strand 0 30 60 90 120 150 180 concentration in the experiment with compartmentalization. The figure shows the average minus-strand RNA concentration after RNA replication. In both experiments, the minus-strand RNA gradually decreased and was no longer recovered after round 17. For comparison, the result of a TcRR Total cycle with compartmentalization (the same experiment represented in Fixed Fig. 2) is also plotted (Compartment). repeated this process for another 48 rounds (rounds 33–80). 0 30 60 90 120 150 180 During this time, the initial concentration of the plus-strand RNA Round was kept below 0.1 nM by adjusting the volume of the fused Figure 2 | Increased replication ability and mutation accumulation in a droplets (Supplementary Fig. S2). The average replication, which TcRR experiment. (a) The TcRR cycle method with RNA amplification decreased to twofold at round 33 because of the change in the (rounds 1–32). After (i) RNA replication in the emulsion, (ii) the synthesized process (see below for details), increased again to B30-fold by minus-strand RNA was recovered and (iii) amplified by reverse transcription round 80 (Fig. 2c). We then decreased the incubation time from followed by PCR (RT-PCR). (iv) The resulting cDNA was converted to 2 h to 1 h for an additional 96 rounds (rounds 81–176). The plus-strand RNA by in vitro transcription (IVT) and then (v) re-encapsulated average replication at round 81 decreased to approximately with the translation system in the emulsion for the next round of replication. fivefold before gradually increasing again. Through all the (b) The simplified TcRR cycle method (rounds 33–176). After (i) RNA long-term replication processes, the genomic RNA replicated replication for 2 h (rounds 33–80) or 1 h (rounds 81–176), (ii) a subfraction B2 -fold, corresponding to 600 generations. of the emulsion was transferred and (iii) directly fused with a large droplet The average fold replication decreased fromB30-fold to 2-fold containing fresh translation system components by vigorous mixing; at the transition from round 32 to 33 (Fig. 2c). This decrease is (iv) the droplet was then divided into droplets of the original size for the next explained by the effect of omitting RNA labelling after round 32. round of replication. (c) The average fold replication of the plus-strand Before round 32 (Fig. 2a), the plus-strand RNA was labelled with RNA population in the RNA replication step. The vertical dashed line a-S GTP in the IVT to selectively degrade the initial plus-strand represents the round at which the incubation time was shortened from 2 h to after RNA replication for selective recovery of newly synthesized 1h. (d) Mutation number. The sequences of 10–15 clones of plus-strand RNA (see Methods), whereas the plus-strand was not labelled RNA were analysed at each round. The average number of total mutations after round 32. The omission of labelling may have affected RNA (Total) and fixed mutations (Fixed) per RNA is plotted. folding, resulting in a decrease in the replication ability of the RNA at round 32 after it had adapted under the labelled condition. during each round (approximately one mutation per RNA per round, Supplementary Table S1). If a mutant RNA appeared with a greater ability to replicate, that RNA was expected to become Mutations are fixed in the genomic RNA. To test whether dominant, increasing the average replication ability of the entire evolution led to the gradual increase in the replication ability RNA population. In fact, the average fold replication (the ratio of (Fig. 2c), we analysed sequences of 10–15 RNA clones during the plus-strand concentration after replication to that before each round. The average number of mutations per clone replication) was B1.2-fold in round 1 and gradually increased to increased by B0.7 per round and 0.1 per round before and after 30-fold in round 32 (Fig. 2c). No increase in the replication ability round 32, respectively (Fig. 2d, total). The higher rate before occurred in the control experiments without compartmentaliza- round 32 resulted from the additional mutations that occurred tion (Fig. 3). during the RT-PCR and IVT processes. We defined the mutations As the replication ability improved, we simplified the TcRR observed in more than half of the analysed clones as ‘fixed.’ These cycle by eliminating the RT-PCR and IVT steps (Fig. 2b). After fixed mutations increased intermittently (Fig. 2d, fixed) and RNA replication, a subfraction of the droplets was transferred and ultimately reached a total of 38 mutations, which included directly fused by vigorous mixing with droplets that contained a 34 point mutations, 1 insertion and 3 deletions (Supplementary fresh translation system. The resulting larger droplets were Table S2). These results (the increased replication ability, or reduced to their original size via filtration for the next round of fitness, and the successive fixation of the mutations) provide replication. Using the RNA population present after round 32, we evidence of RNA evolution according to Darwinian principles. NATURE COMMUNICATIONS | 4:2494 | DOI: 10.1038/ncomms3494 | www.nature.com/naturecommunications 3 & 2013 Macmillan Publishers Limited. All rights reserved. Fold replication Mutation number Minus-strand RNA (nM) ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/ncomms3494 Round # Name 5 8 11 14 17 20 23 26 29 32 44 56 68 80 104 128 152 176 1 A186G 2 C167U 3 U203C 4 1995 delete 5 1998 delete 6 G743A Frequency 7 155 insert 8 G1600A 9 A1523U 10 A2033G 11 G2064A 12 C1895U 13 G1723A 14 G661A 15 G720A 0.5 16 C1099G 17 C2010U 18 G1829U 19 U1913C 20 C163U 21 C163A 22 U1887C 23 U221C 24 U295C 25 C2001U 26 A46G 27 U854C 28 C2019U 29 G40A 30 U1616C 31 C1825U 32 1923 delete 33 A1067G 34 U225C 35 U1317C 36 A1866G 37 U610C 38 A1849G Figure 4 | Varying fixation dynamics of the mutations. The frequency of each mutation in the analysed clones is represented as a heat map. The grey colour indicates mutation regions that were lost in the large deletion that occurred in round 80 (number 32). Each of the fixed mutations increased in frequency throughout As the rounds progressed (round 32, 80 and 128), the replication the population with varying rates and dynamics (Fig. 4). Some continued, and the RNA clone at round 128 replicated up to mutations (for example, numbers 8 and 9) increased slowly from 200-fold after 4 h. In addition, the replication kinetics of round round 8 to 29, but others (for example, numbers 16 and 17) were 32–128 became roughly exponential (that is, linear on a semi- fixed rapidly within three rounds, presumably depending on logarithmic scale), suggesting that the replicated RNA recursively the benefit each mutation offers for the RNA replication. functioned as a template for the next replication cycle. The mutation (number 19) was fixed at round 29 but then dis- We next performed a competition experiment in which the appeared at round 56 and was fixed again at round 80, suggesting genomic plus-strand RNAs (50 nM) were mixed with a small the effect of clonal interference . As the population size in the quantity of parasitic RNA (10 fM) under bulk conditions (that is, 7 10 long-term TcRR experiment is B10 –10 , mutations should without compartmentalization), and the replicated RNA was rarely be fixed by genetic drift in 180 rounds . Hence, each detected by the incorporation of radiolabelled UTP. Unlike example of fixation dynamics is expected to contain at least one the genomic RNA, the parasitic RNA replicated extensively beneficial mutation. In addition, the deletion of 29 amino-acid with the original genomic RNA (round 0; Fig. 5b). In contrast, residues at the C terminus of the replicase subunit (number 32) the genomic RNA replicated more selectively as the rounds exactly matches the deleted region that has been reported to proceeded, indicating that it had higher competence against improve the replicase activity at the cost of template specificity . the parasitic RNA. A similar result was observed in an experi- ment without the addition of parasitic RNA when parasitic RNAs spontaneously developed from each genomic RNA Evolved RNAs are competent against the parasitic RNA.To molecule (Supplementary Fig. S3A). We also analysed the time investigate changes in the reaction network between the genomic course data of the TcRR reaction without compartmentalization RNA, the translated replicase and the parasitic RNA via evolution, (Supplementary Fig. S3B) and found that replication of the we analysed the biochemical properties of four RNA clones (one evolved clone (round 128) is prolonged, most probably because of each from rounds 0, 32, 80 and 128; Supplementary Table S3). We competence against the parasitic RNA. first compared the TcRR kinetics for these clones in the emulsion To quantitatively evaluate these evolutionary changes, we (Fig. 5a). The replication of the original RNA (round 0) stopped measured the kinetic parameters of each genomic plus- and within 0.5 h, and the final replication was less than twofold. minus-strand RNA and the parasitic RNA as substrates for 4 NATURE COMMUNICATIONS | 4:2494 | DOI: 10.1038/ncomms3494 | www.nature.com/naturecommunications & 2013 Macmillan Publishers Limited. All rights reserved. NATURE COMMUNICATIONS | DOI: 10.1038/ncomms3494 ARTICLE a b 100 Round 0 32 80 128 Round 0 kbase Round 32 Genomic Round 80 –2 RNA Round 128 0.1 –0.2 Parasitic 0 0.5 1.0 1.5 2.0 RNA Time (h) Ribosome Double strand (1-R )k ss_minus rep_Minus Plus-strand k translation Replicase R k ss_minus rep_minus Parasitic RNA rep_parasite K K M_Minus M_Plus R k ss_plus rep_plus K K M_parasite M_parasite Minus-strand (1-R )k ss_plus rep_Plus rep_parasite Double strand Parasitic RNA Genome RNA replication Parasitic RNA replication Figure 5 | Biochemical assessment of the genomic RNA clones chosen from rounds 0, 32, 80 and 128. (a) Time course data for TcRR of the plus-strand RNA clones. The TcRR reaction was performed with each plus-strand (0.1 nM) in the emulsion at 37 C. At each time point, plus-strand concentrations in the droplets were measured. The error bars indicate the s.d. (n ¼ 2). (b) Competition experiment between genomic plus-strand RNA and a parasitic RNA. TcRR reactions were performed with each clone (50 nM) and a parasitic RNA (10 fM) without compartmentalization at 37 C for 4 h. The replicated RNAs were detected by radioisotope labelling, followed by non-denatured polyacrylamide gel electrophoresis and autoradiography. The full image of the gel is shown in the Supplementary Fig. S9. (c) A kinetic model of TcRR. A Michaelis–Menten-type reaction was assumed for each RNA replication reaction (that is, the replication rate is represented as k [RNA][Replicase]/(K þ [RNA]), where k and K are the maximum replication rate constant rep M rep M and the Michaelis constant, respectively). During replication, template RNA and newly synthesized RNA hybridize to form double-stranded RNA, a dead-end product of this system . Here R represents the fraction of synthesized RNA that is in the single-stranded form. For simplicity, the formation of ss double-stranded RNA of the parasitic RNA is neglected, and the same parameters are assumed for both complementary strands of the parasitic RNA. Double-stranded RNA formation by collision between the plus- and minus-strand RNA was omitted in this model because the rates are extremely small for all clones (Supplementary Fig. S8). Table 1 | Kinetic parameters of RNA clones at each round. RNA and replicase Round 0 Round 32 Round 80 Round 128 ± ± ± ± R * 0.41 0.03 0.90 0.04 0.82 0.04 0.86 0.07 ss_plus ± ± ± ± R * 0.42 0.03 0.88 0.04 0.87 0.07 0.88 0.05 ss_minus ± ± ± ± k *(min) 0.59 0.13 0.78 0.10 2.0 0.5 1.4 0.3 rep_plus ± ± ± ± k *(min) 0.85 0.20 1.1 0.2 1.6 0.4 1.9 0.3 rep_minus ± ± ± ± K *(nM) 7.2 2.4 5.4 1.5 6.7 2.1 5.1 1.7 M_plus ± ± ± ± K *(nM) 4.7 3.1 5.1 0.6 3.1 0.5 0.52 0.37 M_minus 1  1 ± ± ± ± k (h nM ) 0.00074 0.00004 0.00073 0.00007 0.00099 0.00005 0.00107 0.00003 translation ± ± ± ± k (min) 5.1 1.0 4.4 0.4 7.4 1.7 7.0 0.8 rep_parasite ± ± ± ± K (nM) 7.6 1.9 7.0 2.7 6.8 2.0 7.7 0.8 M_parasite The kinetic parameters shown were measured in independent experiments with each template RNA and purified replicase (Supplementary Figs S5—S7). The s.d. are shown at the right of the parameter values. Parameters that changed 41.4-fold are shown in bold; the reactions that were significantly altered by these changes in the parameters are also highlighted in the reaction flow diagrams in Fig. 1b. *A cognate set of RNA and replicase (that is, round 0 RNA and round 0 replicase, round 32 RNA and round 32 replicase, and so on) was used for measurements. The parameters obtained using a non- cognate set of replicase and RNA are shown in Supplementary Fig. S4. wThe average value (6.0) was used for the flux analysis, shown in Fig. 1b, because the analysis is sensitive to non-significant differences in this parameter. each purified replicase based on the kinetic model shown the replicase enzyme (Supplementary Fig. S4). In round 32, the in Fig. 5c (Table 1). Although the highly variable parameters single-strand ratios of the replication product for both the were dependent on the round, most were related to the ability of genomic plus- and minus-strands (R and R ) ss_plus ss_minus genomic RNA to be replicated rather than the activity of increased from B0.4 to 0.9 (Table 1). In round 80, the genomic NATURE COMMUNICATIONS | 4:2494 | DOI: 10.1038/ncomms3494 | www.nature.com/naturecommunications 5 & 2013 Macmillan Publishers Limited. All rights reserved. Plus-strand RNA (nM) ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/ncomms3494 replication rate constant (k and k ) increased Does the evolution of the artificial system used in this study rep_plus rep_minus approximately twofold. In round 128, the affinity between the display features similar to those of natural organisms? In this replicase and the genomic minus-strand RNA (1/K ) work, we observed two evolutionary patterns that have also been M_minus increased approximately sixfold. observed in the experimental evolution of bacteria and viruses. To visualize the effect of the observed changes in the kinetic First, the rate of increase in fold replication (that is, fitness) parameters on the replication reaction network, we evaluated the decreased as the experiment proceeded (Fig. 2c), a phenomenon reaction flows in the TcRR via computer simulation (Fig. 1b). that is known in bacterial evolution as ‘diminishing return . This simulation demonstrated that in round 0, most of the Second, in contrast to the decreasing rate of increase in fitness, translated replicase was utilized to replicate the parasitic RNA the accumulation of mutations continued at a relatively constant and little was used for genomic replication, primarily leading to rate (Fig. 2d); this type of relationship has been characterized as a 38,39 non-replicable double-stranded RNA. In round 32, more repli- discrepancy between the tempo and the mode of evolution . case was utilized for the genomic replication of the single- The mechanisms that produce these patterns in natural stranded form as reflected in the increased single-strand ratios organisms are still unclear. The similarity of the patterns in the (R and R ). In round 80, even more replicase was artificial replication system studied here to those found in nature ss_plus ss_minus utilized for the genomic replication as evidenced by the increase indicates that these patterns do not depend on the complexity of in the genomic replication rate constant (k and k ). natural cells but instead are common evolutionary features of rep_plus rep_minus This trend was accelerated in round 128 because of the increased asexual self-replicating systems composed of polynucleotides and affinity between the replicase and the genomic minus-strand proteins. The simpler reaction network of the in vitro system RNA (1/K ). These results demonstrate that genomic RNA studied here provides a useful platform for discovering the M_minus can acquire the ability to selectively replicate via evolution by mechanisms underlying these evolutionary patterns. reinforcing a cooperative relationship between the genomic RNA This artificial cell-like system could also provide a useful and a translated replicase. platform to understand how an assembly of chemical molecules could become ‘alive’ through an evolutionary process. In principle, the genomic RNA obtained in this study has an unlimited Discussion potential to acquire new functions and develop a more complex In this study, we constructed an artificial cell-like system in which network by encoding additional genes, including translation the genomic RNA replicates as it does in natural organisms (that factors, that are currently supplied externally. Examining whether is, through translation of self-encoded replicase) and evolves the genomic RNA could (with additional replication cycles) evolve according to Darwinian principles through the continuous fusion to create a system that resembles a natural living organism or and division cycles of a cell-like compartment. The evolutionary whether the evolution would be halted by other obstacles such as self-improving ability differentiates this system from typical an error catastrophe would be of interest. The TcRR provides a enzymatic reactions: the replication reaction repeats over many novel platform for the experimental investigation of evolutionary generations, and its replication reaction network is autonomously scenarios that may lead to the emergence of a ‘living state’ from improved. This process occurs just as it has in natural organisms the assembly of non-living molecules. throughout their long evolutionary history. The evolvable artificial cell-like system constructed in this study represents a Methods step towards the realization of an artificial cell with the same Translation-coupled RNA replication. Plus-strand RNA (0.1 nM) was mixed with the customized translation system (Supplementary Table S4), and 10 ml of the evolutionary potential as natural organisms. mixture was dropped into 1 ml of buffer-saturated oil. The mixture of solution and The evolutionary process of this system provides experimental oil was filtered through a multipore membrane (20 mm hydrophilic SPG pumping insight into the following long-standing question regarding the filter, SPG Techno, Japan) 40 times to prepare a 1–6-mm water-in-oil emulsion origin of life: how can a primitive self-replication system be (Supplementary Fig. S1). The buffer-saturated oil was prepared as follows. The maintained by overcoming the appearance of selfish or parasitic freshly prepared oil phase (95% mineral oil (Sigma), 2% Span 80 (Wako, Japan) and 3% Tween 80 (Wako)) was immediately mixed vigorously for 30 s with replicators in prebiotic evolution ? Theoretically, a self-replicating 50–150 ml of saturation buffer per ml of oil and then incubated for 10 min at 37 C. reaction network with a certain level of complexity, such as the After centrifugation at 20 g at room temperature for 5 min, the upper oil phase was hypercycle , is easily destroyed by the appearance of parasitic collected and used as the buffer-saturated oil phase. The composition of the replicators that selfishly replicate by exploiting the system’s saturation buffer was the same as that used in the cell-free translation system 31,33 except that all proteins, RNAs and NTPs were omitted and the concentration of resources . These parasitic replicators often appear in artificial 34,35 dithiothreitol was increased sixfold (to 36 mM). replication systems . One possible solution for this problem is compartmentalization, which spatially restricts parasite propagation 32,33,36 and allows group selection at the compartment level . RNA measurement. Plus-strand and minus-strand RNA concentrations were measured using RT-qPCR, as described in a previous study . In some experiments, Szathmary and Demeter have explicitly demonstrated the role RNA was detected using autoradiography. In these experiments, cell-free of compartmentalization in the evolution of self-replication translation mixtures containing [ P]-UTP and reaction mixtures were subjected networks using the Stochastic Corrector Model, in which self- to 1% agarose gel electrophoresis in 1 TBE (89 mM Tris-borate, 20 mM EDTA) replication molecules are selected at the individual molecular at 4 C to separate single-stranded and double-stranded forms of genomic RNA and to 8% polyacrylamide gel electrophoresis to separate genomic RNA from level and the group level. Therefore, self-replication networks parasitic RNA. Electrophoresis was followed by fixation, drying and can be sustained and continue to evolve even in the presence autoradiography as described in a previous study . of parasitic replicators. In the current study, we tested this model experimentally using a TcRR system and observed that Methods for TcRR cycle. Rounds 1–32: The original RNA (MDV(  )b( þ )) was compartmentalization sustains genomic replication for many prepared by IVT with the exception of the addition of 1 mM Sp-GTP-a-S (BIO- generations (Figs 2 and 3) and also allows the evolution of LOG Life Science Institute, Germany). The prepared template RNA was mixed competitiveness against the parasitic RNA, supporting the with the cell-free translation system and encapsulated into an emulsion as described. After incubation at 37 C for 2 h, water droplets were collected by validity of the Stochastic Corrector Model. This result provides centrifugation (20 g for 5 min at room temperature) and washed with diethyl ether experimental evidence that self-replication systems can be main- as described previously . At this stage, the plus-strand RNA concentration was tained and further developed through evolution in a cell-like measured using RT-qPCR to quantify the fold change in replication. The recovered compartment, even when they are surrounded by parasitic water droplets were mixed with nine volumes of an iodine solution (10 mM iodine, replicators. 1 mM Tris-HCl (pH, 7.4)) and incubated for 5 min at 37 C to degrade the initial 6 NATURE COMMUNICATIONS | 4:2494 | DOI: 10.1038/ncomms3494 | www.nature.com/naturecommunications & 2013 Macmillan Publishers Limited. All rights reserved. NATURE COMMUNICATIONS | DOI: 10.1038/ncomms3494 ARTICLE plus-strand RNA . This reaction was stopped by the addition of 10 mM 20. Wright, M. C. & Joyce, G. F. Continuous in vitro evolution of catalytic function. dithiothreitol. The newly synthesized RNA was purified using an RNeasy column Science 276, 614–617 (1997). (QIAGEN). An aliquot (0.75 ml) of purified RNA was subjected to reverse 21. Lincoln, T. A. & Joyce, G. F. 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Reprints and permission information is available online at http://npg.nature.com/ 18. Forlin, M., Lentini, R. & Mansy, S. S. Cellular imitations. Curr. Opin. Chem. reprintsandpermissions/ Biol. 16, 586–592 (2012). 19. Mills, D. R., Peterson, R. L. & Spiegelman, S. An extracellular Darwinian How to cite this article: Ichihashi, N. et al. Darwinian evolution in a translation-coupled experiment with a self-duplicating nucleic acid molecule. Proc. Natl Acad. Sci. RNA replication system within a cell-like compartment. Nat. Commun. 4:2494 USA 58, 217–224 (1967). doi: 10.1038/ncomms3494 (2013) NATURE COMMUNICATIONS | 4:2494 | DOI: 10.1038/ncomms3494 | www.nature.com/naturecommunications 7 & 2013 Macmillan Publishers Limited. All rights reserved. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Nature Communications Springer Journals

Darwinian evolution in a translation-coupled RNA replication system within a cell-like compartment

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Copyright © 2013 by Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.
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Science, Humanities and Social Sciences, multidisciplinary; Science, Humanities and Social Sciences, multidisciplinary; Science, multidisciplinary
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Abstract

ARTICLE Received 28 Mar 2013 | Accepted 22 Aug 2013 | Published 3 Oct 2013 DOI: 10.1038/ncomms3494 Darwinian evolution in a translation-coupled RNA replication system within a cell-like compartment 1,2 1 1 1,2 1,2,3 Norikazu Ichihashi , Kimihito Usui , Yasuaki Kazuta , Takeshi Sunami , Tomoaki Matsuura 1,2,4 & Tetsuya Yomo The ability to evolve is a key characteristic that distinguishes living things from non-living chemical compounds. The construction of an evolvable cell-like system entirely from non-living molecules has been a major challenge. Here we construct an evolvable artificial cell model from an assembly of biochemical molecules. The artificial cell model contains artificial genomic RNA that replicates through the translation of its encoded RNA replicase. We perform a long-term (600-generation) replication experiment using this system, in which mutations are spontaneously introduced into the RNA by replication error, and highly replicable mutants dominate the population according to Darwinian principles. During evolution, the genomic RNA gradually reinforces its interaction with the translated replicase, thereby acquiring competitiveness against selfish (parasitic) RNAs. This study provides the first experimental evidence that replicating systems can be developed through Darwinian evolution in a cell-like compartment, even in the presence of parasitic replicators. 1 2 Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Osaka University, Suita, Osaka 565-0871, Japan. Graduate School of Information Science and Technology, Osaka University, Suita, Osaka 565-0871, Japan. Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan. Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan. Correspondence and requests for materials should be addressed to T.Y. (email: yomo@ist.osaka-u.ac.jp). NATURE COMMUNICATIONS | 4:2494 | DOI: 10.1038/ncomms3494 | www.nature.com/naturecommunications 1 & 2013 Macmillan Publishers Limited. All rights reserved. UP: Single-strand ratio UP: Genome UP: Affinity of genomic of genome replication replication rate minus RNA with replicase ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/ncomms3494 he construction of an artificial cell or model protocell Genomic RNA replication Parasitic RNA is hypothesized to provide important insights into replication Translation Tthe emergence of life from an assembly of non-living 1,2 molecules , the basic principles that underlie biological 3–5 6,7 functions and the production of new technology . To date, Parasitic Plus-strand RNA several cellular functions have been reconstructed using simple Replicase compounds, such as fatty acids, that may have existed during 8–12 the prebiotic era . Using other approaches, including the 13 13 Minus-strand semi-synthetic approach and the supramolecular approach , various cellular functions have been reconstituted from purified Double- stranded RNA biological polymers, such as proteins and RNA, in either lipid vesicles or water-in-oil emulsions to determine the conditions b Round 0 14–18 sufficient for achieving the target biological functions . However, the creation of an artificial cell that harbours the same level of evolutionary ability as natural organisms remains a major challenge. 55 The evolution of living organisms is a result of the error-prone replication processes of genetic material, either DNA or RNA, by the replication enzyme translated from its own information. To date, several replication systems have been constructed Round 32 19,20 either from various sets of RNA and proteins or from RNA 21,22 ribozymes only , although these replication systems lack the process by which the genetic information is translated into 0.37 proteins. To construct an artificial system that replicates in the 260 0.37 same manner as natural organisms, through the translation of a replication enzyme, we combined an artificial genomic RNA that encodes an RNA-dependent RNA polymerase, the Qb replicase, 23,24 with a reconstituted translation system . In this translation- Round 80 coupled RNA replication (TcRR) system, the genomic plus-strand RNA (2,125 nucleotides) replicates using an RNA replicase translated from its own sequence via the synthesis of the comple- 0.044 mentary minus-strand (Genomic RNA replication, Fig. 1a). The 0.044 TcRR requires a cell-like compartment to ensure interaction between the translated replicase and the original genomic RNA. In this study, we encapsulated the TcRR system into a microscale 25,26 1–6 mm cell-like compartment, a water-in-oil emulsion . Round 128 Translation coupling increases the complexity of the replica- 140 tion scheme; therefore, the TcRR system becomes vulnerable to selfish or parasitic RNAs, which are continuously generated from 0.0005 genomic RNA by the deletion of the internal replicase-encoding 0.0005 region, while retaining the terminal region for replicase recogni- tion. These small RNAs are selfish and parasitic in that they do not produce replicase but replicate rapidly because of their small size (typically 222 nucleotides), utilizing the already existing replicase, until genome replication is competitively inhibited 27 Figure 1 | A reaction network in a TcRR system. (a) Reaction scheme. The (parasitic RNA replication in Fig. 1a) . The genomic RNA must TcRR system is composed of genomic plus-strand RNA (2,125 nucleotides) overcome the parasitic RNA to recursively replicate in the TcRR encoding the catalytic b-subunit of Qb RNA replicase and a purified system. translation system. The translated replicase replicates the original plus- In the present study, we perform a long-term TcRR experiment strand RNA via complementary minus-strand RNA synthesis, during which in the manual fusion-division cycle of a cell-like compartment the double-stranded RNA is produced via hybridization between the and find that genomic RNA can spontaneously evolve according template and the newly synthesized strand. A parasitic RNA replicates and to Darwinian principles and overcome the parasitic RNA through competes with the genomic RNA for the replicase. (b) The transition of evolution. reaction flow through evolution. The amount of reaction flow was simulated using the parameters shown in Table 1 (initially, 100 nM plus-strand and 10 fM parasitic RNA). The intensity of the colour of the arrows and Results molecules roughly represents the quantities in the reaction. The absolute Long-term TcRR experiment increases replication ability.We values are shown next to the arrows (nM h ). Processes that were first performed a long-term TcRR experiment under conditions governed by the significantly changed parameters are highlighted in orange. in which the RNA amplification was assisted by reverse trans- cription and PCR (RT-PCR) because of the inefficient replication during the initial stage (Fig. 2a). The plus-strand RNA (0.1 nM) was encapsulated with the purified translation system in a amplified the minus-strand RNA by RT-PCR and converted the water-in-oil emulsion with a droplet diameter of 1–6 mm complementary DNA into plus-strand RNA via in vitro trans- (Supplementary Fig. S1);B1 in 10 water droplets was expected to cription (IVT). The plus-strand was then re-encapsulated into the contain a single plus-strand RNA molecule. After incubation at emulsion for the next round of replication cycle. This process was 37 C for 2 h to allow for RNA replication, we recovered and repeated 32 times, and mutations occurred via replication errors 2 NATURE COMMUNICATIONS | 4:2494 | DOI: 10.1038/ncomms3494 | www.nature.com/naturecommunications & 2013 Macmillan Publishers Limited. All rights reserved. Evolution NATURE COMMUNICATIONS | DOI: 10.1038/ncomms3494 ARTICLE (v) Encapsulation ab Compartment (iv) Division Plus-strand Bulk 1.0 (iv) IVT (i) RNA Bulk (i) RNA (iii) Fusion replication replication 0.1 (iii) RT-PCR Fresh 0.01 (ii) Transfer translation Minus-strand (ii) RNA recovery subfraction system c 100 0.001 010 20 30 40 Round Figure 3 | No increase in the replication ability in the control TcRR cycles without compartmentalization. Two independent serial TcRR cycles were performed using the method represented in Fig. 2a, without 2 h reaction 1 h reaction compartmentalization (Bulk); in these cycles, the initial plus-strand 0.1 concentration was 1 nM, corresponding to the effective plus-strand 0 30 60 90 120 150 180 concentration in the experiment with compartmentalization. The figure shows the average minus-strand RNA concentration after RNA replication. In both experiments, the minus-strand RNA gradually decreased and was no longer recovered after round 17. For comparison, the result of a TcRR Total cycle with compartmentalization (the same experiment represented in Fixed Fig. 2) is also plotted (Compartment). repeated this process for another 48 rounds (rounds 33–80). 0 30 60 90 120 150 180 During this time, the initial concentration of the plus-strand RNA Round was kept below 0.1 nM by adjusting the volume of the fused Figure 2 | Increased replication ability and mutation accumulation in a droplets (Supplementary Fig. S2). The average replication, which TcRR experiment. (a) The TcRR cycle method with RNA amplification decreased to twofold at round 33 because of the change in the (rounds 1–32). After (i) RNA replication in the emulsion, (ii) the synthesized process (see below for details), increased again to B30-fold by minus-strand RNA was recovered and (iii) amplified by reverse transcription round 80 (Fig. 2c). We then decreased the incubation time from followed by PCR (RT-PCR). (iv) The resulting cDNA was converted to 2 h to 1 h for an additional 96 rounds (rounds 81–176). The plus-strand RNA by in vitro transcription (IVT) and then (v) re-encapsulated average replication at round 81 decreased to approximately with the translation system in the emulsion for the next round of replication. fivefold before gradually increasing again. Through all the (b) The simplified TcRR cycle method (rounds 33–176). After (i) RNA long-term replication processes, the genomic RNA replicated replication for 2 h (rounds 33–80) or 1 h (rounds 81–176), (ii) a subfraction B2 -fold, corresponding to 600 generations. of the emulsion was transferred and (iii) directly fused with a large droplet The average fold replication decreased fromB30-fold to 2-fold containing fresh translation system components by vigorous mixing; at the transition from round 32 to 33 (Fig. 2c). This decrease is (iv) the droplet was then divided into droplets of the original size for the next explained by the effect of omitting RNA labelling after round 32. round of replication. (c) The average fold replication of the plus-strand Before round 32 (Fig. 2a), the plus-strand RNA was labelled with RNA population in the RNA replication step. The vertical dashed line a-S GTP in the IVT to selectively degrade the initial plus-strand represents the round at which the incubation time was shortened from 2 h to after RNA replication for selective recovery of newly synthesized 1h. (d) Mutation number. The sequences of 10–15 clones of plus-strand RNA (see Methods), whereas the plus-strand was not labelled RNA were analysed at each round. The average number of total mutations after round 32. The omission of labelling may have affected RNA (Total) and fixed mutations (Fixed) per RNA is plotted. folding, resulting in a decrease in the replication ability of the RNA at round 32 after it had adapted under the labelled condition. during each round (approximately one mutation per RNA per round, Supplementary Table S1). If a mutant RNA appeared with a greater ability to replicate, that RNA was expected to become Mutations are fixed in the genomic RNA. To test whether dominant, increasing the average replication ability of the entire evolution led to the gradual increase in the replication ability RNA population. In fact, the average fold replication (the ratio of (Fig. 2c), we analysed sequences of 10–15 RNA clones during the plus-strand concentration after replication to that before each round. The average number of mutations per clone replication) was B1.2-fold in round 1 and gradually increased to increased by B0.7 per round and 0.1 per round before and after 30-fold in round 32 (Fig. 2c). No increase in the replication ability round 32, respectively (Fig. 2d, total). The higher rate before occurred in the control experiments without compartmentaliza- round 32 resulted from the additional mutations that occurred tion (Fig. 3). during the RT-PCR and IVT processes. We defined the mutations As the replication ability improved, we simplified the TcRR observed in more than half of the analysed clones as ‘fixed.’ These cycle by eliminating the RT-PCR and IVT steps (Fig. 2b). After fixed mutations increased intermittently (Fig. 2d, fixed) and RNA replication, a subfraction of the droplets was transferred and ultimately reached a total of 38 mutations, which included directly fused by vigorous mixing with droplets that contained a 34 point mutations, 1 insertion and 3 deletions (Supplementary fresh translation system. The resulting larger droplets were Table S2). These results (the increased replication ability, or reduced to their original size via filtration for the next round of fitness, and the successive fixation of the mutations) provide replication. Using the RNA population present after round 32, we evidence of RNA evolution according to Darwinian principles. NATURE COMMUNICATIONS | 4:2494 | DOI: 10.1038/ncomms3494 | www.nature.com/naturecommunications 3 & 2013 Macmillan Publishers Limited. All rights reserved. Fold replication Mutation number Minus-strand RNA (nM) ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/ncomms3494 Round # Name 5 8 11 14 17 20 23 26 29 32 44 56 68 80 104 128 152 176 1 A186G 2 C167U 3 U203C 4 1995 delete 5 1998 delete 6 G743A Frequency 7 155 insert 8 G1600A 9 A1523U 10 A2033G 11 G2064A 12 C1895U 13 G1723A 14 G661A 15 G720A 0.5 16 C1099G 17 C2010U 18 G1829U 19 U1913C 20 C163U 21 C163A 22 U1887C 23 U221C 24 U295C 25 C2001U 26 A46G 27 U854C 28 C2019U 29 G40A 30 U1616C 31 C1825U 32 1923 delete 33 A1067G 34 U225C 35 U1317C 36 A1866G 37 U610C 38 A1849G Figure 4 | Varying fixation dynamics of the mutations. The frequency of each mutation in the analysed clones is represented as a heat map. The grey colour indicates mutation regions that were lost in the large deletion that occurred in round 80 (number 32). Each of the fixed mutations increased in frequency throughout As the rounds progressed (round 32, 80 and 128), the replication the population with varying rates and dynamics (Fig. 4). Some continued, and the RNA clone at round 128 replicated up to mutations (for example, numbers 8 and 9) increased slowly from 200-fold after 4 h. In addition, the replication kinetics of round round 8 to 29, but others (for example, numbers 16 and 17) were 32–128 became roughly exponential (that is, linear on a semi- fixed rapidly within three rounds, presumably depending on logarithmic scale), suggesting that the replicated RNA recursively the benefit each mutation offers for the RNA replication. functioned as a template for the next replication cycle. The mutation (number 19) was fixed at round 29 but then dis- We next performed a competition experiment in which the appeared at round 56 and was fixed again at round 80, suggesting genomic plus-strand RNAs (50 nM) were mixed with a small the effect of clonal interference . As the population size in the quantity of parasitic RNA (10 fM) under bulk conditions (that is, 7 10 long-term TcRR experiment is B10 –10 , mutations should without compartmentalization), and the replicated RNA was rarely be fixed by genetic drift in 180 rounds . Hence, each detected by the incorporation of radiolabelled UTP. Unlike example of fixation dynamics is expected to contain at least one the genomic RNA, the parasitic RNA replicated extensively beneficial mutation. In addition, the deletion of 29 amino-acid with the original genomic RNA (round 0; Fig. 5b). In contrast, residues at the C terminus of the replicase subunit (number 32) the genomic RNA replicated more selectively as the rounds exactly matches the deleted region that has been reported to proceeded, indicating that it had higher competence against improve the replicase activity at the cost of template specificity . the parasitic RNA. A similar result was observed in an experi- ment without the addition of parasitic RNA when parasitic RNAs spontaneously developed from each genomic RNA Evolved RNAs are competent against the parasitic RNA.To molecule (Supplementary Fig. S3A). We also analysed the time investigate changes in the reaction network between the genomic course data of the TcRR reaction without compartmentalization RNA, the translated replicase and the parasitic RNA via evolution, (Supplementary Fig. S3B) and found that replication of the we analysed the biochemical properties of four RNA clones (one evolved clone (round 128) is prolonged, most probably because of each from rounds 0, 32, 80 and 128; Supplementary Table S3). We competence against the parasitic RNA. first compared the TcRR kinetics for these clones in the emulsion To quantitatively evaluate these evolutionary changes, we (Fig. 5a). The replication of the original RNA (round 0) stopped measured the kinetic parameters of each genomic plus- and within 0.5 h, and the final replication was less than twofold. minus-strand RNA and the parasitic RNA as substrates for 4 NATURE COMMUNICATIONS | 4:2494 | DOI: 10.1038/ncomms3494 | www.nature.com/naturecommunications & 2013 Macmillan Publishers Limited. All rights reserved. NATURE COMMUNICATIONS | DOI: 10.1038/ncomms3494 ARTICLE a b 100 Round 0 32 80 128 Round 0 kbase Round 32 Genomic Round 80 –2 RNA Round 128 0.1 –0.2 Parasitic 0 0.5 1.0 1.5 2.0 RNA Time (h) Ribosome Double strand (1-R )k ss_minus rep_Minus Plus-strand k translation Replicase R k ss_minus rep_minus Parasitic RNA rep_parasite K K M_Minus M_Plus R k ss_plus rep_plus K K M_parasite M_parasite Minus-strand (1-R )k ss_plus rep_Plus rep_parasite Double strand Parasitic RNA Genome RNA replication Parasitic RNA replication Figure 5 | Biochemical assessment of the genomic RNA clones chosen from rounds 0, 32, 80 and 128. (a) Time course data for TcRR of the plus-strand RNA clones. The TcRR reaction was performed with each plus-strand (0.1 nM) in the emulsion at 37 C. At each time point, plus-strand concentrations in the droplets were measured. The error bars indicate the s.d. (n ¼ 2). (b) Competition experiment between genomic plus-strand RNA and a parasitic RNA. TcRR reactions were performed with each clone (50 nM) and a parasitic RNA (10 fM) without compartmentalization at 37 C for 4 h. The replicated RNAs were detected by radioisotope labelling, followed by non-denatured polyacrylamide gel electrophoresis and autoradiography. The full image of the gel is shown in the Supplementary Fig. S9. (c) A kinetic model of TcRR. A Michaelis–Menten-type reaction was assumed for each RNA replication reaction (that is, the replication rate is represented as k [RNA][Replicase]/(K þ [RNA]), where k and K are the maximum replication rate constant rep M rep M and the Michaelis constant, respectively). During replication, template RNA and newly synthesized RNA hybridize to form double-stranded RNA, a dead-end product of this system . Here R represents the fraction of synthesized RNA that is in the single-stranded form. For simplicity, the formation of ss double-stranded RNA of the parasitic RNA is neglected, and the same parameters are assumed for both complementary strands of the parasitic RNA. Double-stranded RNA formation by collision between the plus- and minus-strand RNA was omitted in this model because the rates are extremely small for all clones (Supplementary Fig. S8). Table 1 | Kinetic parameters of RNA clones at each round. RNA and replicase Round 0 Round 32 Round 80 Round 128 ± ± ± ± R * 0.41 0.03 0.90 0.04 0.82 0.04 0.86 0.07 ss_plus ± ± ± ± R * 0.42 0.03 0.88 0.04 0.87 0.07 0.88 0.05 ss_minus ± ± ± ± k *(min) 0.59 0.13 0.78 0.10 2.0 0.5 1.4 0.3 rep_plus ± ± ± ± k *(min) 0.85 0.20 1.1 0.2 1.6 0.4 1.9 0.3 rep_minus ± ± ± ± K *(nM) 7.2 2.4 5.4 1.5 6.7 2.1 5.1 1.7 M_plus ± ± ± ± K *(nM) 4.7 3.1 5.1 0.6 3.1 0.5 0.52 0.37 M_minus 1  1 ± ± ± ± k (h nM ) 0.00074 0.00004 0.00073 0.00007 0.00099 0.00005 0.00107 0.00003 translation ± ± ± ± k (min) 5.1 1.0 4.4 0.4 7.4 1.7 7.0 0.8 rep_parasite ± ± ± ± K (nM) 7.6 1.9 7.0 2.7 6.8 2.0 7.7 0.8 M_parasite The kinetic parameters shown were measured in independent experiments with each template RNA and purified replicase (Supplementary Figs S5—S7). The s.d. are shown at the right of the parameter values. Parameters that changed 41.4-fold are shown in bold; the reactions that were significantly altered by these changes in the parameters are also highlighted in the reaction flow diagrams in Fig. 1b. *A cognate set of RNA and replicase (that is, round 0 RNA and round 0 replicase, round 32 RNA and round 32 replicase, and so on) was used for measurements. The parameters obtained using a non- cognate set of replicase and RNA are shown in Supplementary Fig. S4. wThe average value (6.0) was used for the flux analysis, shown in Fig. 1b, because the analysis is sensitive to non-significant differences in this parameter. each purified replicase based on the kinetic model shown the replicase enzyme (Supplementary Fig. S4). In round 32, the in Fig. 5c (Table 1). Although the highly variable parameters single-strand ratios of the replication product for both the were dependent on the round, most were related to the ability of genomic plus- and minus-strands (R and R ) ss_plus ss_minus genomic RNA to be replicated rather than the activity of increased from B0.4 to 0.9 (Table 1). In round 80, the genomic NATURE COMMUNICATIONS | 4:2494 | DOI: 10.1038/ncomms3494 | www.nature.com/naturecommunications 5 & 2013 Macmillan Publishers Limited. All rights reserved. Plus-strand RNA (nM) ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/ncomms3494 replication rate constant (k and k ) increased Does the evolution of the artificial system used in this study rep_plus rep_minus approximately twofold. In round 128, the affinity between the display features similar to those of natural organisms? In this replicase and the genomic minus-strand RNA (1/K ) work, we observed two evolutionary patterns that have also been M_minus increased approximately sixfold. observed in the experimental evolution of bacteria and viruses. To visualize the effect of the observed changes in the kinetic First, the rate of increase in fold replication (that is, fitness) parameters on the replication reaction network, we evaluated the decreased as the experiment proceeded (Fig. 2c), a phenomenon reaction flows in the TcRR via computer simulation (Fig. 1b). that is known in bacterial evolution as ‘diminishing return . This simulation demonstrated that in round 0, most of the Second, in contrast to the decreasing rate of increase in fitness, translated replicase was utilized to replicate the parasitic RNA the accumulation of mutations continued at a relatively constant and little was used for genomic replication, primarily leading to rate (Fig. 2d); this type of relationship has been characterized as a 38,39 non-replicable double-stranded RNA. In round 32, more repli- discrepancy between the tempo and the mode of evolution . case was utilized for the genomic replication of the single- The mechanisms that produce these patterns in natural stranded form as reflected in the increased single-strand ratios organisms are still unclear. The similarity of the patterns in the (R and R ). In round 80, even more replicase was artificial replication system studied here to those found in nature ss_plus ss_minus utilized for the genomic replication as evidenced by the increase indicates that these patterns do not depend on the complexity of in the genomic replication rate constant (k and k ). natural cells but instead are common evolutionary features of rep_plus rep_minus This trend was accelerated in round 128 because of the increased asexual self-replicating systems composed of polynucleotides and affinity between the replicase and the genomic minus-strand proteins. The simpler reaction network of the in vitro system RNA (1/K ). These results demonstrate that genomic RNA studied here provides a useful platform for discovering the M_minus can acquire the ability to selectively replicate via evolution by mechanisms underlying these evolutionary patterns. reinforcing a cooperative relationship between the genomic RNA This artificial cell-like system could also provide a useful and a translated replicase. platform to understand how an assembly of chemical molecules could become ‘alive’ through an evolutionary process. In principle, the genomic RNA obtained in this study has an unlimited Discussion potential to acquire new functions and develop a more complex In this study, we constructed an artificial cell-like system in which network by encoding additional genes, including translation the genomic RNA replicates as it does in natural organisms (that factors, that are currently supplied externally. Examining whether is, through translation of self-encoded replicase) and evolves the genomic RNA could (with additional replication cycles) evolve according to Darwinian principles through the continuous fusion to create a system that resembles a natural living organism or and division cycles of a cell-like compartment. The evolutionary whether the evolution would be halted by other obstacles such as self-improving ability differentiates this system from typical an error catastrophe would be of interest. The TcRR provides a enzymatic reactions: the replication reaction repeats over many novel platform for the experimental investigation of evolutionary generations, and its replication reaction network is autonomously scenarios that may lead to the emergence of a ‘living state’ from improved. This process occurs just as it has in natural organisms the assembly of non-living molecules. throughout their long evolutionary history. The evolvable artificial cell-like system constructed in this study represents a Methods step towards the realization of an artificial cell with the same Translation-coupled RNA replication. Plus-strand RNA (0.1 nM) was mixed with the customized translation system (Supplementary Table S4), and 10 ml of the evolutionary potential as natural organisms. mixture was dropped into 1 ml of buffer-saturated oil. The mixture of solution and The evolutionary process of this system provides experimental oil was filtered through a multipore membrane (20 mm hydrophilic SPG pumping insight into the following long-standing question regarding the filter, SPG Techno, Japan) 40 times to prepare a 1–6-mm water-in-oil emulsion origin of life: how can a primitive self-replication system be (Supplementary Fig. S1). The buffer-saturated oil was prepared as follows. The maintained by overcoming the appearance of selfish or parasitic freshly prepared oil phase (95% mineral oil (Sigma), 2% Span 80 (Wako, Japan) and 3% Tween 80 (Wako)) was immediately mixed vigorously for 30 s with replicators in prebiotic evolution ? Theoretically, a self-replicating 50–150 ml of saturation buffer per ml of oil and then incubated for 10 min at 37 C. reaction network with a certain level of complexity, such as the After centrifugation at 20 g at room temperature for 5 min, the upper oil phase was hypercycle , is easily destroyed by the appearance of parasitic collected and used as the buffer-saturated oil phase. The composition of the replicators that selfishly replicate by exploiting the system’s saturation buffer was the same as that used in the cell-free translation system 31,33 except that all proteins, RNAs and NTPs were omitted and the concentration of resources . These parasitic replicators often appear in artificial 34,35 dithiothreitol was increased sixfold (to 36 mM). replication systems . One possible solution for this problem is compartmentalization, which spatially restricts parasite propagation 32,33,36 and allows group selection at the compartment level . RNA measurement. Plus-strand and minus-strand RNA concentrations were measured using RT-qPCR, as described in a previous study . In some experiments, Szathmary and Demeter have explicitly demonstrated the role RNA was detected using autoradiography. In these experiments, cell-free of compartmentalization in the evolution of self-replication translation mixtures containing [ P]-UTP and reaction mixtures were subjected networks using the Stochastic Corrector Model, in which self- to 1% agarose gel electrophoresis in 1 TBE (89 mM Tris-borate, 20 mM EDTA) replication molecules are selected at the individual molecular at 4 C to separate single-stranded and double-stranded forms of genomic RNA and to 8% polyacrylamide gel electrophoresis to separate genomic RNA from level and the group level. Therefore, self-replication networks parasitic RNA. Electrophoresis was followed by fixation, drying and can be sustained and continue to evolve even in the presence autoradiography as described in a previous study . of parasitic replicators. In the current study, we tested this model experimentally using a TcRR system and observed that Methods for TcRR cycle. Rounds 1–32: The original RNA (MDV(  )b( þ )) was compartmentalization sustains genomic replication for many prepared by IVT with the exception of the addition of 1 mM Sp-GTP-a-S (BIO- generations (Figs 2 and 3) and also allows the evolution of LOG Life Science Institute, Germany). The prepared template RNA was mixed competitiveness against the parasitic RNA, supporting the with the cell-free translation system and encapsulated into an emulsion as described. After incubation at 37 C for 2 h, water droplets were collected by validity of the Stochastic Corrector Model. This result provides centrifugation (20 g for 5 min at room temperature) and washed with diethyl ether experimental evidence that self-replication systems can be main- as described previously . At this stage, the plus-strand RNA concentration was tained and further developed through evolution in a cell-like measured using RT-qPCR to quantify the fold change in replication. 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Reprints and permission information is available online at http://npg.nature.com/ 18. Forlin, M., Lentini, R. & Mansy, S. S. Cellular imitations. Curr. Opin. Chem. reprintsandpermissions/ Biol. 16, 586–592 (2012). 19. Mills, D. R., Peterson, R. L. & Spiegelman, S. An extracellular Darwinian How to cite this article: Ichihashi, N. et al. Darwinian evolution in a translation-coupled experiment with a self-duplicating nucleic acid molecule. Proc. Natl Acad. Sci. RNA replication system within a cell-like compartment. Nat. Commun. 4:2494 USA 58, 217–224 (1967). doi: 10.1038/ncomms3494 (2013) NATURE COMMUNICATIONS | 4:2494 | DOI: 10.1038/ncomms3494 | www.nature.com/naturecommunications 7 & 2013 Macmillan Publishers Limited. All rights reserved.

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Published: Oct 3, 2013

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