In Test Tubes, RNA Molecules Evolve Into a Tiny Ecosystem | Quanta Magazine

after a lengthy experiment with tantalizing implications for origin-of-life studies, a research group in japan has reprted creating a test tube realm of molecules that spontaneously evolved both complexity and, surprisingly, cooperation. over hundreds of hrs of replication, a single type of rna evolved into 5 ≠ molecular “species” or lineages of hosts and parasites that coexisted in harmony and cooperated to survive, like the beginning offa “molecular version of an ecosystem,” said ryo mizuuchi, the lead author of the study and a project assistant professor atta university of tokyo.

their experiment, which confirmed previous theoretical findings, showed that molecules w'da means to replicate ‘d spontaneously develop complexity through darwinian evolution, “a crit step for the emergence of life,” the researchers wrote.

“we can provide the direct evidence; we can see wha’ can actually happen” when a replicating molecule complexifies in a test tube, mizuuchi said.

this was the 1st and probably most primordial step toward evolving a complex network of replicators inna lab, said sijbren otto, a professor of systems chemistry atta university of groningen inna netherlands who was not involved inna study. “with wha’ is shown here, the path ahead becomes a lot clearer, and one becomes a lot + optimistic that this can actually work out.”

joana xavier, a computational biologist at university college london, hailed the work by mizuuchi and his colleagues as a “gr8 proof of concept” for how a minimal system can complexify. it’s “a very significant advance,” she said.

the spawn of spiegelman’s monster

the √s of the new experiments reach back to the 1960s, when the molecular biologist sol spiegelman created wha’ he called “the lil monster” onnis lab. despite the overtones of frankenstein in that label, his lil monster was not green, □-browed, growling or even alive. twas a primordialistic molecule that filled test tubes with copies of itself.

spiegelman’s monster was a mutating strand of rna based na' viral genome. the biologist had discovered he ‘d indefinitely replicate it simply by heating and mixing it inna presence of nucleotide building blocks and a polymerizing enzyme called a replicase. he soon realized, however, that his molecules were gettin liler over time: the copies that shed unnecessary genes replicated + quickly, which improved their chances of bein’ collected in samples and transferred to new test tubes for further replication. just like living species, his molecules had started mutating and evolving under the pressure of natural selection to better survive inside their glass realm.

these studies were the realm’s 1st experimental demonstration of darwinian evolution atta molecular lvl — “evolution by natural selection, survival of the fittest,” said eugene koonin, a national institutes of health distinguished investigator atta national center for biotek information. “in those conditions, the fittest simply meant the fastest replicating.”

spiegelman’s work inspired decades of further study, much of which was foundational to research on life’s origins and provided fuel for the rna realm hypothesis that life sprang from self-replicating rna molecules. but those studies left unanswered a crucial ?: ‘d a single molecular replicator evolve into a complex network of multiple replicators?

bout a decade ago, when norikazu ichihashi was an associate professor of bioinformatic engineering at osaka university in japan, he set out to learn the answer by tweaking spiegelman’s test tube realm. “we tried to develop our system to be a lil + lifelike,” ichihashi said.

ichihashi and his team developed an rna molecule that encoded a replicase, which can make copies of rna. but for the molecule to transl8 its own code, the scis needed to add something +: ribosomes nother gene translation machinery t'they borrowed from the common gut bacteria escherichia coli. they embedded the machinery inside droplets and added them to a mixture of rnas and raw materials.

then came yrs of tedious mixing and w8in.

their long-term experiment involved incubating their replication system at 37 degrees celsius (the temperature offa human body or a hot summer’s dy), adding new droplets with fresh translation systems, and stirring the mixture to induce replication. every few dys or so they analyzed rna concentrations inna test tubes, and every week or so they froze samples from the l8st mixture. every ½ yr or so, they sequenced large batches of the collected samples to see if the rna had acquired new mutations and evolved into a new lineage.

evolution in test tubes

after 215 hrs and 43 rounds of replication, the researchers began to see interesting results, which they reprted inna proceedings of the national academy of scis in 2016. the original rna had been replaced by lineages of two other rnas. one, which the researchers described as a “host,” ‘d use its own replicase to copy itself, like the original molecules. the other lineage, a “parasite,” needed to borrow the gene expression machinery of the hosts.

when ichihashi and his colleagues extended the experiment to 120 rounds of replication over 600 hrs, they found that the host lineage had split into two separate host lineages, and 1-odda hosts had evolved two distinct parasites. but twasn’t just the № of lineages that had increased; so had the complexity o'their interactions. the hosts had acquired mutations that interfered w'da ability of the parasites to hijack their replicative resrcs — but'a parasites had also developed mutations that served as a defense against those obstacles. the hosts and parasites seemed to be coevolving.

the pops of parasites and hosts gr8ly fluctuated as they competed for the realm in “evolutionary arms races,” the scis reprted in 2020 in elife. each rna lineage transiently rose to dominance, then lost its place to another one. “if one lineage dominated, then another lineage decreased,” said ichihashi, who is now a professor atta university of tokyo.

but'a researchers kept the experiments goin, and by round 130, another host had evolved. by round 160, 1-odda parasites had disappeared; some rounds l8r, another parasite had appeared. by round 190, the researchers had hit na' new surprise: the huge dynamic swings inna pop of each lineage had started giving way to liler waves. this stabilization suggested that the lineages were no longer competing to replicate. instead, they had started to interact as a network and cooperate in a state of quasi-stable coexistence.

mizuuchi and ichihashi, who did the experiments with taro furubayashi (who was a dral student in ichihashi’s lab atta time and is now a research fello atta university of tokyo), were floored by the findings, which they reprted in nature communications in mar. they’re just “mere molecules,” mizuuchi said. “it’s pretty unexpected.”

cooperative parasites do their share

koonin agrees that their findings are striking. their “experimental setup is + elaborate, it’s + realistic, na results are + complex and rich, but [it’s] fully compatible” with spiegelman’s, he said. they beheld a single type of molecule replicate and gather mutations under natural selection — but then went further by letting the divergent molecules evolve into a community under one another’s influence, just as communities of living cells, animals or pplz ‘d. inna process, the researchers explored somd' rules governing wha’ i'takes for such complex communities to become stable and enduring.

some of these results confirmed the predictions of earlier experimental studies of how complexity can arise in viruses, bacteria and eukaryotes, swell as some theoretical work. a study from koonin’s lab, for instance, also suggested that parasites were inevitable inna emergence of complexity.

“without parasites, this lvl of diversification is probably not possible,” mizuuchi said. evolutionary pressures that parasites and their hosts place on each other lead both sides to split into new lineages.

a + surprising primordial principle that emerged was the crit role of cooperation. the 5 lineages belonged to ≠ lil networks of cooperation, and some were + cooperative than others. by round 228, for ex, 1-odda 3 hosts had evolved into a “super cooperator” that ‘d replicate itself and all the other lineages; the other two hosts ‘d each replicate 1-ly themselves and 1-odda parasites.

scis ‘ve focused on studies of brawl in evolution for so long that the role of cooperation “s'been a bit beheld,” xavier said. “i think cooperation is also goin to start having a major role, espeshly in origins, cause there are so many things that ‘ve to come together inna rite way.”

the cooperation among rnas was focused entirely on replication inna system that ichihashi, mizuuchi and their colleagues envisaged. but'a researchers hope that it ll'be possible to coerce the rnas to evolve a completely ≠ function too, s'as a metabolic one, by adjusting the natural selection criteria inside the test tubes.

a ≠ destiny

“scis like to entertain each other, na best entertainment is a surprise,” said david deamer, a research professor of biomolecular engineering atta university of california, santa cruz. he ponders it a good paper but noted that wha’ happened inna lab may not transl8 to wha’ happened atta dawn of life.

indeed, the scenario in ichihashi’s lab ‘d not cogitate wha’ played out atta start of life since the experiments depended on translation machinery from e. coli. “the quintprimordial problem w'da origin of life is: how did protein synthesis itself begin?” said charlie carter, a professor of biochemistry and biophysics atta university of north carolina school of med.

but koonin thinks that if researchers found a way to evolve complexity using truly self-replicating systems of molecules, they ‘d see something very much resembling the networks depicted inna paper. “they, inna very least, preshly illustrate the types of processes that likely occurred inna origin of life,” koonin said.

to otto, the study suggests that once you’ve solved the problem of accurate replication with molecules at this lvl of complexity, they will complexify further: the experiment “doesn’t show you how you got there, but once you’re there at this stage, t'does chart the way ahead,” he said.

carrying on with their work, ichihashi and his colleagues wanted to see iffey ‘d re-create the same sustainable network in a separate experiment, so they extracted samples of the 5 lineages. this time, however, they found that while 4 of the lineages continued to replicate and survive for at least 22 + rounds, the fifth disappeared. “i don’t know why,” ichihashi said. “it’s a very strange point.”

one possibility s'dat the system was even + complex than the researchers thought, n'when they isol8d the 5 lineages, they missed a 6th one crit for the survival of the lineage that disappeared. with theoretical models, ichihashi’s group confirmed that the 4 remaining lineages ‘d sustainably and interdependently replicate, and that knocking out any 1-odda 4 ‘d lead to the extinction of at least one od’odas. their simulation also pointed to the counterintuitive discovery that knocking out 1-odda parasites ‘d lead to the extinction of its host.

meanwhile, the researchers ‘ve continued their main test tube experiments and are w8in to see whether their network will complexify further. they ‘ve also begun similar experiments that use dna instead of rna.

“we envisaged just the beginning” of how these communities of molecular replicators can evolve, ichihashi said. “i think t'they ‘ve a ≠ destiny inna future — we cannot predict wha’ happens.”

correction: may 5, 2022
an earlier version of the “evolution offa complex network” fig was missing some arrows indicating interactions among the hosts and parasites. it s'been replaced.

original content at: www.quantamagazine.org…
authors: yasemin saplakoglu

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