Despite being one of the central components of both life and industrial protein production, little is known about the ribosome’s origin at the dawn of life. To investigate ribosomal evolution, we treat it like a molecular fossil, using pre-existing phylogenetic models to identify sites of expansion in the modern rRNA, and removing them, thus producing variants of what could be considered proto-ribosomes in vitro. Many of these proto-ribosomes were initially inactive, but we were able to optimize the deletion sites through an in vitro ribosome synthesis and evolution method developed in the Jewett lab. The rescued deletion variants were then characterized in their assembly and function, e.g. their ability to perform synthesis of large and smaller reporter proteins. This retro-evolution approach yielded proto-ribosome variants with much smaller rRNA, while still being capable of protein synthesis. While these findings are inherently relevant to the study of the origins of life, they can also be applied in biological engineering, such as ongoing efforts to produce a minimal cell and continue to shrink the genetic code. A functional minimal ribosome would represent major resource- and energy savings in both recombinant and cell-free protein production, since prokaryotic rRNA can account for up to 80% of total RNA mass. Furthermore, our top-down ribosome minimization provides a valuable counterpoint to the bottom-up work from Nobel Laureate Prof. Ada Yonath’s group, which demonstrates peptide bond catalysis is possible with merely the most ancient inner core of the primitive ribosome’s active site. 

In our future work, we will continue examining some of the active proto-ribosome variants discovered prior, diving deeper into the quest for the origin of life and possible applications for minimal ribosomes:

• What are the characteristics of the discovered proto-ribosomes? How do individual and combined rRNA deletions influence structure and function of translation?

• Does minimized rRNA also allow for the deletion of ribosomal proteins which have co-evolved, perhaps even essential ones?

• Can minimal ribosomes sustain life? If no, why not? Can accompanying translation factors be retro-evolved as well?

• Can minimal ribosomes be combined with minimal cell systems for even further minimization?

• Can minimal proto-ribosomes provide a starting point for evolving novel ribosomes under selection pressures different from those of early life?

While fundamental research into the origin of life may appear purely intellectual, this experimental foray into the evolutionary history of the translation system has already yielded several functional “missing links” and will continue to yield practical applications for synthetic biology and development of a minimal cell.

Further reading:

• History of the ribosome and the origin of translation, and Evolution of the Ribosome at Atomic Resolution, both Petrov et al, PNAS 2015/2014

• Origin of life: protoribosome forms peptide bonds and links RNA and protein dominated worlds, Bose et al, NAR 2022

• Williams lab: origin of life and RNA world

• Yonath lab: origin of life and ribosome structure