Sunday, 5 November 2017

The Chemical Origin of Life

Accretion of SSU rRNA as illustrated by helices 7–10/es3 from species of increasing complexity. A four-way junction at the surface of the common core, formed by helices 7–10, has expanded by accretion. Accretion adds to the previous rRNA core, leaving insertion fingerprints. (A and B) Secondary (A) and 3D (B) structures are preserved upon the addition of new rRNA. (C) Superimposition of the 3D structures highlights how new rRNA accretes with preservation of ancestral rRNA. (D) A characteristic insertion fingerprint is shown in red and blue boxes. In all panels, the rRNA that approximates the common core is blue. An expansion observed in both archaea and eukaryotes is green. An expansion that is observed only in eukaryotes is gold. An additional expansion in higher eukaryotes (mammals) is red.*
History of the ribosome and the origin of translation

A team of scientist from Georgia Institute of Technology, Atlanta, GA, USA believe they are close to solving one of the mysteries of how living systems first arose from chemical precursors. They believe they have identified a small section of the ribosome which is so fundamental that it is common to all living organisms, from the simplest single-celled organisms to the most complex multicellular plants and animals

In short, this looks to be the starting point for life and a structure that was present in LUCA and maybe before it.

Rather than the bottom up approach where scientists have attempted, with limited success so far, to reconstruct the fundamental units from which living systems could have arisen, the team took a top down approach by reverse engineering the cell organelle common to all living cells and therefore almost certainly present from the first moments, maybe even before something that could be called 'living' existed, the ribosome.

Ribosomes are composed of a tangle of RNA and proteins and are fundamental to living cells in that they only perform one task - they translate the code in DNA and construct proteins from amino acids. They differ from one species to another only in the 'ornamentation' present on their surface, and this gave the clue to the method of reverse engineering the team used.

By successive removal of this ornamentation they arrived at the starting point from which this accretion process probably began some 4 billion years ago. This core functional unit performs the task of joining amino acids together to form a protein chain.

The accretion model mapped onto SSU and LSU secondary structures of E. coli rRNAs. (A and B) Ancestral expansion segments of the SSU (A) and the LSU (B) are numbered by order of acquisition. Insertion fingerprints are located at the seams between the AES or aes. AES/aes colors are arbitrary, chosen to distinguish expansion segments so that no AES or aes is the color of its neighbors. Some ancestral expansion segments appear discontinuous in the secondary structure and so are labeled multiple times. (C) Ancestral bridges B2b, B2c, and B3 mapped onto rRNA secondary structures. (D and E) SSU (D) and LSU (E) common cores are built by the addition of ancestral expansion segments in six phases. Each phase contains ancestral expansion segments that are associated in time and function.*
The ribosome, in analogy with a tree, contains a record of its history, spanning 4 billion years of life on earth. The information contained within ribosomes connects us to the prehistory of biology. Details of ribosomal RNA variation, observed by comparing three-dimensional structures of ribosomes across the tree of life, form the basis of our molecular-level model of the origins and evolution of the translational system. We infer many steps in the evolution of translation, mapping out acquisition of structure and function, revealing much about how modern biology originated from ancestral chemical systems.

We present a molecular-level model for the origin and evolution of the translation system, using a 3D comparative method. 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. In this model, ribosomal proteinization was a driving force for the broad adoption of proteins in other biological processes. The exit tunnel was clearly a central theme of all phases of ribosomal evolution and was continuously extended and rigidified. In the primitive noncoding ribosome, proto-mRNA and the small ribosomal subunit acted as cofactors, positioning the activated ends of tRNAs within the peptidyl transferase center. This association linked the evolution of the large and small ribosomal subunits, proto-mRNA, and tRNA.

Contrary to creationists' touchingly hopeful assertions that if ever we do discover the origins of life on Earth, for the first time ever, science will discover it required a special form of magic called god-magic, no such evidence was found. Just like every other gap science has ever examined, it's looking very much like no god(s) will be found in this one either.

Contrary also to intelligent (sic) design advocates insistence that 'irreducibly complex' structures could not have arisen gradually by an evolutionary process, the ribosome shows evidence of having done just that. As layers of ornamentation and complexity were added, the ribosomes would have become more efficient and even more specific in their function (otherwise they would have lost out to those that were), but an early version was working with minimal complexity and continued to work as ornamentation was added.

Initially, the core functional unit would not even need a DNA code as its function is simply to join amino acids together to form protein chains. By creating random proteins, these units over millions of years could have chanced upon proteins that stuck to them and modified their activity making it more efficient and less random, so building a fully functional ribosome.

Biologically, an interesting aspect of this approach is that it supports the view that life might not have arisen in water but in conditions which were dry for part of the time, such as on the edge of tidal mudflats. This is an alternative (but not exclusive) hypothesis to the deep ocean hot smokers origin which is the currently favoured hypothesis for the origin of living organisms.

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