Evolution of the Organelle Assembly Line

 Background​

Proteins are made in cells in a complex system. A protein is a long sequence of amino acids. There are twenty different amino acids used in nature; different sequences give different proteins.

The sequence is encoded in DNA, with a set of three bases signalling a specific amino acid. The sequence is transcribed into mRNA (messenger RNA), and passed to a ribosome. The ribosome then assembles the protein, using rather shorter tRNA (transfer RNA) to select the right amino acid.

Evolution​

How could such a complex system possibly evolve?

The simple answer is that we do not know. This is something that happened maybe 4 billion years ago, and by its nature will not leave any fossils. However, the theory of evolution is real science, so real scientists are looking at how it might have happened. I present here a number of science papers that discuss how the organelle assembly line could have evolved.

Real Science​

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1894784

We describe a stepwise model for the origin of the translation system in the ancient RNA world such that each step confers a distinct advantage onto an ensemble of co-evolving genetic elements. Under this scenario, the primary cause for the emergence of translation was the ability of amino acids and peptides to stimulate reactions catalyzed by ribozymes. Thus, the translation system might have evolved as the result of selection for ribozymes capable of, initially, efficient amino acid binding, and subsequently, synthesis of increasingly versatile peptides. Several aspects of this scenario are amenable to experimental testing

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Put another way, the conservation of the core of the translation machinery is the strongest available evidence that some form of LUCA actually existed.​

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​https://www.pnas.org/doi/10.1073/pnas.1509761112

In this model, the ribosome evolved by accretion, recursively adding expansion segments, iteratively growing, subsuming, and freezing the rRNA. Functions of expansion segments in the ancestral ribosome are assigned by correspondence with their functions in the extant ribosome. The model explains the evolution of the large ribosomal subunit, the small ribosomal subunit, tRNA, and mRNA. Prokaryotic ribosomes evolved in six phases, sequentially acquiring capabilities for RNA folding, catalysis, subunit association, correlated evolution, decoding, energy-driven translocation, and surface proteinization. Two additional phases exclusive to eukaryotes led to tentacle-like rRNA expansions.​

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​https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3312679/

Two specific suggestions are made here to help to address this, involving separate evolution of the peptidyl transferase and decoding functions. First, it is proposed that translation originally arose not to synthesize functional proteins, but to provide simple (perhaps random) peptides that bound to RNA, increasing its available structure space, and therefore its functional capabilities. Second, it is proposed that the decoding site of the ribosome evolved from a mechanism for duplication of RNA. This process involved homodimeric “duplicator RNAs,” resembling the anticodon arms of tRNAs, which directed ligation of trinucleotides in response to an RNA template.​

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​https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0032776

We find that components of the small subunit involved in ribosomal processivity evolved earlier than the catalytic peptidyl transferase center responsible for protein synthesis. Remarkably, subunit RNA and proteins coevolved, starting with interactions between the oldest proteins (S12 and S17) and the oldest substructure (the ribosomal ratchet) in the small subunit and ending with the rise of a modern multi-subunit ribosome. Ancestral ribonucleoprotein components show similarities to in vitro evolved RNA replicase ribozymes and protein structures in extant replication machinery. 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.​

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​https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2926754/

To understand pre-LUCA developments, it is argued that events that are coupled in time are especially useful if one can infer a likely order in which they occurred. Using such timing events, the relative age of various proteins and individual regions within the large rRNA are inferred. An examination of the properties of modern ribosomes strongly suggests that the initial peptides made by the primitive ribosomes were likely enriched for l-amino acids, but did not completely exclude d-amino acids. This has implications for the nature of peptides made by the first ribosomes. From the perspective of ribosome origins, the immediate question regarding coding is when did it arise rather than how did the assignments evolve. The modern ribosome is very dynamic with tRNAs moving in and out and the mRNA moving relative to the ribosome. These movements may have become possible as a result of the addition of a template to hold the tRNAs. That template would subsequently become the mRNA, thereby allowing the evolution of the code and making an RNA genome useful.​

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​https://biologydirect.biomedcentral.com/articles/10.1186/1745-6150-5-15

Our analysis reveals a structural expansion of translation proteins immediately following the RNA world and well before the establishment of the DNA genome. Subsequent functional annotation shows that representatives of the ten most ancestral protein architectures are responsible for all of the core protein functions found in modern translation.​

We propose that this early robust translation system evolved by virtue of a positive feedback cycle in which the system was able to create increasingly complex proteins to further enhance its own function.​

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​https://www.frontiersin.org/articles/10.3389/fevo.2015.00129/full

We examine here whether RNA is indispensable for coded protein synthesis, or whether an all-protein “ribosome” (or “synthosome”) might be possible, with a protein enzyme catalyzing peptide synthesis, and release factor-like protein adaptors able to read a message composed of deoxyribonucleotides. We also compare the RNA world hypothesis with the alternative “proteins first” hypothesis in terms of their different understandings of the evolution of the ribosome, specifically whether ribosomal protein synthesis carried out by RNA might have been preceded by an ancestral form of nonribosomal peptide synthesis carried out by protein enzymes.