Commentary: History of the ribosome and the origin of translation

Archaeological approaches to RNA virus evolution

Studies with RNA enzymes (ribozymes) and protein enzymes have identified certain structural elements that are present in some cellular mRNAs and viral RNAs. These elements do not share a primary structure and, thus, are not phylogenetically related. However, they have common (secondary/tertiary) structural folds that, according to some lines of evidence, may have an ancient and common origin. The term 'mRNA archaeology' has been coined to refer to the search for such structural/functional relics that may be informative of early evolutionary developments in the cellular and viral worlds and have lasted to the present day. Such identified RNA elements may have developed as biological signals with structural and functional relevance (as if they were buried objects with archaeological value), and coexist with the standard linear information of nucleic acid molecules that is translated into proteins. However, there is a key difference between the methods that extract information from either the primary structure of mRNA or the signals provided by secondary and tertiary structures. The former (sequence comparison and phylogenetic analysis) requires strict continuity of the material vehicle of information during evolution, whereas the archaeological method does not require such continuity. The tools of RNA archaeology (including the use of ribozymes and enzymes to investigate the reactivity of the RNA elements) establish links between the concepts of communication and language theories that have not been incorporated into knowledge of virology, as well as experimental studies on the search for functionally relevant RNA structures.

Menzerath-Altmann's Law of Syntax in RNA Accretion History

RNA evolves by adding substructural parts to growing molecules. Molecular accretion history can be dissected with phylogenetic methods that exploit structural and functional evidence. Here, we explore the statistical behaviors of lengths of double-stranded and single-stranded segments of growing tRNA, 5S rRNA, RNase P RNA, and rRNA molecules. The reconstruction of character state changes along branches of phylogenetic trees of molecules and trees of substructures revealed strong pushes towards an economy of scale. In addition, statistically significant negative correlations and strong associations between the average lengths of helical double-stranded stems and their time of origin (age) were identified with the Pearson's correlation and Spearman's rho methods. The ages of substructures were derived directly from published rooted trees of substructures. A similar negative correlation was detected in unpaired segments of rRNA but not for the other molecules studied. These results suggest a principle of diminishing returns in RNA accretion history. We show this principle follows a tendency of substructural parts to decrease their size when molecular systems enlarge that follows the Menzerath-Altmann's law of language in full generality and without interference from the details of molecular growth.

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.

Comparisons between small ribosomal RNA and theoretical minimal RNA ring secondary structures confirm phylogenetic and structural accretion histories

Ribosomal RNAs are complex structures that presumably evolved by tRNA accretions. Statistical properties of tRNA secondary structures correlate with genetic code integration orders of their cognate amino acids. Ribosomal RNA secondary structures resemble those of tRNAs with recent cognates. Hence, rRNAs presumably evolved from ancestral tRNAs. Here, analyses compare secondary structure subcomponents of small ribosomal RNA subunits with secondary structures of theoretical minimal RNA rings, presumed proto-tRNAs. Two independent methods determined different accretion orders of rRNA structural subelements: (a) classical comparative homology and phylogenetic reconstruction, and (b) a structural hypothesis assuming an inverted onion ring growth where the three-dimensional ribosome's core is most ancient and peripheral elements most recent. Comparisons between (a) and (b) accretions orders with RNA ring secondary structure scales show that recent rRNA subelements are: 1. more like RNA rings with recent cognates, indicating ongoing coevolution between tRNA and rRNA secondary structures; 2. less similar to theoretical minimal RNA rings with ancient cognates. Our method fits (a) and (b) in all examined organisms, more with (a) than (b). Results stress the need to integrate independent methods. Theoretical minimal RNA rings are potential evolutionary references for any sequence-based evolutionary analyses, independent of the focal data from that study.

Deamination gradients within codons after 1<->2 position swap predict amino acid hydrophobicity and parallel β-sheet conformational preference

Deaminations C->T and A->G are frequent mutations producing nucleotide content gradients across genomes proportional to singlestrandedness during replication/transcription. Hence, within single codons, deamination risks increase from first to third codon positions, while second codon positions are functionally most crucial. Here genetic codes are analyzed assuming that after anticodons protected codons from deaminations, first and second codon positions swapped (N2N1N3->N1N2N3), with lowest deamination risks for N2 in presumed primitive N2N1N3 codons. N2N1N3, not standard N1N2N3, codon structure minimizes deaminations inversely proportionally to cognate amino acid hydrophobicity and parallel betasheet conformational preference. For N1N2N3, deamination minimization increases with genetic code integration order of cognate amino acids: during the presumed N2N1N3->N1N2N3 codon structure transition, protein synthesis combined direct codon-amino acid interactions for late amino acids and tRNA-based translation for early amino acids. Hence N2N1N3 codons would correspond to tRNA-free translation by spontaneous codon-amino acid affinities, and tRNA-mediated translation presumably caused N2N1N3->N1N2N3 swaps. Results show that rational, not arbitrary rules link codon and amino acid structures. Some analyses detect mitochondrial RNAs and peptides in public data corresponding to systematic position swaps, suggesting occasional swapping polymerase activity.

Accretion history of large ribosomal subunits deduced from theoretical minimal RNA rings is congruent with histories derived from phylogenetic and structural methods

Accretions of tRNAs presumably formed the large complex ribosomal RNA structures. Similarities of tRNA secondary structures with rRNA secondary structures increase with the integration order of their cognate amino acid in the genetic code, indicating tRNA evolution towards rRNA-like structures. Here analyses rank secondary structure subelements of three large ribosomal RNAs (Prokaryota: Archaea: Thermus thermophilus; Bacteria: Escherichia coli; Eukaryota: Saccharomyces cerevisiae) in relation to their similarities with secondary structures formed by presumed proto-tRNAs, represented by 25 theoretical minimal RNA rings. These ranks are compared to those derived from two independent methods (ranks provide a relative evolutionary age to the rRNA substructure), (a) cladistic phylogenetic analyses and (b) 3D-crystallography where core subelements are presumed ancient and peripheral ones recent. Comparisons of rRNA secondary structure subelements with RNA ring secondary structures show congruence between ranks deduced by this method and both (a) and (b) (more with (a) than (b)), especially for RNA rings with predicted ancient cognate amino acid. Reconstruction of accretion histories of large rRNAs will gain from adequately integrating information from independent methods. Theoretical minimal RNA rings, sequences deterministically designed in silico according to specific coding constraints, might produce adequate scales for prebiotic and early life molecular evolution.

Chimeric Translation for Mitochondrial Peptides: Regular and Expanded Codons

Frameshifting protein translation occasionally results from insertion of amino acids at isolated mono- or dinucleotide-expanded codons by tRNAs with expanded anticodons. Previous analyses of two different types of human mitochondrial MS proteomic data (Fisher and Waters technologies) detect peptides entirely corresponding to expanded codon translation. Here, these proteomic data are reanalyzed searching for peptides consisting of at least eight consecutive amino acids translated according to regular tricodons, and at least eight adjacent consecutive amino acids translated according to expanded codons. Both datasets include chimerically translated peptides (mono- and dinucleotide expansions, 42 and 37, respectively). The regular tricodon-encoded part of some chimeric peptides corresponds to standard human mitochondrial proteins (mono- and dinucleotide expansions, six (AT6, CytB, ND1, 2xND2, ND5) and one (ND1), respectively). Chimeric translation probably increases the diversity of mitogenome-encoded proteins, putatively producing functional proteins. These might result from translation by tRNAs with expanded anticodons, or from regular tricodon translation of RNAs where transcription/posttranscriptional edition systematically deleted mono- or dinucleotides after each trinucleotide. The pairwise matched combination of adjacent peptide parts translated from regular and expanded codons strengthens the hypothesis that translation of stretches of consecutive expanded codons occurs. Results indicate statistical translation producing distributions of alternative proteins. Genetic engineering should account for potential unexpected, unwanted secondary products.

Evolution of macromolecular structure: a 'double tale' of biological accretion and diversification

The evolution of structure in biology is driven by accretion and diversification. Accretion brings together disparate parts to form bigger wholes. Diversification provides opportunities for growth and innovation. Here, we review patterns and processes that are responsible for a 'double tale' of accretion and diversification at various levels of complexity, from proteins and nucleic acids to high-rise building structures in cities. Parts are at first weakly linked and associate variously. As they diversify, they compete with each other and are selected for performance. The emerging interactions constrain their structure and associations. This causes parts to self-organise into modules with tight linkage. In a second phase, variants of the modules evolve and become new parts for a new generative cycle of higher-level organisation. Evolutionary genomics and network biology support the 'double tale' of structural module creation and validate an evolutionary principle of maximum abundance that drives the gain and loss of modules.

In the Beginning was a Mutualism - On the Origin of Translation

The origin of translation is critical for understanding the evolution of life, including the origins of life. The canonical genetic code is one of the most dominant aspects of life on this planet, while the origin of heredity is one of the key evolutionary transitions in living world. Why the translation apparatus evolved is one of the enduring mysteries of molecular biology. Assuming the hypothesis, that during the emergence of life evolution had to first involve autocatalytic systems which only subsequently acquired the capacity of genetic heredity, we propose and discuss possible mechanisms, basic aspects of the emergence and subsequent molecular evolution of translation and ribosomes, as well as enzymes as we know them today. It is possible, in this sense, to view the ribosome as a digital-to-analogue information converter. The proposed mechanism is based on the abilities and tendencies of short RNA and polypeptides to fold and to catalyse biochemical reactions. The proposed mechanism is in concordance with the hypothesis of a possible chemical co-evolution of RNA and proteins in the origin of the genetic code or even more generally at the early evolution of life on Earth. The possible abundance and availability of monomers at prebiotic conditions are considered in the mechanism. The hypothesis that early polypeptides were folding on the RNA scaffold is also considered and mutualism in molecular evolutionary development of RNA and peptides is favoured.