This paper presents a reformulation of the submarine alkaline hydrothermal theory for the emergence of life in response to recent experimental findings. The theory views life, like other self-organizing systems in the Universe, as an inevitable outcome of particular disequilibria. In this case, the disequilibria were two: (1) in redox potential, between hydrogen plus methane with the circuit-completing electron acceptors such as nitrite, nitrate, ferric iron, and carbon dioxide, and (2) in pH gradient between an acidulous external ocean and an alkaline hydrothermal fluid. Both CO2 and CH4 were equally the ultimate sources of organic carbon, and the metal sulfides and oxyhydroxides acted as protoenzymatic catalysts. The realization, now 50 years old, that membrane-spanning gradients, rather than organic intermediates, play a vital role in life's operations calls into question the idea of “prebiotic chemistry.” It informs our own suggestion that experimentation should look to the kind of nanoengine...

/pdf/the-drive-to-life-on-wet-and-icy-worlds-4esffzvhl9.pdf

The Drive to Life on Wet and Icy Worlds

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.

https://www.pnas.org/content/pnas/112/50/15396.full.pdf

History of the ribosome and the origin of translation

A major commonality of all cellular life is the coupling between translation and transcription mediated by the genetic code. Comparative genomics has further refined this by revealing the presence of an “RNA metabolism” (Anantharaman et al. 2002) or “Persistent proteome” (Danchin et al. 2007) that is basically a compendium of essentially universal genes involved in translation, transcription, RNA processing and degradation, intermediary and RNA metabolism, and compartmentalization. DNA replication likely arose later because the core enzymes involved in the process are not related (Bailey et al. 2006 and others). Together these universal genes comprise what is frequently referred to as LUCA, the last universal common ancestor (Benner et al. 1993; Lazcano 1994; Mushegian and Koonin 1996; Kyrpides et al. 1999). It is noteworthy that no matter how they are defined, by far the largest numbers of genes in LUCA are associated with translation. Indeed, the translation machinery as represented in LUCA is essentially complete indicating that major events in its origins occurred before LUCA. Thus, it might appear that the origins of the translation machinery would be hopelessly obscured by time. Nevertheless, as will be discussed herein, substantial although necessarily incomplete, evidence relating to the origins and early development of the translation machinery and its relation to other core cellular processes continues to exist in the primary sequences, three-dimensional folding, and functional interactions of the various macromolecules involved in the modern versions of the translation machinery.

The modern ribosome consists of small and large subunits (30S and 50S in Bacteria and Archaea) that come together during the initiation of protein synthesis remain together as individual amino acids are added to a growing peptide according to information encoded on the mRNA, and finally separate again in conjunction with the release of the finished protein. Each subunit is an RNA/protein complex. In Bacteria and Archaea, the 50S subunit typically contains a 23S rRNA and a 5S rRNA whereas the 30S subunit contains the 16S rRNA. Peptide bond synthesis occurs in the 50S subunit at the peptidyl transferase center, (PTC), and codon recognition occurs at the decoding site, which is in the small subunit. Transfer RNAs, (tRNA), bridge the two subunits occupying, at various times in the synthesis cycle, the A, P, or E (exit) sites of the 50S subunit and the decoding site in the 30S subunit. A universal CCA sequence at the 3′ end of the tRNA is the point of attachment of the amino acid and later the growing peptide chain to the tRNA. The A, P, and E sites are partly in the small subunit and partly in the large subunit such that a tRNA can be in a hybrid site (e.g., the A site in the 30S and P site in the 50S. The mRNA is exclusively found in the small subunit where it interacts with the anticodon loops of the tRNAs. As the nascent protein is synthesized it passes through an exit tunnel that begins at the PTC center and ultimately exits from the back of the 50S subunit. Synthesis is a dynamic cyclic process in which tRNAs enter the ribosome bringing amino acids as specified by the mRNA and move through the machinery, which undergoes a series of coordinated motions that drive the process (Steitz 2008). These include the movements of the tRNAs between sites, opening and closing of the L1 stalk on the 50S subunit and the ratcheting of the small subunit relative to the large subunit (Frank and Agrawal, 2000), which has recently been elucidated in structural detail (Zhang et al. 2009).

Diverse species (Escherichia coli, Haloarcula marismortui, Thermus thermophiles, and Deinococcus radiodurans) are represented among the various atomic resolution ribosome structures now available (Ban et al. 2000; Yusupov et al. 2000; Wimberly et al. 2000; Schuwirth et al. 2005; Selmer et al. 2006; and others). These structures encompass 30S and 50S subunits as well as the whole 70S ribosome. In addition, cryoelectron microscopy studies have revealed dynamic motions associated with the ribosome (Frank and Agrawal 2000; Connell et al. 2007; and others). These ongoing high resolution structural studies provide the opportunity to examine the relative age of features within the ribosome such as the A, P, and E sites, the exit tunnel, the L7/L12 region, and the L1 region that facilitate the entry and exit of tRNAs.

/pdf/origin-and-evolution-of-the-ribosome-krtlwpvhgs.pdf

Origin and Evolution of the Ribosome

The seemingly limitless diversity of proteins in nature arose from only a few thousand domain prototypes, but the origin of these themselves has remained unclear. We are pursuing the hypothesis that they arose by fusion and accretion from an ancestral set of peptides active as co-factors in RNA-dependent replication and catalysis. Should this be true, contemporary domains may still contain vestiges of such peptides, which could be reconstructed by a comparative approach in the same way in which ancient vocabularies have been reconstructed by the comparative study of modern languages. To test this, we compared domains representative of known folds and identified 40 fragments whose similarity is indicative of common descent, yet which occur in domains currently not thought to be homologous. These fragments are widespread in the most ancient folds and enriched for iron-sulfur- and nucleic acid-binding. We propose that they represent the observable remnants of a primordial RNA-peptide world.

A vocabulary of ancient peptides at the origin of folded proteins

Cations in charge: magnesium ions in RNA folding and catalysis.

We describe a method to establish chronologies of ancient ribosomal evolution. The method uses structure-based and sequence-based comparison of the large subunits (LSUs) of Haloarcula marismortui and Thermus thermophilus. These are the highest resolution ribosome structures available and represent disparate regions of the evolutionary tree. We have sectioned the superimposed LSUs into concentric shells, like an onion, using the site of peptidyl transfer as the origin (the PT-origin). This spherical approximation combined with a shell-by-shell comparison captures significant information along the evolutionary time line revealing, for example, that sequence and conformational similarity of the 23S rRNAs are greatest near the PT-origin and diverge smoothly with distance from it. The results suggest that the conformation and interactions of both RNA and protein can be described as changing, in an observable manner, over evolutionary time. The tendency of macromolecules to assume regular secondary structural elements such as A-form helices with Watson-Crick base pairs (RNA) and alpha-helices and beta-sheets (protein) is low at early time points but increases as time progresses. The conformations of ribosomal protein components near the PT-origin suggest that they may be molecular fossils of the peptide ancestors of ribosomal proteins. Their abbreviated length may have proscribed formation of secondary structure, which is indeed nearly absent from the region of the LSU nearest the PT-origin. Formation and evolution of the early PT center may have involved Mg(2+)-mediated assembly of at least partially single-stranded RNA oligomers or polymers. As one moves from center to periphery, proteins appear to replace magnesium ions. The LSU is known to have undergone large-scale conformation changes upon assembly. The T. thermophilus LSU analyzed here is part of a fully assembled ribosome, whereas the H. marismortui LSU analyzed here is dissociated from other ribosomal components. Large-scale conformational differences in the 23S rRNAs are evident from superimposition and prevent structural alignment of some portions of the rRNAs, including the L1 stalk.

Peeling the Onion: Ribosomes Are Ancient Molecular Fossils

The conversion of a nucleic acid from single strands to double strands is thought to involve slow nucleation followed by fast double-strand propagation. Here, for RNA double-strand propagation, we propose an atomic resolution reaction mechanism. This mechanism, called the stack-ratchet, is based on data-mining of threedimensional structures and on available thermodynamic information. The stack-ratchet mechanism extends and adds detail to the classic zipper model proposed by Porschke (Porschke, D. Biophysical Chemistry 1974, 2, pp. 97-101). Porschke’s zipper model describes the addition of a base pair to a nucleated helix in terms of a single type of elementary reaction; a concerted process in which the two bases, one from each strand, participate in the transition state. In the stack-ratchet mechanism proposed here a net base-pairing step consists of two elementary reactions. Motions of only one strand are required to achieve a given transition state. One elementary reaction preorganizes and stacks the 3′single-strand, driven by base-base stacking interactions. A second elementary reaction stacks the 5′strand and pairs it with the preorganized 3′strand. In the stackratchet mechanism, a variable length 3′stack leads the single-strand/double-strand junction. The stack-ratchet mechanism is not a two-state process. A base can be (i) unstacked and unpaired, (ii) stacked and paired, or (ii) stacked and unpaired (only on the 3′strand). The data suggests that helices of DNA and of RNA do not propagate by similar mechanisms.

Benson K Kalahar

Papers

Peeling the Onion: Ribosomes Are Ancient Molecular Fossils

Mechanism of RNA double helix-propagation at atomic resolution.