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A New Study Questions RNA World

A new study in PLoS One shows that RNA and the proteins involved in protein synthesis must have co-evolved. This flies in the face of RNA-world theories, which presume that RNA formed first and that catalytic function (usually performed by proteins) was completed by catalytic RNA, known as ribozymes.
Researchers at the University of Illinois used phylogenetic modeling methods to evaluate the evolutionary history of the ribosome by correlating RNA structure and the ribosome protein structure. Their studies reveal several things of interest.
One of the assumptions in the RNA first hypothesis is that the active site of the ribosome, the peptidyl transferase center (PTC), which is the key player in protein synthesis, evolved first. However, Harish et al.‘s studies reveal that the ribosome subunits actually evolved before the PTC active site and those subunits co-evolved with RNA, or what would eventually be sections of tRNA.
The authors conclude that their study answers some of the difficult questions associated with the RNA First World, while suggesting that there may have been a ribonuceloprotien primordial world:

Our study therefore provides important clues about the chicken-or-egg dilemma associated with the central dogma of molecular biology by showing that ribosomal history is driven by the gradual structural accretion of protein and RNA structures. Most importantly, results suggest that functionally important and conserved regions of the ribosome were recruited and could be relics of an ancient ribonucleoprotein world.

RNA World
The RNA world or RNA-first hypothesis is arguably one of the stronger origin-of-life scenarios to date. While the field is still rife with inexplicable gaps in the progression from non-life to life, this hypothesis at least recognizes the fundamental need to explain the origin of the nucleotide sequence and subsequent coding for protein construction.
The cell has many types of RNA (messenger RNA, transfer RNA, ribosomal RNA, etc.), indicating that RNA can perform various functions. One particular function, when it was discovered, seemed to affirm notions that RNA may have preceded DNA and, therefore, preceded proteins. This function was the catalytic abilities of RNA. Catalysts, in short, speed a reaction. Proteins that act as catalysts are called enzymes, so catalytic RNA was thus named a ribozyme. Enzymes tend to be highly complex and specific to their particular functions.
The ribozyme seemed to answer the “chicken-or-egg” problem for origin-of-life theorists. Proteins are needed to make nucleic acids (RNA or DNA) and nucleic acids are needed to make proteins. Determining how this closed loop got started would provide answers to this most difficult origin-of-life conundrum.
However, while ribozymes were appealing in theory, they have many limitations that preclude their role as the initiators of early life. For example, RNA can cleave or link other RNA molecules, but this is only under specific laboratory conditions. Furthermore, RNA is limited in its capabilities compared to proteins. Ribozymes perform few functions, but protein synthesis requires multiple proteins, each often performing multiple functions.
This poses problems for how the first protein was produced. As the authors point out:

Thus far, in vitro peptidyl transferase activity catalyzed by protein-free rRNA derived from extant rRNA or ribozymes is not demonstrated. Perhaps, the primordial cooperative property of the RNP [ribonucleoprotein] complex explains why such attempts have failed.

In other words, the authors believe that the closely tied interaction between the ribosome and RNA cannot be separated.
The Ribosome
The ribosome is an intricate, complex protein and RNA structure containing two subunits that fit together like two hands in a cupped clap. The “cup” that the hands make is an empty space through which messenger RNA (mRNA) passes, is read, and translated into an amino acid connected to transfer RNA (tRNA).
The authors of the study propose that the individual sub units of the ribosome evolved separately but each subunit co-evolved with ribosomal RNA (rRNA) and then with the portion of the tRNA molecule that the modern-day subunit interacts with (the particular binding sites). The authors propose that these separate and simpler systems were co-opted very early in primordial history to form the machinery that we see today.
Co-Evolution of Ribosomal Proteins and RNA
The authors provide the following lines of evidence for the co-evolution of ribosomal proteins and RNA:
(1) Traditionally, the PTC active site has been considered the oldest part of the ribosomal protein. The idea behind stems from function, as well as an assumption that the proteins were built up in a step-by-step fashion. If this was the case, the outer components are likely “newer.” The authors instead looked at the tertiary structure and employed studies using structural similarities to determine evolutionary age:

In contrast, here we infer the history of the complete RNP ensemble using phylogenetic methods that employ standard cladistics principles widely used for example in the analysis of morphological characteristics of organisms. Shared-derived features of structure defined by crystallography and comparative sequence analysis are treated as phylogenetic characters and used to build structural phylogenies.

The authors found that due to the age difference in portions of the ribosome, there was likely a functional core that pre-dates the PTC active site. This particular study raises some red flags, however, because homology (structural or genetic similarities) is a tricky thing. Usually evolutionary biologists apply homology to organisms.
(2) The authors’ studies indicate that the ribosome subunits may have originally interacted separately until a “major transition” occurred that brought the subunits together. This “major transition” coincided with the evolution of tRNA. These studies dealt with the supposed evolution of the inter-subunit bridge through which the two subunits interact. The authors note that any mutations to this bridge leads to non-functionality.
(3) Tertiary interactions between RNA-RNA and RNA-protein occurred after the first major transition.

We propose that A-minor and other tertiary interactions evolved to stabilize and maintain the ribosome structure during elongation, leading to increased ribosomal processivity. Scarcity of A-minor interactions before the major transition implies that the early proto-ribosome structure was mostly stabilized by r-proteins or their precursors.

(4) According to authors’ studies, tRNA is at the center of ribosomal evolution. There are two major sections of tRNA and each one interacts almost exclusively with a particular subunit of the ribosome. These RNA/subunit partners evolved individually, then came together to form the modern-day complex sometime after the first major transition. The modern-day complex was built around tRNA:

These remarkable patterns suggest that subunit interactions with a full modern cloverleaf tRNA structure were recruited for translation after the major transition and that the ribosome was built around tRNA or tRNA-like structures…

(5) Phylogenetic studies show that the oldest parts of the ribosome interact with the oldest parts of the ribosomal RNA (rRNA), and the evolution of these two are “linked” in such a way that as one evolves so does the other. The authors state that this is evidence for their co-evolution and believe that this intimate interaction is the reason why ribozyme studies have not progressed:

We propose complex ribosomal functionality emerged from the cooperative interaction of rRNA and r-proteins (or their precursors), which existed from the earliest stages of ribosome evolution. Thus far, in vitro peptidyl transferase activity catalyzed by protein-free rRNA derived from extant rRNA or ribozymes is not demonstrated. Perhaps, the primordial cooperative property of the RNP complex explains why such attempts have failed.

The same evidence, however, could also show that these structures are irreducibly complex, rather than that they co-evolved.
(6) A second major transition occurred in which ribosome evolution coincides with the emergence of a particular protein complex that “stimulates the GTPase activity of EF-G, a ribosomal factor that catalyzes elongation and is responsible for marked increases in the processivity of the ribosome.” In other words, this transition has to do with important specific activities involved in building proteins.
(7) The ribosomal core has components that are similar to ribozyme-like activity and therefore provide evidence for recruiting various parts to form the translation system, or co-option:

Thus, it is likely that the ribosomal catalytic core had origins in processive substructures common to replication and translation and is a descendant of a primitive templating complex…Since structural components of a proto-ribosome involved in tRNA, mRNA and intersubunit interactions are older than others, these results also support the replicative origin of tRNA.

(8) Certain components, such as translation initiation factors, tRNA binding proteins, DNA binding proteins, and telomere binding proteins have a similar folding arrangement, and therefore likely have a common origin:

RNA binding and DNA binding proteins therefore have a common evolutionary origin, suggesting ancient r-proteins and homologs were originally part of primitive replication machinery, which diversified and was co-opted for modern translation. This ancient replicative function most likely involved processivity and biosynthetic activities that we believe remain hidden today in ribosome function.” (emphasis added)

Unfortunately, while the authors suggest co-option, they do not have a model system on which to base the prior function of these mechanical parts, which makes this highly speculative.
Overall, the authors appeal to co-option and co-evolution and justify this using phylogenetic homology studies. They contend as many in the ID camp do that “the de novo appearance of complex functions is highly unlikely. Similarly, it is highly unlikely that a multi-component molecular complex harboring several functional processes needed for modern translation could emerge in a single or only a few events of evolutionary novelty.” Their explanation, however, is that a simpler system was performing a different function, and then was recruited into the complex protein translation machine.
The question that follows is what exactly did the recruiting? What provokes recruitment to another system? The authors labeled this time of recruitment the “first major transition” but their explanation of the transition is a little cloudy.
They seem to answer the question of “motivation to recruitment” by appealing to co-evolution. The RNA and ribosome proteins are co-dependent such that as one evolves, the other does too and somehow it reached a point where a “major transition” occurs.
There are many striking features of this study, such as the authors’ acknowledgement of the deficiency of ribozymes to account for the “chicken-and-egg” problem with protein synthesis, and their recognition of the improbable evolution of RNA apart from the ribosomal protein in view of the fact that the relevant functions are so intimately intertwined.
While these results show a relationship and even a correlation between tRNA and the ribosome, it is still unclear what exactly promoted recruitment, what attracted the tRNA to the proto-ribosome, or why co-option must be the conclusion. Could this not also be a case of an irreducibly complex machine?

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