The ancient heart of the ribosomal large subunit: a response to Caetano-Anolles

Origin of life: Drawing the big picture

Trying to provide a broad overview about the origin of life in Earth, the most significant transitions of life before cells are listed and discussed. The current approach emphasizes the symbiotic relationships that emerged with life. We propose a rational, stepwise scenario for the origin of life that starts with the origin of the first biomolecules and steps forward until the origins of the first cells. Along this path, we aim to provide a brief, though comprehensive theoretical model that will consider the following steps: (i) how nucleotides and other biomolecules could be made prebiotically in specific prebiotic refuges; (ii) how the first molecules of RNAs were formed; (iii) how the proto-peptidyl transferase center was built by the concatenation of proto-tRNAs; (iv) how the ribosome and the genetic code could be structured; (v) how progenotes could live and reproduce as "naked" ribonucleoprotein molecules; (vi) how peptides started to bind molecules in the prebiotic soup allowing biochemical pathways to evolve from those bindings; (vii) how genomes got bigger by the symbiotic relationship of progenotes and lateral transference of genetic material; (viii) how the progenote LUCA has been formed by assembling most biochemical routes; (ix) how the first virion capsids probably emerged and evolved; (x) how phospholipid membranes emerged probably twice by the evolution of lipid-binding proteins; (xi) how DNA synthesis have been formed in parallel in Bacteria and Archaea; and, finally, (xii) how DNA-based cells of Bacteria and Archaeabacteria have been constituted. The picture provided is conjectural and present epistemological gaps. Future research will help to advance into the elucidation of gaps and confirmation/refutation of current statements.

A Short Tale of the Origin of Proteins and Ribosome Evolution

Proteins are the workhorses of the cell and have been key players throughout the evolution of all organisms, from the origin of life to the present era. How might life have originated from the prebiotic chemistry of early Earth? This is one of the most intriguing unsolved questions in biology. Currently, however, it is generally accepted that amino acids, the building blocks of proteins, were abiotically available on primitive Earth, which would have made the formation of early peptides in a similar fashion possible. Peptides are likely to have coevolved with ancestral forms of RNA. The ribosome is the most evident product of this coevolution process, a sophisticated nanomachine that performs the synthesis of proteins codified in genomes. In this general review, we explore the evolution of proteins from their peptide origins to their folding and regulation based on the example of superoxide dismutase (SOD1), a key enzyme in oxygen metabolism on modern Earth.

Codon assignment evolvability in theoretical minimal RNA rings

Genetic code codon-amino acid assignments evolve for 15 (AAA, AGA, AGG, ATA, CGG, CTA, CTG. CTC, CTT, TAA, TAG, TCA, TCG, TGA and TTA (GNN codons notably absent)) among 64 codons (23.4%) across the 31 genetic codes (NCBI list completed with recently suggested green algal mitochondrial genetic codes). Their usage in 25 theoretical minimal RNA rings is examined. RNA rings are designed in silico to code once over the shortest length for all 22 coding signals (start and stop codons and each amino acid according to the standard genetic code). Though designed along coding constraints, RNA rings resemble ancestral tRNA loops, assigning to each RNA ring a putative anticodon, a cognate amino acid and an evolutionary genetic code integration rank for that cognate amino acid. Analyses here show 1. biases against/for evolvable codons in the two first vs last thirds of RNA ring coding sequences, 2. RNA rings with evolvable codons have recent cognates, and 3. evolvable codon and cytosine numbers in RNA ring compositions are positively correlated. Applying alternative genetic codes to RNA rings designed for nonredundant coding according to the standard genetic code reveals unsuspected properties of the standard genetic code and of RNA rings, notably on codon assignment evolvability and the special role of cytosine in relation to codon assignment evolvability and of the genetic code's coding structure.

José M. The Ancient History of Peptidyl Transferase Center Formation as Told by Conservation and Information Analyses

The peptidyl transferase center (PTC) is the catalytic center of the ribosome and forms part of the 23S ribosomal RNA. The PTC has been recognized as the earliest ribosomal part and its origins embodied the First Universal Common Ancestor (FUCA). The PTC is frequently assumed to be highly conserved along all living beings. In this work, we posed the following questions: (i) How many 100% conserved bases can be found in the PTC? (ii) Is it possible to identify clusters of informationally linked nucleotides along its sequence? (iii) Can we propose how the PTC was formed? (iv) How does sequence conservation reflect on the secondary and tertiary structures of the PTC? Aiming to answer these questions, all available complete sequences of 23S ribosomal RNA from Bacteria and Archaea deposited on GenBank database were downloaded. Using a sequence bait of 179 bp from the PTC of Thermus termophilus, we performed an optimum pairwise alignment to retrieve the PTC region from 1424 filtered 23S rRNA sequences. These PTC sequences were multiply aligned, and the conserved regions were assigned and observed along the primary, secondary, and tertiary structures. The PTC structure was observed to be more highly conserved close to the adenine located at the catalytical site. Clusters of interrelated, co-evolving nucleotides reinforce previous assumptions that the PTC was formed by the concatenation of proto-tRNAs and important residues responsible for its assembly were identified. The observed sequence variation does not seem to significantly affect the 3D structure of the PTC ribozyme.

Root of the Tree: The Significance, Evolution, and Origins of the Ribosome

The ribosome is an ancient molecular fossil that provides a telescope to the origins of life. Made from RNA and protein, the ribosome translates mRNA to coded protein in all living systems. Universality, economy, centrality and antiquity are ingrained in translation. The translation machinery dominates the set of genes that are shared as orthologues across the tree of life. The lineage of the translation system defines the universal tree of life. The function of a ribosome is to build ribosomes; to accomplish this task, ribosomes make ribosomal proteins, polymerases, enzymes, and signaling proteins. Every coded protein ever produced by life on Earth has passed through the exit tunnel, which is the birth canal of biology. During the root phase of the tree of life, before the last common ancestor of life (LUCA), exit tunnel evolution is dominant and unremitting. Protein folding coevolved with evolution of the exit tunnel. The ribosome shows that protein folding initiated with intrinsic disorder, supported through a short, primitive exit tunnel. Folding progressed to thermodynamically stable β-structures and then to kinetically trapped α-structures. The latter were enabled by a long, mature exit tunnel that partially offset the general thermodynamic tendency of all polypeptides to form β-sheets. RNA chaperoned the evolution of protein folding from the very beginning. The universal common core of the ribosome, with a mass of nearly 2 million Daltons, was finalized by LUCA. The ribosome entered stasis after LUCA and remained in that state for billions of years. Bacterial ribosomes never left stasis. Archaeal ribosomes have remained near stasis, except for the superphylum Asgard, which has accreted rRNA post LUCA. Eukaryotic ribosomes in some lineages appear to be logarithmically accreting rRNA over the last billion years. Ribosomal expansion in Asgard and Eukarya has been incremental and iterative, without substantial remodeling of pre-existing basal structures. The ribosome preserves information on its history.

Interdependence, Reflexivity, Fidelity, Impedance Matching, and the Evolution of Genetic Coding

Genetic coding is generally thought to have required ribozymes whose functions were taken over by polypeptide aminoacyl-tRNA synthetases (aaRS). Two discoveries about aaRS and their interactions with tRNA substrates now furnish a unifying rationale for the opposite conclusion: that the key processes of the Central Dogma of molecular biology emerged simultaneously and naturally from simple origins in a peptide•RNA partnership, eliminating the epistemological utility of a prior RNA world. First, the two aaRS classes likely arose from opposite strands of the same ancestral gene, implying a simple genetic alphabet. The resulting inversion symmetries in aaRS structural biology would have stabilized the initial and subsequent differentiation of coding specificities, rapidly promoting diversity in the proteome. Second, amino acid physical chemistry maps onto tRNA identity elements, establishing reflexive, nanoenvironmental sensing in protein aaRS. Bootstrapping of increasingly detailed coding is thus intrinsic to polypeptide aaRS, but impossible in an RNA world. These notions underline the following concepts that contradict gradual replacement of ribozymal aaRS by polypeptide aaRS: 1) aaRS enzymes must be interdependent; 2) reflexivity intrinsic to polypeptide aaRS production dynamics promotes bootstrapping; 3) takeover of RNA-catalyzed aminoacylation by enzymes will necessarily degrade specificity; and 4) the Central Dogma's emergence is most probable when replication and translation error rates remain comparable. These characteristics are necessary and sufficient for the essentially de novo emergence of a coupled gene-replicase-translatase system of genetic coding that would have continuously preserved the functional meaning of genetically encoded protein genes whose phylogenetic relationships match those observed today.

Insuperable problems of the genetic code initially emerging in an RNA world

Differential equations for error-prone information transfer (template replication, transcription or translation) are developed in order to consider, within the theory of autocatalysis, the advent of coded protein synthesis. Variations of these equations furnish a basis for comparing the plausibility of contrasting scenarios for the emergence of specific tRNA aminoacylation, ultimately by enzymes, and the relationship of this process with the origin of the universal system of molecular biological information processing embodied in the Central Dogma. The hypothetical RNA World does not furnish an adequate basis for explaining how this system came into being, but principles of self-organisation that transcend Darwinian natural selection furnish an unexpectedly robust basis for a rapid, concerted transition to genetic coding from a peptide·RNA world.

Peptidyl Transferase Center and the Emergence of the Translation System

In this work, the three-dimensional (3D) structure of the ancestral Peptidyl Transferase Center (PTC) built by concatamers of ancestral sequences of tRNAs was reconstructed, and its possible interactions with tRNAs molecules were analyzed. The 3D structure of the ancestral PTC was also compared with the current PTC of T. thermophilus. Docking experiments between the ancestral PTC and tRNAs suggest that in the origin of the translation system, the PTC functioned as an adhesion center for tRNA molecules. The approximation of tRNAs charged with amino acids to the PTC permitted peptide synthesis without the need of a genetic code.

Coding of Class I and II Aminoacyl-tRNA Synthetases

The aminoacyl-tRNA synthetases and their cognate transfer RNAs translate the universal genetic code. The twenty canonical amino acids are sufficiently diverse to create a selective advantage for dividing amino acid activation between two distinct, apparently unrelated superfamilies of synthetases, Class I amino acids being generally larger and less polar, Class II amino acids smaller and more polar. Biochemical, bioinformatic, and protein engineering experiments support the hypothesis that the two Classes descended from opposite strands of the same ancestral gene. Parallel experimental deconstructions of Class I and II synthetases reveal parallel losses in catalytic proficiency at two novel modular levels-protozymes and Urzymes-associated with the evolution of catalytic activity. Bi-directional coding supports an important unification of the proteome; affords a genetic relatedness metric-middle base-pairing frequencies in sense/antisense alignments-that probes more deeply into the evolutionary history of translation than do single multiple sequence alignments; and has facilitated the analysis of hitherto unknown coding relationships in tRNA sequences. Reconstruction of native synthetases by modular thermodynamic cycles facilitated by domain engineering emphasizes the subtlety associated with achieving high specificity, shedding new light on allosteric relationships in contemporary synthetases. Synthetase Urzyme structural biology suggests that they are catalytically-active molten globules, broadening the potential manifold of polypeptide catalysts accessible to primitive genetic coding and motivating revisions of the origins of catalysis. Finally, bi-directional genetic coding of some of the oldest genes in the proteome places major limitations on the likelihood that any RNA World preceded the origins of coded proteins.

Computing the origin and evolution of the ribosome from its structure - Uncovering processes of macromolecular accretion benefiting synthetic biology

Accretion occurs pervasively in nature at widely different timeframes. The process also manifests in the evolution of macromolecules. Here we review recent computational and structural biology studies of evolutionary accretion that make use of the ideographic (historical, retrodictive) and nomothetic (universal, predictive) scientific frameworks. Computational studies uncover explicit timelines of accretion of structural parts in molecular repertoires and molecules. Phylogenetic trees of protein structural domains and proteomes and their molecular functions were built from a genomic census of millions of encoded proteins and associated terminal Gene Ontology terms. Trees reveal a ‘metabolic-first’ origin of proteins, the late development of translation, and a patchwork distribution of proteins in biological networks mediated by molecular recruitment. Similarly, the natural history of ancient RNA molecules inferred from trees of molecular substructures built from a census of molecular features shows patchwork-like accretion patterns. Ideographic analyses of ribosomal history uncover the early appearance of structures supporting mRNA decoding and tRNA translocation, the coevolution of ribosomal proteins and RNA, and a first evolutionary transition that brings ribosomal subunits together into a processive protein biosynthetic complex. Nomothetic structural biology studies of tertiary interactions and ancient insertions in rRNA complement these findings, once concentric layering assumptions are removed. Patterns of coaxial helical stacking reveal a frustrated dynamics of outward and inward ribosomal growth possibly mediated by structural grafting. The early rise of the ribosomal ‘turnstile’ suggests an evolutionary transition in natural biological computation. Results make explicit the need to understand processes of molecular growth and information transfer of macromolecules.

Ribosomal accretion, apriorism and the phylogenetic method: a response to Petrov and Williams

Historical (ideographic) and non-historical (nomothetic) studies of ribosomal accretion appear to arrive at diametrically opposite conclusions. Phylogenetic analysis of thousands of RNA molecules and protein structures in hundreds of genomes supports the structural origin of the ribosome in RNA decoding and ribosomal mechanics. Predictions from extant features in a handful of rRNA structural models of the large ribosomal subunit support its origin in protein biosynthesis. In recent correspondence, one of us reported that correcting dismissals of conflicting data and avoiding unwarranted assumptions of the nomothetic method reconciled conclusions. In response, Petrov and Williams dismissed our arguments claiming we did not understand their algorithmic model of ribosomal apical growth. Instead, they controverted the historical approach. Here we show that their objections to the phylogenetic method are unjustified, that their algorithm subjectively guarantees back-in-time molecular deconstructions toward the protein biosynthetic core, and that processes of ribosomal growth are much more complex. We prompt abandoning apriorism, decreasing ad hoc hypotheses and integrating historical and non-historical scientific methods.