Swinger RNAs in the Human Mitochondrial Transcriptome

Transcriptomes include coding and non-coding RNAs and RNA fragments with no apparent homology to parent genomes. Non-canonical transcriptions systematically transforming template DNA sequences along precise rules explain some transcripts. Among these systematic transformations, 23 systematic exchanges between nucleotides, i.e. 9 symmetric (X ↔ Y, e.g. C ↔ T) and 14 asymmetric (X → Y → Z → X, e.g. A → T → G → A) exchanges. Here, comparisons between mitochondrial swinger RNAs previously detected in a complete human transcriptome dataset (including cytosolic RNAs) and swinger RNAs detected in purified mitochondrial transcriptomic data (not including cytosolic RNAs) show high reproducibility and exclude cytosolic contaminations. These results based on next-generation sequencing Illumina technology confirm detections of mitochondrial swinger RNAs in GenBank’s EST database sequenced by the classical Sanger method, assessing the existence of swinger polymerizations

Directed Mutations Recode Mitochondrial Genes: From Regular to Stopless Genetic Codes

Mitochondrial genetic codes evolve as side effects of stop codon ambiguity: suppressor tRNAs with anticodons translating stops transform genetic codes to stopless genetic codes. This produces peptides from frames other than regular ORFs, potentially increasing protein numbers coded by single sequences. Previous descriptions of marine turtle Olive Ridley mitogenomes imply directed stop-depletion of noncoding +1 gene frames, stop-creation recodes regular ORFs to stopless genetic codes. In this analysis, directed stop codon depletion in usually noncoding gene frames of the spiraling whitefly Aleurodicus dispersusʼ mitogenome produces new ORFs, introduces stops in regular ORFs, and apparently increases coding redundancy between different gene frames. Directed stop codon mutations switch between peptides coded by regular and stopless genetic codes. This process seems opposite to directed stop creation in HIV ORFs within genomes of immunized elite HIV controllers. Unknown DNA replication/edition mechanisms probably direct stop creation/depletion beyond natural selection on stops. Switches between genetic codes regulate translation of different gene frames

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

Leiocephalus personatus

Number of pages=30Geological SciencesIntegrative Biolog

Tetracoding increases with body temperature in Lepidosauria

Codons expanded by a silent position (quadruplet or tetracodons) may solve the conundrum that at life's origins, the weak tricodon-anticodon interactions could not promote translation in the absence of complex ribosomes. Modern genomes have isolated tetracodons resulting from insertion mutations. Some bioinformatic analyses suggest that tetracoding stretches overlap with regular mitochondrial protein coding genes. These tetragenes are probably decoded by (antisense) tRNAs with expanded anticodons. They are GC-rich, which produce stronger basepairs than A:T interactions, suggesting expression at high temperatures. The hypothesis that tetracoding is an adaptation to high temperatures is tested here by comparing predicted mitochondrial tetracoding in Lepidosauria (lizards, amphisbaenia, and Sphenodon), in relation to body temperature, expecting more tetracoding in species with high body temperature. The association between tRNAs with expanded anticodons and tetracoding previously describ

The Origin and Early Evolution of Life

What is life? How, where, and when did life arise? These questions have remained most fascinating over the last hundred years. Systems chemistry is the way to go to better understand this problem and to try and answer the unsolved question regarding the origin of Life. Self-organization, thanks to the role of lipid boundaries, made possible the rise of protocells. The role of these boundaries is to separate and co-locate micro-environments, and make them spatially distinct; to protect and keep them at defined concentrations; and to enable a multitude of often competing and interfering biochemical reactions to occur simultaneously. The aim of this Special Issue is to summarize the latest discoveries in the field of the prebiotic chemistry of biomolecules, self-organization, protocells and the origin of life. In recent years, thousands of excellent reviews and articles have appeared in the literature and some breakthroughs have already been achieved. However, a great deal of work remains to be carried out. Beyond the borders of the traditional domains of scientific activity, the multidisciplinary character of the present Special Issue leaves space for anyone to creatively contribute to any aspect of these and related relevant topics. We hope that the presented works will be stimulating for a new generation of scientists that are taking their first steps in this fascinating field