Ribosome in the Light of Evolution

The ribosome is an enormous machine that has gone through many changes since the time of its conception. Not much is really known about its origins. The ribosome field has gone through many research studies to arrive at what is considered currently as the dominant theory: the ribosome originates in the so-called ‘RNA world’.

Before the catalytic RNA was discovered, a number of theories existed about the role of RNA in the ribosome. At the beginning it was clear that since known enzymes were proteins, the proteins are responsible for the peptide-bond-formation. It was puzzling therefore why the ribosome would need RNA. rRNA was considered either a scaffold or a determinant for the

4 Conclusions and Discussion sequence of proteins the ribosome was producing. The first theory was considered to be faulty, since it made no evolutionary sense and when mRNA was discovered, the second theory was disproved as well. Therefore, the idea of RNA participating directly in the protein synthesis was steadily gaining ground until the discovery of RNA with a catalytic activity (Cech et al., 1981; Guerrier-Takada et al., 1983). The full certitude of the importance of RNA was reached with the emergence of high resolution structures pointing directly to rRNA as the active part in protein synthesis. The same structures pointed to the role of ribosomal proteins as largely structural (Moore and Steitz, 2002).

This makes us ask an unavoidable question: what is the start point of the ribosome, its ‘Big Bang’ and what is the future of the structure?

As stated in ref. Tamura and Alexander, 2004: “[…] emergence from the RNA world into the protein world could have been mediated by catalytic RNAs, first in a nontemplated fashion,

then according to a developing genetic code”. In ref. Bokov and Steinberg, 2009, it was

shown that the primary domain for the ribosome activity was a part of the domain V, in which the peptide bond formation occurs. The ribosome possibly was a simple catalytic RNA, (ie. hammerhead RNA (Pley et al., 1994)), which through sequential additions of layers of proteins and RNA was gaining more stability, functions and precision. It was maybe also better in dealing with undesired molecules – an added layer of proteins or RNA that are not active during the translation might supply the binding surface for antibiotics, without influencing the synthesis.

A previous comparison of archaeal and bacterial large subunits illustrated examples of potential convergent evolution, where evolutionarily unrelated r proteins have evolved to stabilize the same region of 23S rRNA (Klein et al., 2004). Many such examples are also found by comparing the models of the yeast and T. aestivum 80S ribosome with the archaeal and bacterial crystal structures: The N-terminal domain of S4e overlaps the binding position of S16p (Figure 45), and the extended N-terminus of L32e overlaps regions of bacterial- specific r proteins L20p and L21p. Likewise, L18ae has two ubiquitin-like α/β roll domains (ULDs), with the N-terminal ULD overlapping bacterial L25p, and like L25p also interacting with the 5S rRNA, whereas alpha-helix 1 of the C-terminal ULD inserts in the minor groove of H41. Furthermore, L29e sits in an RNA pocket at the P0-P1/P2 stalk base, which in Bacteria is occupied by L36p (Figure 41) and devoid of proteins in Archaea (Klein et al., 2004). A comparison of genomic sequences from diverse organisms, ranging from Bacteria to mammals, indicates additional mass with increasing organism complexity (Figure 49).

4 Conclusions and Discussion However, the composition of mammalian ribosomes, e.g. from human, is surprisingly similar to those of other Eukaryotes, such as yeast and plants described here. Evolution has, thus, favored the development of two apparently distinct layers of mass gain for the ribosome: A first layer of tightly intertwined additional proteins and rRNA expansions rigidly positioned on the subunit surfaces (with the only exception of the mobile ES27L), that was followed by a second layer comprising a few drastically extended highly mobile rRNA elements with hitherto unknown function (Figure 48). The information gained from the T. aestivum and yeast 80S models (Figure 50) should, therefore, not only provide a resource for researchers working with these model organisms, but may also provide useful information when studying mammalian systems. However, it will not shed light on whether there is a size limit to the ribosome. Will it continue to grow forever, continuously gaining size and functions for the extensions, acquiring new proteins and more factors needed for the control over synthesis, or has it reached its limit?

Figure 48. Cryo-EM map of the T. aestivum 80S ribosome, with rRNA ES and variable regions colored green and Eukaryote-specific r proteins and extensions colored orange

4 Conclusions and Discussion

Figure 49. Cryo-EM reconstructions of ribosomes from (A) the eubacterium Escherichia coli (Seidelt et al., 2009), (B) the yeast S. cerevisiae (Becker et al., 2009), (C) T. aestivum this work), and (D) Homo sapiens (Spahn et al., 2004b). The small and large subunits are shown in yellow and gray, respectively and the P-tRNA (green) is indicated for reference. The dashed lines and numbers indicate the number of nucleotides of the rRNA expansion segments that are not visualized.