True Mitochondrial tRNA Punctuation and Initiation Using Overlapping Stop and Start Codons at Specific and Conserved Positions

Faure, Éric; Barthélémy, Roxane

doi:10.5772/intechopen.75555

Cited by 11 publications

(6 citation statements)

References 100 publications

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“…The observation that RNA rings, designed according to coding properties, coincide with tRNAs, strengthens the hypothesis of protein coding functions for tRNAs [15,16]. This could explain biases in tRNAs (and rRNAs) for nucleotide triplets corresponding to circular code codons which are overrepresented in protein coding genes (tRNAs [17,18]; rRNAs [19][20][21]).…”

Section: Introductionsupporting

confidence: 54%

The primordial tRNA acceptor stem code from theoretical minimal RNA ring clusters

Demongeot

Seligmann

2020

BMC Genet

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Background: Theoretical minimal RNA rings code by design over the shortest length once for each of the 20 amino acids, a start and a stop codon, and form stem-loop hairpins. This defines at most 25 RNA rings of 22 nucleotides. As a group, RNA rings mimick numerous prebiotic and early life biomolecular properties: tRNAs, deamination gradients and replication origins, emergence of codon preferences for the natural circular code, and contents of early protein coding genes. These properties result from the RNA ring's in silico design, based mainly on coding nonredundancy among overlapping translation frames, as the genetic code's codon-amino acid assignments determine. RNA rings resemble ancestral tRNAs, defining RNA ring anticodons and corresponding cognate amino acids. Surprisingly, all examined RNA ring properties coevolve with genetic code integration ranks of RNA ring cognates, as if RNA rings mimick prebiotic and early life evolution. Methods: Distances between RNA rings were calculated using different evolutionary models. Associations between these distances and genetic code evolutionary hypotheses detect evolutionary models best describing RNA ring diversification. Results: Here pseudo-phylogenetic analyses of RNA rings produce clusters corresponding to the primordial code in tRNA acceptor stems, more so when substitution matrices from neutrally evolving pseudogenes are used rather than from functional protein coding genes reflecting selection for conserving amino acid properties. Conclusions: Results indicate RNA rings with recent cognates evolved from those with early cognates. Hence RNA rings, as designed by the genetic code's structure, simulate tRNA stem evolution and prebiotic history along neutral chemistry-driven mutation regimes.

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Section: Introductionsupporting

confidence: 54%

The primordial tRNA acceptor stem code from theoretical minimal RNA ring clusters

Demongeot

Seligmann

2020

BMC Genet

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“…The majority of Opithokonthes organisms use the punctuation model for the maturation of the polycistronic primary transcripts where maturation of tRNA extremities liberate coding and non-coding RNAs [ 31 ]. In addition, even if other eukaryote clades do not use this model, tRNAs or tRNA-like sequences (TLS) can account for the maturation of some polycistrons or mRNA extremities [ 32 , 33 ].…”

Section: Mitochondrial Rnases Involved In Rna Maturationmentioning

confidence: 99%

How RNases Shape Mitochondrial Transcriptomes

Cartalas

Coudray

Gobert

2022

IJMS

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Mitochondria are the power houses of eukaryote cells. These endosymbiotic organelles of prokaryote origin are considered as semi-autonomous since they have retained a genome and fully functional gene expression mechanisms. These pathways are particularly interesting because they combine features inherited from the bacterial ancestor of mitochondria with characteristics that appeared during eukaryote evolution. RNA biology is thus particularly diverse in mitochondria. It involves an unexpectedly vast array of factors, some of which being universal to all mitochondria and others being specific from specific eukaryote clades. Among them, ribonucleases are particularly prominent. They play pivotal functions such as the maturation of transcript ends, RNA degradation and surveillance functions that are required to attain the pool of mature RNAs required to synthesize essential mitochondrial proteins such as respiratory chain proteins. Beyond these functions, mitochondrial ribonucleases are also involved in the maintenance and replication of mitochondrial DNA, and even possibly in the biogenesis of mitochondrial ribosomes. The diversity of mitochondrial RNases is reviewed here, showing for instance how in some cases a bacterial-type enzyme was kept in some eukaryotes, while in other clades, eukaryote specific enzymes were recruited for the same function.

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“…Several hypotheses suggest different historical scenarios for tRNA evolution, all assuming accretions of smaller sequences [22][23][24][25][26][27][28][29][30][31][32][33][34][35][36][37][38][39][40][41] . A similar hypothesis exists for 5S rRNAs 42 .…”

Section: Trna Accretionmentioning

confidence: 99%

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

Demongeot

Seligmann

2020

Sci Rep

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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. Ribosomes presumably evolved through serial accretions of tRNAs and tRNA-like RNAs 1-11. The ribosomal dimeric RNA core surrounding the peptide synthesis site 12-14 also resembles tRNA dimers linked by complementary anticodons, according to the self-referential hypothesis on the origin of translation 15-19. Evidence for this process exists also in modern vertebrate mitochondrial ribosomes: regular mitochondrial tRNAs constitutively fulfill 5S rRNA functions 20,21. In the latter case, extreme mitogenome reduction perhaps reversed evolution to a tRNA-insertion stage, enabling further mitogenome reduction. These evidences suggest that rRNAs derived from tRNAs.

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True Mitochondrial tRNA Punctuation and Initiation Using Overlapping Stop and Start Codons at Specific and Conserved Positions

Cited by 11 publications

References 100 publications

The primordial tRNA acceptor stem code from theoretical minimal RNA ring clusters

The primordial tRNA acceptor stem code from theoretical minimal RNA ring clusters

How RNases Shape Mitochondrial Transcriptomes

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

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