Why Is AUG the Start Codon?: Theoretical Minimal RNA Rings: Maximizing Coded Information Biases 1st Codon for the Universal Initiation Codon AUG

Integrative Multi-OMICs Identifies Therapeutic Response Biomarkers and Confirms Fidelity of Clinically Annotated, Serially Passaged Patient-Derived Xenografts Established from Primary and Metastatic Pediatric and AYA Solid Tumors

Establishment of clinically annotated, molecularly characterized, patient-derived xenografts (PDXs) from treatment-naïve and pretreated patients provides a platform to test precision genomics-guided therapies. An integrated multi-OMICS pipeline was developed to identify cancer-associated pathways and evaluate stability of molecular signatures in a panel of pediatric and AYA PDXs following serial passaging in mice. Original solid tumor samples and their corresponding PDXs were evaluated by whole-genome sequencing, RNA-seq, immunoblotting, pathway enrichment analyses, and the drug−gene interaction database to identify as well as cross-validate actionable targets in patients with sarcomas or Wilms tumors. While some divergence between original tumor and the respective PDX was evident, majority of alterations were not functionally impactful, and oncogenic pathway activation was maintained following serial passaging. CDK4/6 and BETs were prioritized as biomarkers of therapeutic response in osteosarcoma PDXs with pertinent molecular signatures. Inhibition of CDK4/6 or BETs decreased osteosarcoma PDX growth (two-way ANOVA, p < 0.05) confirming mechanistic involvement in growth. Linking patient treatment history with molecular and efficacy data in PDX will provide a strong rationale for targeted therapy and improve our understanding of which therapy is most beneficial in patients at diagnosis and in those already exposed to therapy.

Sulfur Amino Acids: From Prebiotic Chemistry to Biology and Vice Versa

Two sulfur-containing amino acids are included in the list of the 20 classical protein amino acids. A methionine residue is introduced at the start of the synthesis of all current proteins. Cysteine, thanks to its thiol function, plays an essential role in a very large number of catalytic sites. Here we present what is known about the prebiotic synthesis of these two amino acids and homocysteine, and we discuss their introduction into primitive peptides and more elaborate proteins.

1 Introduction

2 Sulfur Sources

3 Prebiotic Synthesis of Cysteine

4 Prebiotic Synthesis of Methionine

5 Homocysteine and Its Thiolactone

6 Methionine and Cystine in Proteins

7 Prebiotic Scenarios Using Sulfur Amino Acids

8 Introduction of Cys and Met in the Genetic Code

9 Conclusion

Combinatorial Fusion Rules to Describe Codon Assignment in the Standard Genetic Code

We propose combinatorial fusion rules that describe the codon assignment in the standard genetic code simply and uniformly for all canonical amino acids. These rules become obvious if the origin of the standard genetic code is considered as a result of a fusion of four protocodes: Two dominant AU and GC protocodes and two recessive AU and GC protocodes. The biochemical meaning of the fusion rules consists of retaining the complementarity between cognate codons of the small hydrophobic amino acids and large charged or polar amino acids within the protocodes. The proto tRNAs were assembled in form of two kissing hairpins with 9-base and 10-base loops in the case of dominant protocodes and two 9-base loops in the case of recessive protocodes. The fusion rules reveal the connection between the stop codons, the non-canonical amino acids, pyrrolysine and selenocysteine, and deviations in the translation of mitochondria. Using fusion rules, we predicted the existence of additional amino acids that are essential for the development of the standard genetic code. The validity of the proposed partition of the genetic code into dominant and recessive protocodes is considered referring to state-of-the-art hypotheses. The formation of two aminoacyl-tRNA synthetase classes is compatible with four-protocode partition.

Negative CG dinucleotide bias: An explanation based on feedback loops between Arginine codon assignments and theoretical minimal RNA rings

Theoretical minimal RNA rings are candidate primordial genes evolved for non-redundant coding of the genetic code's 22 coding signals (one codon per biogenic amino acid, a start and a stop codon) over the shortest possible length: 29520 22-nucleotide-long RNA rings solve this min-max constraint. Numerous RNA ring properties are reminiscent of natural genes. Here we present analyses showing that all RNA rings lack dinucleotide CG (a mutable, chemically instable dinucleotide coding for Arginine), bearing a resemblance to known CG-depleted genomes. CG in "incomplete" RNA rings (not coding for all coding signals, with only 3-12 nucleotides) gradually decreases towards CG absence in complete, 22-nucleotide-long RNA rings. Presumably, feedback loops during RNA ring growth during evolution (when amino acid assignment fixed the genetic code) assigned Arg to codons lacking CG (AGR) to avoid CG. Hence, as a chemical property of base pairs, CG mutability restructured the genetic code, thereby establishing itself as genetically encoded biological information.

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.

Theoretical minimal RNA rings mimick molecular evolution before tRNA-mediated translation: codon-amino acid affinities increase from early to late RNA rings

Nucleotide affinities for noncovalent interactions with amino acids produce associations between mRNAs and cognate peptides, potentially regulating ribosomal translation. Correlations between nucleotide affinities and residue hydrophobicity are explored for 25 theoretical minimal RNA rings, 22 nucleotide-long RNAs designed in silico to code for each amino acid once after three translation rounds, and forming stem-loop hairpins. This design presumably mimicks life's first RNAs. RNA rings resemble consensual tRNAs, suggesting proto-tRNA function, predicted anticodon and cognate amino acid. The 25 RNA rings and their presumed evolutionary order, deduced from the genetic code integration order of the amino acid cognate to their predicted anticodon, produces noteworthy associations with several ancient properties of the cell's translational machinery. Here we use this system to explore the evolution of codon affinity-residue hydrophobicity correlations, assuming these reflect pre-tRNA and pre-ribosomal translations. This hypothesis expects that correlations decrease with genetic code inclusion orders of RNA ring cognates. RNA ring associations between nucleotide affinities and residue hydrophobicities resemble those from modern natural genes/proteins. Association strengths decrease with genetic code inclusion ranks of proto-tRNA cognate amino acids. In silico design of minimal RNA rings didn't account for affinities between RNA and peptides coded by these RNAs. Yet, interactions between RNA rings and translated cognate peptides resemble modern natural genes. This property is strongest for ancient RNA rings, weakest for recent RNA rings, spanning a period during which modern tRNA- and ribosome-based translation presumably evolved. Results indicate that translation lacking tRNA-like adaptors based on codon-amino acid affinities and the genetic code pre-existed tRNA-mediated translation. Theoretical minimal RNA rings appear valid prebiotic peptide-RNA world models for the transition between pre-tRNA- and tRNA-mediated translations.

Footprints of a Singular 22-Nucleotide RNA Ring at the Origin of Life

(1) Background: Previous experimental observations and theoretical hypotheses have been providing insight into a hypothetical world where an RNA hairpin or ring may have debuted as the primary informational and functional molecule. We propose a model revisiting the architecture of RNA-peptide interactions at the origin of life through the evolutionary dynamics of RNA populations. (2) Methods: By performing a step-by-step computation of the smallest possible hairpin/ring RNA sequences compatible with building up a variety of peptides of the primitive network, we inferred the sequence of a singular docosameric RNA molecule, we call the ALPHA sequence. Then, we searched for any relics of the peptides made from ALPHA in sequences deposited in the different public databases. (3) Results: Sequence matching between ALPHA and sequences from organisms among the earliest forms of life on Earth were found at high statistical relevance. We hypothesize that the frequency of appearance of relics from ALPHA sequence in present genomes has a functional necessity. (4) Conclusions: Given the fitness of ALPHA as a supportive sequence of the framework of all existing theories, and the evolution of Archaea and giant viruses, it is anticipated that the unique properties of this singular archetypal ALPHA sequence should prove useful as a model matrix for future applications, ranging from synthetic biology to DNA computing.

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.