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

Demongeot, Jacques; Seligmann, Hervé

doi:10.5802/crbiol.1

Cited by 9 publications

(5 citation statements)

References 105 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…All other tRNA Pri sequences are known with very high confidence (essential certainty). When this model was first considered, it was a surprise to its originators, because tRNA was previously thought to arise by a chaotic process [6,[8][9][10][11][12][13][14]21]. Because the entire tRNA Pri and entire tRNAomes from ancient organisms are ordered, however, no chaotic model can possibly be correct for tRNA evolution [1][2][3].…”

Section: Resultsmentioning

confidence: 99%

“…Because the 3-31 nt mini-36 helix model explains all features, sequences and segments of type I and type II tRNAs, the 37 model has been described as a proven theorem [3]. Competing models for tRNA evolution are all accretion models [6][7][8][9][10][11][12][13][14], in which tRNA segments expand and/or contract by random insertions and/or deletions (indels) to a final form. Because the entire primordial tRNA (tRNA Pri ) sequence is ordered as discrete segments of RNA repeats and inverted repeats, however, no accretion model with random indels can adequately describe tRNA 2 of 15 [5,15].…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Realignment of tRNA Variable Loops, the 3-31 nt Minihelix Theorem and Consequences for the Origin of Life

Lei¹,

Burton²

2022

Preprint

View full text Add to dashboard Cite

Evolutionary, sequence and structural analyses of tRNA variable (V) loops provides a new understanding. Type I tRNA V loops have a primordial length of 5 nt, and type II tRNA V loops have a primordial length of 14 nt. Sequence-based alignments of type I and type II V loops gave deceptive results. Type II V loops are characterized by the trajectory of the V arm, the size and sequence of the loop and the first and last V loop nucleotides and their known contacts. Depending on the V arm trajectory, type II V stems and loops can be interaction sites for aminoacyl-tRNA synthetases. So, type II V arms for tRNALeu, tRNASer and tRNATyr (found in Bacteria) were coevolved and selected to distinguish determinants to support cognate tRNA charging. The alignment of type I and type II V loops was adjusted based on tRNA evolution. Results are consistent with Archaea being an older and simpler life form than Bacteria. TRNAome sequences were derived from radiation of an ordered tRNAPri (Pri for primordial) sequence comprised of known RNA repeats and inverted repeats. V loop and tRNA sequences, therefore, convey a history of the primary successful pathway in the origin of life.

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Realignment of tRNA Variable Loops, the 3-31 nt Minihelix Theorem and Consequences for the Origin of Life

Lei¹,

Burton²

2022

Preprint

View full text Add to dashboard Cite

show abstract

“…Intriguingly, the sequences of the 25 primordial rings turn out to maximize the affinity between their nucleotide triplets and the corresponding cognate amino acids. Moreover, the calculated interactions between these RNA rings and their cognate peptides are strongest for ancient RNA rings and weakest for recent RNA rings, consistent with their putative role in pre-tRNA- to tRNA-mediated translation [ 51 , 52 , 53 ].…”

Section: Evidencementioning

confidence: 85%

The Ring World: Eversion of Small Double-Stranded Polynucleotide Circlets at the Origin of DNA Double Helix, RNA Polymerization, Triplet Code, Twenty Amino Acids, and Strand Asymmetry

Norris

Demongeot²

2022

IJMS

View full text Add to dashboard Cite

It is not entirely clear why, at some stage in its evolution, terrestrial life adopted double-stranded DNA as the hereditary material. To explain this, we propose that small, double-stranded, polynucleotide circlets have special catalytic properties. We then use this proposal as the basis for a ‘view from here’ that we term the Circlet hypothesis as part of a broader Ring World. To maximize the potential explanatory value of this hypothesis, we speculate boldly about the origins of several of the fundamental characteristics and briefly describe the main methods or treatments applied. The principal prediction of the paper is that the highly constrained, conformational changes will occur preferentially in dsDNA, dsRNA and hybrid RNA-DNA circlets that are below a critical size (e.g., 306 bp) and that these will favor the polymerization of precursors into RNA and DNA. We can conclude that the Circlet hypothesis and the Ring World therefore have the attraction of offering the same solution to the fundamental problems that probably confront both the earliest cells and the most recent ones.

show abstract

“…Circular RNAs (circRNAs) are endogenous RNAs with a covalently closed cyclic structure [8,9]. Intracellular circRNAs with competing endogenous RNA (ceRNA) activity may act as microRNA (miRNA/miR) inhibitors by interacting with miRNA recognition elements (MREs) on target mRNAs [10,11].…”

Section: Introductionmentioning

confidence: 99%

Knockdown of hsa_circ_0001275 reverses dexamethasone-induced osteoblast growth inhibition via mediation of miR-377/CDKN1B axis

Sun

et al. 2021

PLoS ONE

View full text Add to dashboard Cite

Background Osteoporosis affects the quality of life among middle-aged and elderly individuals. In addition, dysfunction of osteoblasts can lead to the progression of osteoporosis. Circular (circ)RNAs are involved in various types of diseases, including osteoporosis. Moreover, it has been reported that hsa_circ_0001275 expression is upregulated in osteoporosis. However, the effects of hsa_circ_0001275 on the growth of osteoblasts remain unclear. Methods In the present study, the gene and protein expression levels in hFOB1.19 cells were detected via reverse transcription-quantitative (RT-qPCR) and western blot analyses, respectively. In addition, alkaline phosphatase (ALP) activity and calcium nodules were examined by ALP and alizarin red staining, respectively. Cell proliferation was measured using the Cell Counting Kit-8 assay. Cell apoptosis and cell cycle were analyzed by flow cytometry. Furthermore, dual luciferase reporter and RNA pull-down assay were used to confirm the association among hsa_circ_0001275, microRNA (miR)-377 and CDKN1B. Results DEX-induced hFOB1.19 cell growth inhibition was significantly reversed by silencing hsa_circ_0001275. Moreover, DEX significantly increased ALP activity and calcium nodules in hFOB1.19 cells, while this effect was significantly reversed in the presence of hsa_circ_0001275 small interfering RNA. In addition, miR-377 was sponged by hsa_circ_0001275 and CDKN1B was directly targeted by miR-377 in hFOB1.19 cells. Furthermore, the therapeutic effect of hsa_circ_0001275 knockdown on osteoporosis was notably reversed by miR-377 antagomir. Conclusion The data demonstrated that knockdown of hsa_circ_0001275 reversed DEX-induced osteoblast growth inhibition via activation of the miR-377/CDKN1B axis. Therefore, this study might shed new lights on the treatment of osteoporosis.

show abstract

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

Cited by 9 publications

References 105 publications

Realignment of tRNA Variable Loops, the 3-31 nt Minihelix Theorem and Consequences for the Origin of Life

Realignment of tRNA Variable Loops, the 3-31 nt Minihelix Theorem and Consequences for the Origin of Life

The Ring World: Eversion of Small Double-Stranded Polynucleotide Circlets at the Origin of DNA Double Helix, RNA Polymerization, Triplet Code, Twenty Amino Acids, and Strand Asymmetry

Knockdown of hsa_circ_0001275 reverses dexamethasone-induced osteoblast growth inhibition via mediation of miR-377/CDKN1B axis

Contact Info

Product

Resources

About