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Demongeot J, Seligmann H. Evolution of small and large ribosomal RNAs from accretion of tRNA subelements. Biosystems 2022; 222:104796. [DOI: 10.1016/j.biosystems.2022.104796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 10/19/2022] [Indexed: 11/02/2022]
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2
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Seligmann H, Vuillerme N, Demongeot J. Unpredictable, Counter-Intuitive Geoclimatic and Demographic Correlations of COVID-19 Spread Rates. Biology (Basel) 2021; 10:623. [PMID: 34356478 PMCID: PMC8301123 DOI: 10.3390/biology10070623] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 06/16/2021] [Accepted: 06/29/2021] [Indexed: 11/17/2022]
Abstract
We present spread parameters for first and second waves of the COVID-19 pandemic for USA states, and for consecutive nonoverlapping periods of 20 days for the USA and 51 countries across the globe. We studied spread rates in the USA states and 51 countries, and analyzed associations between spread rates at different periods, and with temperature, elevation, population density and age. USA first/second wave spread rates increase/decrease with population density, and are uncorrelated with temperature and median population age. Spread rates are systematically inversely proportional to those estimated 80-100 days later. Ascending/descending phases of the same wave only partially explain this. Directions of correlations with factors such as temperature and median age flip. Changes in environmental trends of the COVID-19 pandemic remain unpredictable; predictions based on classical epidemiological knowledge are highly uncertain. Negative associations between population density and spread rates, observed in independent samples and at different periods, are most surprising. We suggest that systematic negative associations between spread rates 80-100 days apart could result from confinements selecting for greater contagiousness, a potential double-edged sword effect of confinements.
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Affiliation(s)
- Hervé Seligmann
- Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical & Labcom CNRS/UGA/OrangeLabs Telecom4Health, Faculty of Medicine, University Grenoble Alpes (UGA), 38700 La Tronche, France;
- The National Natural History Collections, The Hebrew University of Jerusalem, Jerusalem 91404, Israel;
| | - Nicolas Vuillerme
- Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical & Labcom CNRS/UGA/OrangeLabs Telecom4Health, Faculty of Medicine, University Grenoble Alpes (UGA), 38700 La Tronche, France;
| | - Jacques Demongeot
- The National Natural History Collections, The Hebrew University of Jerusalem, Jerusalem 91404, Israel;
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Nesterov-Mueller A, Popov R, Seligmann H. Combinatorial Fusion Rules to Describe Codon Assignment in the Standard Genetic Code. Life (Basel) 2020; 11:life11010004. [PMID: 33374866 PMCID: PMC7824455 DOI: 10.3390/life11010004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/15/2020] [Accepted: 12/21/2020] [Indexed: 11/16/2022] Open
Abstract
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.
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Affiliation(s)
- Alexander Nesterov-Mueller
- Institute of Microstructure Technology, Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany; (R.P.); (H.S.)
- Correspondence:
| | - Roman Popov
- Institute of Microstructure Technology, Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany; (R.P.); (H.S.)
| | - Hervé Seligmann
- Institute of Microstructure Technology, Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany; (R.P.); (H.S.)
- The National Natural History Collections, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
- Laboratory AGEIS EA 7407, Team Tools for e-GnosisMedical & LabcomCNRS/UGA/OrangeLabs Telecoms4Health, Faculty of Medicine, Université Grenoble Alpes, F-38700 La Tronche, France
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Demongeot J, Moreira A, Seligmann H. Negative CG dinucleotide bias: An explanation based on feedback loops between Arginine codon assignments and theoretical minimal RNA rings. Bioessays 2020; 43:e2000071. [PMID: 33319381 DOI: 10.1002/bies.202000071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 11/23/2020] [Accepted: 11/26/2020] [Indexed: 01/05/2023]
Abstract
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.
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Affiliation(s)
- Jacques Demongeot
- Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical & Labcom CNRS/UGA/OrangeLabs Telecom4Health, Faculty of Medicine, Université Grenoble Alpes, La Tronche, France
| | - Andrés Moreira
- Departamento de Informática, Universidad Técnica Federico Santa María, Santiago, Chile
| | - Hervé Seligmann
- Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical & Labcom CNRS/UGA/OrangeLabs Telecom4Health, Faculty of Medicine, Université Grenoble Alpes, La Tronche, France.,The National Natural History Collections, The Hebrew University of Jerusalem, Jerusalem, Israel.,Institute of Microstructure Technology, Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
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Abstract
(1) Background: RNA viruses and especially coronaviruses could act inside host cells not only by building their own proteins, but also by perturbing the cell metabolism. We show the possibility of miRNA-like inhibitions by the SARS-CoV-2 concerning for example the hemoglobin and type I interferons syntheses, hence highly perturbing oxygen distribution in vital organs and immune response as described by clinicians; (2) Hypothesis: We hypothesize that short RNA sequences (about 20 nucleotides in length) from the SARS-CoV-2 virus genome can inhibit the translation of human proteins involved in oxygen metabolism, olfactory perception and immune system. (3) Methods: We compare RNA subsequences of SARS-CoV-2 protein S and RNA-dependent RNA polymerase genes to mRNA sequences of beta-globin and type I interferons; (4) Results: RNA subsequences longer than eight nucleotides from SARS-CoV-2 genome could hybridize subsequences of the mRNA of beta-globin and of type I interferons; (5) Conclusions: Beyond viral protein production, COVID-19 might affect vital processes like host oxygen transport and immune response.
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Affiliation(s)
- Jacques Demongeot
- Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical & Labcom CNRS/UGA/OrangeLabs Telecom4Health, Faculty of Medicine, University Grenoble Alpes (UGA), 38700 La Tronche, France.
| | - Hervé Seligmann
- Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical & Labcom CNRS/UGA/OrangeLabs Telecom4Health, Faculty of Medicine, University Grenoble Alpes (UGA), 38700 La Tronche, France; The National Natural History Collections, The Hebrew University of Jerusalem, 91404 Jerusalem, Israel
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6
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Demongeot J, Seligmann H. Codon assignment evolvability in theoretical minimal RNA rings. Gene 2020; 769:145208. [PMID: 33031892 DOI: 10.1016/j.gene.2020.145208] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 09/28/2020] [Accepted: 09/29/2020] [Indexed: 12/28/2022]
Abstract
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.
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Affiliation(s)
- Jacques Demongeot
- Université Grenoble Alpes, Faculty of Medicine, Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical, F-38700 La Tronche, France
| | - Hervé Seligmann
- The National Natural History Collections, The Hebrew University of Jerusalem, 91404 Jerusalem, Israel.
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Seligmann H, Iggui S, Rachdi M, Vuillerme N, Demongeot J. Inverted Covariate Effects for First versus Mutated Second Wave Covid-19: High Temperature Spread Biased for Young. Biology (Basel) 2020; 9:E226. [PMID: 32823981 PMCID: PMC7464149 DOI: 10.3390/biology9080226] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 08/12/2020] [Accepted: 08/13/2020] [Indexed: 12/23/2022]
Abstract
(1) Background: Here, we characterize COVID-19's waves, following a study presenting negative associations between first wave COVID-19 spread parameters and temperature. (2) Methods: Visual examinations of daily increases in confirmed COVID-19 cases in 124 countries, determined first and second waves in 28 countries. (3) Results: The first wave spread rate increases with country mean elevation, median population age, time since wave onset, and decreases with temperature. Spread rates decrease above 1000 m, indicating high ultraviolet lights (UVs) decrease the spread rate. The second wave associations are the opposite, i.e., spread increases with temperature and young age, and decreases with time since wave onset. The earliest second waves started 5-7 April at mutagenic high elevations (Armenia, Algeria). The second waves also occurred at the warm-to-cold season transition (Argentina, Chile). Second vs. first wave spread decreases in most (77%) countries. In countries with late first wave onset, spread rates better fit second than first wave-temperature patterns. In countries with ageing populations (for example, Japan, Sweden, and Ukraine), second waves only adapted to spread at higher temperatures, not to infect the young. (4) Conclusions: First wave viruses evolved towards lower spread. Second wave mutant COVID-19 strain(s) adapted to higher temperature, infecting younger ages and replacing (also in cold conditions) first wave COVID-19 strains. Counterintuitively, low spread strains replace high spread strains, rendering prognostics and extrapolations uncertain.
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Affiliation(s)
- Hervé Seligmann
- Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical & Labcom CNRS/UGA/OrangeLabs Telecom4Health, Faculty of Medicine, University Grenoble Alpes (UGA), 38700 La Tronche, France; (S.I.); (M.R.); (N.V.); (J.D.)
- The National Natural History Collections, The Hebrew University of Jerusalem, Jerusalem 91404, Israel
| | - Siham Iggui
- Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical & Labcom CNRS/UGA/OrangeLabs Telecom4Health, Faculty of Medicine, University Grenoble Alpes (UGA), 38700 La Tronche, France; (S.I.); (M.R.); (N.V.); (J.D.)
| | - Mustapha Rachdi
- Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical & Labcom CNRS/UGA/OrangeLabs Telecom4Health, Faculty of Medicine, University Grenoble Alpes (UGA), 38700 La Tronche, France; (S.I.); (M.R.); (N.V.); (J.D.)
| | - Nicolas Vuillerme
- Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical & Labcom CNRS/UGA/OrangeLabs Telecom4Health, Faculty of Medicine, University Grenoble Alpes (UGA), 38700 La Tronche, France; (S.I.); (M.R.); (N.V.); (J.D.)
| | - Jacques Demongeot
- Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical & Labcom CNRS/UGA/OrangeLabs Telecom4Health, Faculty of Medicine, University Grenoble Alpes (UGA), 38700 La Tronche, France; (S.I.); (M.R.); (N.V.); (J.D.)
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Seligmann H, Warthi G. Natural pyrrolysine-biased translation of stop codons in mitochondrial peptides entirely coded by expanded codons. Biosystems 2020; 196:104180. [PMID: 32534170 DOI: 10.1016/j.biosystems.2020.104180] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/02/2020] [Accepted: 06/02/2020] [Indexed: 12/31/2022]
Abstract
During the noncanonical deletion transcription, k nucleotides are systematically skipped/deleted after each transcribed trinucleotide producing deletion-RNAs (delRNAs). Peptides matching delRNAs either result from (a) canonical translation of delRNAs; or (b) noncanonical translation of regular transcripts along expanded codons. Only along frame "0" (start site) (a) and (b) produce identical peptides. Here, mitochondrial mass spectrometry data analyses assume expanded codon/del-transcription with 3 + k (k from 0 to 12) nucleotides. Detected peptides map preferentially on previously identified delRNAs. More peptides were detected for k (1-12) when del-transcriptional and expanded codon translations start sites coincide (i.e. the 0th frame) than for frames +1 or +2. Hence, both (a) and (b) produced peptides identified here. Biases for frame 0 decrease for k > 2, reflecting codon/anticodon expansion limits. Further analyses find preferential pyrrolysine insertion at stop codons, suggesting Pyl-specific mitochondrial suppressor tRNAs loaded by Pyl-specific tRNA synthetases with unknown origins. Pyl biases at stops are stronger for regular than expanded codons suggesting that Pyl-tRNAs are less competitive with near-cognate tRNAs in expanded codon contexts. Statistical biases for these findings exclude that detected peptides are experimental and/or bioinformatic artefacts implying both del-transcription and expanded codons translation occur in human mitochondria.
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Affiliation(s)
- Hervé Seligmann
- The National Natural History Collections, The Hebrew University of Jerusalem, 91404, Jerusalem, Israel; Université Grenoble Alpes, Faculty of Medicine, Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical, F-38700, La Tronche, France.
| | - Ganesh Warthi
- Aix-Marseille University, IRD, VITROME, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France.
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Demongeot J, Seligmann H. Theoretical minimal RNA rings mimick molecular evolution before tRNA-mediated translation: codon-amino acid affinities increase from early to late RNA rings. C R Biol 2020; 343:111-122. [PMID: 32720493 DOI: 10.5802/crbiol.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Accepted: 02/21/2020] [Indexed: 12/11/2022]
Abstract
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.
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Affiliation(s)
- Jacques Demongeot
- Université Grenoble Alpes, Faculty of Medicine, Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical, F-38700 La Tronche, France
| | - Hervé Seligmann
- Université Grenoble Alpes, Faculty of Medicine, Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical, F-38700 La Tronche, France.,The National Natural History Collections, The Hebrew University of Jerusalem, 9190401 Jerusalem, Israel
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Demongeot J, Seligmann H. Comparisons between small ribosomal RNA and theoretical minimal RNA ring secondary structures confirm phylogenetic and structural accretion histories. Sci Rep 2020; 10:7693. [PMID: 32376895 PMCID: PMC7203183 DOI: 10.1038/s41598-020-64627-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 04/01/2020] [Indexed: 12/16/2022] Open
Abstract
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.
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Affiliation(s)
- Jacques Demongeot
- Université Grenoble Alpes, Faculty of Medicine, Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical & Labcom CNRS/UGA/OrangeLabs Telecoms4Health, F-38700, La Tronche, France.
| | - Hervé Seligmann
- Université Grenoble Alpes, Faculty of Medicine, Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical & Labcom CNRS/UGA/OrangeLabs Telecoms4Health, F-38700, La Tronche, France
- The National Natural History Collections, The Hebrew University of Jerusalem, 91404, Jerusalem, Israel
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Seligmann H. First arrived, first served: competition between codons for codon-amino acid stereochemical interactions determined early genetic code assignments. Naturwissenschaften 2020; 107:20. [PMID: 32367155 DOI: 10.1007/s00114-020-01676-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 03/10/2020] [Accepted: 04/05/2020] [Indexed: 12/12/2022]
Abstract
Stereochemical nucleotide-amino acid interactions, in the form of noncovalent nucleotide-amino acid interactions, potentially produced the genetic code's codon-amino acid assignments. Empirical estimates of single nucleotide-amino acid affinities on surfaces and in solution are used to test whether trinucleotide-amino acid affinities determined genetic code assignments pending the principle "first arrived, first served": presumed early amino acids have greater codon-amino acid affinities than ulterior ones. Here, these single nucleotide affinities are used to approximate all 64 × 20 trinucleotide-amino acid affinities. Analyses show that (1) on surfaces, genetic code codon-amino acid assignments tend to match high affinities for the amino acids that integrated earliest the genetic code (according to Wong's metabolic coevolution hypothesis between nucleotides and amino acids) and (2) in solution, the same principle holds for the anticodon-amino acid assignments. Affinity analyses match best genetic code assignments when assuming that trinucleotides competed for amino acids, rather than amino acids for trinucleotides. Codon-amino acid affinities stick better to genetic code assignments than anticodon-amino acid affinities. Presumably, two independent coding systems, on surfaces and in solution, converged, and formed the current translation system. Proto-translation on surfaces by direct codon-amino acid interactions without tRNA-like adaptors coadapted with a system emerging in solution by proto-tRNA anticodon-amino acid interactions. These systems assigned identical or similar cognates to codons on surfaces and to anticodons in solution. Results indicate that a prebiotic metabolism predated genetic code self-organization.
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Affiliation(s)
- Hervé Seligmann
- The National Natural History Collections, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel. .,Faculty of Medicine, Université Grenoble Alpes, Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical & Labcom CNRS/UGA/OrangeLabs Telecoms4Health, F-38700, La Tronche, France.
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Demongeot J, Flet-Berliac Y, Seligmann H. Temperature Decreases Spread Parameters of the New Covid-19 Case Dynamics. Biology (Basel) 2020; 9:E94. [PMID: 32375234 PMCID: PMC7284740 DOI: 10.3390/biology9050094] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/24/2020] [Accepted: 04/30/2020] [Indexed: 12/15/2022]
Abstract
(1) Background: The virulence of coronavirus diseases due to viruses like SARS-CoV or MERS-CoV decreases in humid and hot weather. The putative temperature dependence of infectivity by the new coronavirus SARS-CoV-2 or covid-19 has a high predictive medical interest. (2) Methods: External temperature and new covid-19 cases in 21 countries and in the French administrative regions were collected from public data. Associations between epidemiological parameters of the new case dynamics and temperature were examined using an ARIMA model. (3) Results: We show that, in the first stages of the epidemic, the velocity of contagion decreases with country- or region-wise temperature. (4) Conclusions: Results indicate that high temperatures diminish initial contagion rates, but seasonal temperature effects at later stages of the epidemy remain questionable. Confinement policies and other eviction rules should account for climatological heterogeneities, in order to adapt the public health decisions to possible geographic or seasonal gradients.
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Affiliation(s)
- Jacques Demongeot
- Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical & Labcom CNRS/UGA/OrangeLabs Telecom4Health, Faculty of Medicine, Université Grenoble Alpes, F-38700 La Tronche, France;
| | - Yannis Flet-Berliac
- Laboratory CRIStAL, UMR 9189, CNRS, Université de Lille, Campus Scientifique, Avenue Henri Poincaré, F-59655 Villeneuve d’Ascq, France;
| | - Hervé Seligmann
- Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical & Labcom CNRS/UGA/OrangeLabs Telecom4Health, Faculty of Medicine, Université Grenoble Alpes, F-38700 La Tronche, France;
- The National Natural History Collections, The Hebrew University of Jerusalem, Jerusalem 91404, Israel
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Demongeot J, Seligmann H. Why Is AUG the Start Codon?: Theoretical Minimal RNA Rings: Maximizing Coded Information Biases 1st Codon for the Universal Initiation Codon AUG. Bioessays 2020; 42:e1900201. [PMID: 32227358 DOI: 10.1002/bies.201900201] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 02/09/2020] [Indexed: 01/04/2023]
Abstract
The rational design of theoretical minimal RNA rings predetermines AUG as the universal start codon. This design maximizes coded amino acid diversity over minimal sequence length, defining in silico theoretical minimal RNA rings, candidate ancestral genes. RNA rings code for 21 amino acids and a stop codon after three consecutive translation rounds, and form a degradation-delaying stem-loop hairpin. Twenty-five RNA rings match these constraints, ten start with the universal initiation codon AUG. No first codon bias exists among remaining RNA rings. RNA ring design predetermines AUG as initiation codon. This is the only explanation yet for AUG as start codon. RNA ring design determines additional RNA ring gene- and tRNA-like properties described previously, because it presumably mimics constraints on life's primordial RNAs.
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Affiliation(s)
- Jacques Demongeot
- Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical & Labcom CNRS/UGA/OrangeLabs Telecom4Health, Faculty of Medicine, Université Grenoble Alpes, La Tronche, F-38700, France
| | - Hervé Seligmann
- Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical & Labcom CNRS/UGA/OrangeLabs Telecom4Health, Faculty of Medicine, Université Grenoble Alpes, La Tronche, F-38700, France.,The National Natural History Collections, The Hebrew University of Jerusalem, Jerusalem, 91404, Israel
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14
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Demongeot J, Seligmann H. Deamination gradients within codons after 1<->2 position swap predict amino acid hydrophobicity and parallel β-sheet conformational preference. Biosystems 2020; 191-192:104116. [PMID: 32081715 DOI: 10.1016/j.biosystems.2020.104116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 12/04/2019] [Accepted: 02/10/2020] [Indexed: 12/16/2022]
Abstract
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.
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Affiliation(s)
- Jacques Demongeot
- Université Grenoble Alpes, Faculty of Medicine, Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical, F-38700, La Tronche, France.
| | - Hervé Seligmann
- Université Grenoble Alpes, Faculty of Medicine, Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical, F-38700, La Tronche, France; The National Natural History Collections, The Hebrew University of Jerusalem, 91404, Jerusalem, Israel.
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15
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Warthi G, Fournier PE, Seligmann H. Systematic Nucleotide Exchange Analysis of ESTs From the Human Cancer Genome Project Report: Origins of 347 Unknown ESTs Indicate Putative Transcription of Non-Coding Genomic Regions. Front Genet 2020; 11:42. [PMID: 32117454 PMCID: PMC7027195 DOI: 10.3389/fgene.2020.00042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 01/15/2020] [Indexed: 12/16/2022] Open
Abstract
Expressed sequence tags (ESTs) provide an imprint of cellular RNA diversity irrespectively of sequence homology with template genomes. NCBI databases include many unknown RNAs from various normal and cancer cells. These are usually ignored assuming sequencing artefacts or contamination due to their lack of sequence homology with template DNA. Here, we report genomic origins of 347 ESTs previously assumed artefacts/unknown, from the FAPESP/LICR Human Cancer Genome Project. EST template detection uses systematic nucleotide exchange analyses called swinger transformations. Systematic nucleotide exchanges replace systematically particular nucleotides with different nucleotides. Among 347 unknown ESTs, 51 ESTs match mitogenome transcription, 17 and 2 ESTs are from nuclear chromosome non-coding regions, and uncharacterized nuclear genes. Identified ESTs mapped on 205 protein-coding genes, 10 genes had swinger RNAs in several biosamples. Whole cell transcriptome searches for 17 ESTs mapping on non-coding regions confirmed their transcription. The 10 swinger-transcribed genes identified more than once associate with cancer induction and progression, suggesting swinger transformation occurs mainly in highly transcribed genes. Swinger transformation is a unique method to identify noncanonical RNAs obtained from NGS, which identifies putative ncRNA transcribed regions. Results suggest that swinger transcription occurs in highly active genes in normal and genetically unstable cancer cells.
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Affiliation(s)
- Ganesh Warthi
- Aix Marseille Univ, IRD, APHM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Pierre-Edouard Fournier
- Aix Marseille Univ, IRD, APHM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Hervé Seligmann
- The National Natural History Collections, The Hebrew University of Jerusalem, Jerusalem, Israel.,Université Grenoble Alpes, Faculty of Medicine, Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical & Labcom CNRS/UGA/OrangeLabs Telecoms4Health, La Tronche, France
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16
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Demongeot J, Seligmann H. Accretion history of large ribosomal subunits deduced from theoretical minimal RNA rings is congruent with histories derived from phylogenetic and structural methods. Gene 2020; 738:144436. [PMID: 32027954 DOI: 10.1016/j.gene.2020.144436] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 01/24/2020] [Accepted: 02/01/2020] [Indexed: 12/17/2022]
Abstract
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.
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Affiliation(s)
- Jacques Demongeot
- Université Grenoble Alpes, Faculty of Medicine, Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical & Labcom CNRS/UGA/OrangeLabs Telecoms4Health, F-38700 La Tronche, France.
| | - Hervé Seligmann
- Université Grenoble Alpes, Faculty of Medicine, Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical & Labcom CNRS/UGA/OrangeLabs Telecoms4Health, F-38700 La Tronche, France; The National Natural History Collections, The Hebrew University of Jerusalem, 91404 Jerusalem, Israel.
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17
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Abstract
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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Affiliation(s)
- Jacques Demongeot
- Faculty of Medicine, Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical & Labcom CNRS/UGA/OrangeLabs Telecoms4Health, Université Grenoble Alpes, F-38700 La Tronche, France
| | - Hervé Seligmann
- Faculty of Medicine, Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical & Labcom CNRS/UGA/OrangeLabs Telecoms4Health, Université Grenoble Alpes, F-38700 La Tronche, France
- The National Natural History Collections, The Hebrew University of Jerusalem, 91404 Jerusalem, Israel
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18
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Abstract
Background: Codon directional asymmetry (CDA) classifies the 64 codons into palindromes (XYX, CDA = 0), and 5'- and 3'-dominant (YXX and XXY, CDA < 0 and CDA > 0, respectively). Previously, CDA was defined by the purine/pyrimidine divide (A,G/C,T), where X is either a purine or a pyrimidine. For the remaining codons with undefined CDA, CDA was defined by the 5' or 3' nucleotide complementary to Y. This CDA correlates with cognate amino acid tRNA synthetase classes, antiparallel beta sheet conformation index and the evolutionary order defined by the self-referential genetic code evolution model (CDA < 0: class I, high beta sheet index, late genetic code inclusion). Methods: We explore associations of CDAs defined by nucleotide classifications according to complementarity strengths (A:T, weak; C:G, strong) and keto-enol/amino-imino groupings (G,T/A,C), also after swapping 1st and 2nd codon positions with amino acid physicochemical and structural properties. Results: Here, analyses show that for the eight codons whose purine/pyrimidine-based CDA requires using the rule of complementarity with the midposition, using weak interactions to define CDA instead of complementarity increases associations with tRNA synthetase classes, antiparallel beta sheet index and genetic code evolutionary order. CDA defined by keto-enol/amino-imino groups, 1st and 2nd codon positions swapped, correlates with amino acid parallel beta sheet formation indices and Doolittle's hydropathicities. Conclusions: Results suggest (a) prebiotic swaps from N2N1N3 to N1N2N3 codon structures, (b) that tRNA-mediated translation replaced direct codon-amino acid interactions, and (c) links between codon structures and cognate amino acid properties.
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Affiliation(s)
- Hervé Seligmann
- The National Natural History Collections, The Hebrew University of Jerusalem, 91404 Jerusalem, Israel
- Faculty of Medicine, Université Grenoble Alpes, Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical, F-38700 La Tronche, France;
| | - Jacques Demongeot
- Faculty of Medicine, Université Grenoble Alpes, Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical, F-38700 La Tronche, France;
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19
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Warthi G, Fournier PE, Seligmann H. Identification of Noncanonical Transcripts Produced by Systematic Nucleotide Exchanges in HIV-Associated Centroblastic Lymphoma. DNA Cell Biol 2019; 39:1444-1448. [PMID: 31750730 DOI: 10.1089/dna.2019.5066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Noncanonical transcriptions include transcriptions that systematically exchange nucleotides, also called bijective transformations or swinger transformations. Swinger transformation A↔T+C↔G recovers identities of 8 among 9 unknown RNAs differentially expressed in centroblastic lymphoma, a human immunodeficiency virus (HIV)-associated non-Hodgkin's lymphoma. The identified RNAs align with human genes with known anti-HIV1 or oncogenic activities. Function disruption through swinger-transformed transcription potentially enables avoiding antiviral responses and contributes to cancer induction.
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Affiliation(s)
- Ganesh Warthi
- IRD, APHM, Aix Marseille Univ, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Pierre-Edouard Fournier
- IRD, APHM, Aix Marseille Univ, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Hervé Seligmann
- The National Natural History Collections, The Hebrew University of Jerusalem, Jerusalem, Israel
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20
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Seligmann H. Syntenies Between Cohosted Mitochondrial, Chloroplast, and Phycodnavirus Genomes: Functional Mimicry and/or Common Ancestry? DNA Cell Biol 2019; 38:1257-1268. [DOI: 10.1089/dna.2019.4858] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Hervé Seligmann
- The National Natural History Collections, The Hebrew University of Jerusalem, Jerusalem, Israel
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21
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Seligmann H, Warthi G. Chimeric Translation for Mitochondrial Peptides: Regular and Expanded Codons. Comput Struct Biotechnol J 2019; 17:1195-1202. [PMID: 31534643 PMCID: PMC6742854 DOI: 10.1016/j.csbj.2019.08.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/19/2019] [Accepted: 08/21/2019] [Indexed: 02/07/2023] Open
Abstract
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.
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Affiliation(s)
- Hervé Seligmann
- The National Natural History Collections, The Hebrew University of Jerusalem, 91404 Jerusalem, Israel
| | - Ganesh Warthi
- Aix-Marseille University, IRD, VITROME, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
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22
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Demongeot J, Seligmann H. Theoretical minimal RNA rings designed according to coding constraints mimic deamination gradients. Sci Nat 2019; 106:44. [DOI: 10.1007/s00114-019-1638-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 06/18/2019] [Accepted: 06/19/2019] [Indexed: 11/27/2022]
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23
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Demongeot J, Seligmann H. Spontaneous evolution of circular codes in theoretical minimal RNA rings. Gene 2019; 705:95-102. [DOI: 10.1016/j.gene.2019.03.069] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 03/08/2019] [Accepted: 03/29/2019] [Indexed: 02/06/2023]
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24
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Abstract
The ambush hypothesis speculates that off-frame stop codons increase translational efficiency after ribosomal frameshifts by stopping early frameshifted translation. Some evidences fit this hypothesis: (1) synonymous codon usages increase with their potential contribution to off-frame stops; (2) the genetic code assigns frequent amino acids to codon families contributing to off-frame stops; (3) positive biases for off-frame stops (AT rich) occur despite adverse nucleotide (GC) biases; and (4) mitochondrial off-frame stop codon densities increase with ribosomal structural instability, potential proxy of frameshift frequencies. In this study, analyses of vertebrate mitogenes and tRNA synthetase genes from all superkingdoms and viruses test a new prediction of the ambush hypothesis: sequences immediately downstream of frameshift-inducing homopolymer codons (AAA, CCC, GGG, and TTT) are off-frame stop rich. Codons immediately downstream of homopolymer codons form more than average off-frame stops, biases are stronger than for corresponding upstream distances and for any other group of synonymous codons. Sequences downstream of that high-density region are off-frame stop depleted. This decrease suggests that off-frame stops, combined with suppressor tRNAs regulate translation of overlapping coding sequences. Results show the predictive power of the ambush hypothesis, from macroevolutionary (genetic code structure) to detailed gene sequence anatomy.
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Affiliation(s)
- Hervé Seligmann
- The National Natural History Collections, The Hebrew University of Jerusalem, Jerusalem, Israel
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25
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Demongeot J, Seligmann H. Theoretical minimal RNA rings recapitulate the order of the genetic code's codon-amino acid assignments. J Theor Biol 2019; 471:108-116. [DOI: 10.1016/j.jtbi.2019.03.024] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 09/19/2018] [Accepted: 03/28/2019] [Indexed: 12/21/2022]
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26
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Warthi G, Seligmann H. Transcripts with systematic nucleotide deletion of 1-12 nucleotide in human mitochondrion suggest potential non-canonical transcription. PLoS One 2019; 14:e0217356. [PMID: 31120958 PMCID: PMC6532905 DOI: 10.1371/journal.pone.0217356] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 05/09/2019] [Indexed: 11/22/2022] Open
Abstract
Raw transcriptomic data contain numerous RNA reads whose homology with template DNA doesn't match canonical transcription. Transcriptome analyses usually ignore such noncanonical RNA reads. Here, analyses search for noncanonical mitochondrial RNAs systematically deleting 1 to 12 nucleotides after each transcribed nucleotide triplet, producing deletion-RNAs (delRNAs). We detected delRNAs in the human whole cell and purified mitochondrial transcriptomes, and in Genbank's human EST database corresponding to systematic deletions of 1 to 12 nucleotides after each transcribed trinucleotide. DelRNAs detected in both transcriptomes mapped along with 55.63% of the EST delRNAs. A bias exists for delRNAs covering identical mitogenomic regions in both transcriptomic and EST datasets. Among 227 delRNAs detected in these 3 datasets, 81.1% and 8.4% of delRNAs were mapped on mitochondrial coding and hypervariable region 2 of dloop. Del-transcription analyses of GenBank's EST database confirm observations from whole cell and purified mitochondrial transcriptomes, eliminating the possibility that detected delRNAs are false positives matches, cytosolic DNA/RNA nuclear contamination or sequencing artefacts. These detected delRNAs are enriched in frameshift-inducing homopolymers and are poor in frameshift-preventing circular code codons (a set of 20 codons which regulate reading frame detection, over- and underrepresented in coding and other frames of genes, respectively) suggesting a motif-based regulation of non-canonical transcription. These findings show that rare non-canonical transcripts exist. Such non canonical del-transcription does increases mitochondrial coding potential and non-coding regulation of intracellular mechanisms, and could explain the dark DNA conundrum.
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Affiliation(s)
- Ganesh Warthi
- Aix-Marseille Université, IRD, VITROME, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Hervé Seligmann
- Aix-Marseille Université, IRD, MEPHI, Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Marseille, France
- The National Natural History Collections, The Hebrew University of Jerusalem, Jerusalem, Israel
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27
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Abstract
Aminoacyl tRNA synthetases ligate tRNAs specifically with their cognate amino acid. These synthetases are among life's earliest proteins, class II tRNA synthetases (cognates A, D, F, G, H, K, N, P, S, and T) presumably preceding class I tRNA synthetases (cognates C, E, I, L, M, Q, R, V, W, and Y). Classification of codons into palindromic (structure XYX), 5'-dominant (YXX), and 3'-dominant (XXY) (Codon Directional Asymmetry [CDA]) shows that class II tRNA synthetases aminoacylate amino acids associated with XXY. Our working hypothesis expects bias for XXY codons in primordial RNAs, such as theoretical minimal RNA rings, designed in silico to mimic life's earliest RNAs. Twenty-five RNA rings have been computed, which code over a minimal length (22 nucleotides) for a start codon, stop codon, and one and only one codon for each of the 20 amino acids, and form stem-loop hairpins preventing degradation; these 25 minimal RNAs are the only ones matching these constraints and they seem homologous to consensus tRNA sequences. This similarity defined candidate RNA ring anticodons and corresponding cognate amino acids. Here, analyses of RNA ring codon contents confirm bias for XXY codons in 13 among 14 RNA rings with unequal XXY and YXX codon numbers. This bias increases with the genetic code integration order of the RNA ring's cognate amino acid across and within tRNA synthetase classes, suggesting that evolutionary processes, and not physicochemical constraints, produced the association between CDA and tRNA synthetase classes. The self-referential hypothesis for genetic code origin, a very complete genetic code evolutionary hypothesis integrating many translational machinery components, predicts best among genetic code evolutionary hypotheses CDA biases in RNA rings. The RNA rings' simple design inadvertently reproduces CDAs predicted by the genetic code's structure, confirming theoretical minimal RNA rings as good proxies for life's earliest RNAs.
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Affiliation(s)
- Jacques Demongeot
- Laboratory AGEIS EA 7407, Faculty of Medicine, Team Tools for e-Gnosis Medical, Université Grenoble Alpes, La Tronche, France
| | - Hervé Seligmann
- The National Natural History Collections, The Hebrew University of Jerusalem, Jerusalem, Israel
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28
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Demongeot J, Seligmann H. More Pieces of Ancient than Recent Theoretical Minimal Proto-tRNA-Like RNA Rings in Genes Coding for tRNA Synthetases. J Mol Evol 2019; 87:152-174. [DOI: 10.1007/s00239-019-09892-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 03/22/2019] [Indexed: 12/19/2022]
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29
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Seligmann H. Giant viruses: spore‐like missing links betweenRickettsiaand mitochondria? Ann N Y Acad Sci 2019; 1447:69-79. [DOI: 10.1111/nyas.14022] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 01/10/2019] [Accepted: 01/16/2019] [Indexed: 12/27/2022]
Affiliation(s)
- Hervé Seligmann
- The National Natural History Collectionsthe Hebrew University of Jerusalem Jerusalem Israel
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30
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El Houmami N, Durand GA, Bzdrenga J, Darmon A, Minodier P, Seligmann H, Raoult D, Fournier PE. A New Highly Sensitive and Specific Real-Time PCR Assay Targeting the Malate Dehydrogenase Gene of Kingella kingae and Application to 201 Pediatric Clinical Specimens. J Clin Microbiol 2018; 56:e00505-18. [PMID: 29875189 PMCID: PMC6062779 DOI: 10.1128/jcm.00505-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 05/29/2018] [Indexed: 12/21/2022] Open
Abstract
Kingella kingae is a significant pediatric pathogen responsible for bone and joint infections, occult bacteremia, and endocarditis in early childhood. Past efforts to detect this bacterium using culture and broad-range 16S rRNA gene PCR assays from clinical specimens have proven unsatisfactory; therefore, by the late 2000s, these were gradually phased out to explore the benefits of specific real-time PCR tests targeting the groEL gene and the RTX locus of K. kingae However, recent studies showed that real-time PCR (RT-PCR) assays targeting the Kingella sp. RTX locus that are currently available for the diagnosis of K. kingae infection lack specificity because they could not distinguish between K. kingae and the recently described Kingella negevensis species. Furthermore, in silico analysis of the groEL gene from a large collection of 45 K. kingae strains showed that primers and probes from K. kingaegroEL-based RT-PCR assays display a few mismatches with K. kingae groEL variations that may result in decreased detection sensitivity, especially in paucibacillary clinical specimens. In order to provide an alternative to groEL- and RTX-targeting RT-PCR assays that may suffer from suboptimal specificity and sensitivity, a K. kingae-specific RT-PCR assay targeting the malate dehydrogenase (mdh) gene was developed for predicting no mismatch between primers and probe and 18 variants of the K. kingae mdh gene from 20 distinct sequence types of K. kingae This novel K. kingae-specific RT-PCR assay demonstrated high specificity and sensitivity and was successfully used to diagnose K. kingae infections and carriage in 104 clinical specimens from children between 7 months and 7 years old.
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Affiliation(s)
- Nawal El Houmami
- UMR VITROME, Aix-Marseille Université, IRD, Service de Santé des Armées, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Guillaume André Durand
- UMR VITROME, Aix-Marseille Université, IRD, Service de Santé des Armées, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Janek Bzdrenga
- Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Anne Darmon
- UMR VITROME, Aix-Marseille Université, IRD, Service de Santé des Armées, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Philippe Minodier
- Department of Pediatric Emergency Medicine, North Hospital, Marseille, France
| | - Hervé Seligmann
- UMR VITROME, Aix-Marseille Université, IRD, Service de Santé des Armées, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Didier Raoult
- UMR VITROME, Aix-Marseille Université, IRD, Service de Santé des Armées, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Pierre-Edouard Fournier
- UMR VITROME, Aix-Marseille Université, IRD, Service de Santé des Armées, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
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31
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Abstract
Several hypotheses predict ranks of amino acid assignments to genetic code's codons. Analyses here show that average positions of amino acid species in proteins correspond to assignment ranks, in particular as predicted by Juke's neutral mutation hypothesis for codon assignments. In all tested protein groups, including co- and post-translationally folding proteins, 'recent' amino acids are on average closer to gene 5' extremities than 'ancient' ones. Analyses of pairwise residue contact energies matrices suggest that early amino acids stereochemically selected late ones that stablilize residue interactions within protein cores, presumably producing 5'-late-to-3'-early amino acid protein sequence gradients. The gradient might reduce protein misfolding, also after mutations, extending principles of neutral mutations to protein folding. Presumably, in self-perpetuating and self-correcting systems like the genetic code, initial conditions produce similarities between evolution of the process (the genetic code) and 'ontogeny' of resulting structures (here proteins), producing apparent teleonomy between process and product.
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Affiliation(s)
- Hervé Seligmann
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR MEPHI, Aix-Marseille Université, IRD, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France.
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Seligmann H, Raoult D. Stem-Loop RNA Hairpins in Giant Viruses: Invading rRNA-Like Repeats and a Template Free RNA. Front Microbiol 2018; 9:101. [PMID: 29449833 PMCID: PMC5799277 DOI: 10.3389/fmicb.2018.00101] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 01/16/2018] [Indexed: 12/31/2022] Open
Abstract
We examine the hypothesis that de novo template-free RNAs still form spontaneously, as they did at the origins of life, invade modern genomes, contribute new genetic material. Previously, analyses of RNA secondary structures suggested that some RNAs resembling ancestral (t)RNAs formed recently de novo, other parasitic sequences cluster with rRNAs. Here positive control analyses of additional RNA secondary structures confirm ancestral and de novo statuses of RNA grouped according to secondary structure. Viroids with branched stems resemble de novo RNAs, rod-shaped viroids resemble rRNA secondary structures, independently of GC contents. 5' UTR leading regions of West Nile and Dengue flavivirid viruses resemble de novo and rRNA structures, respectively. An RNA homologous with Megavirus, Dengue and West Nile genomes, copperhead snake microsatellites and levant cotton repeats, not templated by Mimivirus' genome, persists throughout Mimivirus' infection. Its secondary structure clusters with candidate de novo RNAs. The saltatory phyletic distribution and secondary structure of Mimivirus' peculiar RNA suggest occasional template-free polymerization of this sequence, rather than noncanonical transcriptions (swinger polymerization, posttranscriptional editing).
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Affiliation(s)
- Hervé Seligmann
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR MEPHI, Aix-Marseille Université, IRD, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR MEPHI, Aix-Marseille Université, IRD, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
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El Houmami N, Bzdrenga J, Durand GA, Minodier P, Seligmann H, Prudent E, Bakour S, Bonacorsi S, Raoult D, Yagupsky P, Fournier PE. Molecular Tests That Target the RTX Locus Do Not Distinguish between Kingella kingae and the Recently Described Kingella negevensis Species. J Clin Microbiol 2017; 55:3113-3122. [PMID: 28794176 PMCID: PMC5625396 DOI: 10.1128/jcm.00736-17] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 07/31/2017] [Indexed: 11/20/2022] Open
Abstract
Kingella kingae is an important invasive pathogen in early childhood. The organism elaborates an RTX toxin presumably restricted to this species. Consequently, real-time quantitative PCR (qPCR) assays targeting the RTX locus have been developed in recent years and are gaining increasing use for the molecular diagnosis of K. kingae infections. However, the present study shows that Kingella negevensis, a Kingella species newly identified in young children, harbors an identical Kingella RTX locus, raising the question of whether K. negevensis can be misidentified as K. kingae by clinical microbiology laboratories. In silico comparison of Kingella sp. RTX and groEL genes and in vitro studies provided evidence that targeting the rtxA and rtxB genes could not differentiate between strains of K. kingae and K. negevensis, whereas targeting the groEL gene could. This prompted the design of a highly specific and sensitive qPCR assay targeting K. negevensis groEL (kngroEL). Ninety-nine culture-negative osteoarticular specimens from 99 children younger than 4 years of age were tested with a conventional 16S rRNA gene-based broad-range PCR assay and Kingella-specific rtxB, K. kingae-specific groEL (kkgroEL), and kngroEL qPCR assays. Forty-two specimens were rtxB positive, including 41 that were also kkgroEL positive and 1 (the remaining one) that was kngroEL positive. Thus, this study discloses an invasive infection caused by K. negevensis in humans and demonstrates that targeting the RTX locus cannot be used for the formal diagnosis of K. kingae infections. These findings stress the need for further studies on the epidemiology of asymptomatic carriage and invasive infections caused by K. negevensis in humans.
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Affiliation(s)
- Nawal El Houmami
- Aix-Marseille Université, Research Unit on Infectious and Emerging Tropical Diseases (URMITE), UM63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Janek Bzdrenga
- Aix-Marseille Université, Research Unit on Infectious and Emerging Tropical Diseases (URMITE), UM63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Marseille, France
- Université Grenoble Alpes, CEA, CNRS, IBS, F-38000, Grenoble, France
| | - Guillaume André Durand
- Aix-Marseille Université, Research Unit on Infectious and Emerging Tropical Diseases (URMITE), UM63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Philippe Minodier
- Department of Pediatric Emergency, North Hospital, Marseille, France
| | - Hervé Seligmann
- Aix-Marseille Université, Research Unit on Infectious and Emerging Tropical Diseases (URMITE), UM63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Elsa Prudent
- Aix-Marseille Université, Research Unit on Infectious and Emerging Tropical Diseases (URMITE), UM63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Sofiane Bakour
- Aix-Marseille Université, Research Unit on Infectious and Emerging Tropical Diseases (URMITE), UM63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Stéphane Bonacorsi
- Inserm, IAME, UMR 1137, Université Paris-Diderot, Sorbonne Paris Cité, Laboratoire de Microbiologie, Hôpital Robert-Debré, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Didier Raoult
- Aix-Marseille Université, Research Unit on Infectious and Emerging Tropical Diseases (URMITE), UM63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Pablo Yagupsky
- Clinical Microbiology Laboratory, Soroka University Medical Center, Beer-Sheva, Israel
| | - Pierre-Edouard Fournier
- Aix-Marseille Université, Research Unit on Infectious and Emerging Tropical Diseases (URMITE), UM63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Marseille, France
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Osei L, El Houmami N, Minodier P, Sika A, Basset T, Seligmann H, Terraz A, Demar M, Pochard J, Clouzeau J, Fournier PE, Elenga N. Paediatric Bone and Joint Infections in French Guiana: A 6 Year Retrospective Review. J Trop Pediatr 2017; 63:380-388. [PMID: 28204806 DOI: 10.1093/tropej/fmw102] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The epidemiology of paediatric bone and joint infections from South America is poorly known. We herein report a retrospective study conducted in whole French Guiana from January 2010 to December 2015. Medical charts of 55 previously healthy children were analysed, identifying 27 with osteomyelitis, 22 with septic arthritis and 6 with multifocal infections and/or osteoarthritis. The male:female ratio was 2.2:1, and the mean age was 7.5 years. Eighty percent children were ≥36 months old who had predominantly osteomyelitis related to methicillin-susceptible Staphylococcus aureus (p < 0.05) in the course of neglected skin infections. Five children presented with multi-systemic infections resulting in one fatality, mainly caused by S. aureus producing Panton-Valentine leucocidin (p < 0.01). In contrast, children aged 6-36 months had more likely culture-negative infections (p < 0.05), septic arthritis and mild clinical and biological features. Further prospective studies are required to better guide rational diagnostic and therapeutic strategies.
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Affiliation(s)
- Lindsay Osei
- Department of Pediatrics, Andrée Rosemon Hospital, French Guiana, Cayenne, France
| | - Nawal El Houmami
- URMITE "Research Unit on Infectious and Emerging Diseases", Inserm 1095, CNRS 7278, IRD 198, UMR 63, Institut Hospitalo-Universitaire Méditerranée-Infection, APHM Public Hospitals, Aix-Marseille University, Marseille, France.,Department of Accident and Emergency, Andrée Rosemon Hospital, Cayenne, French Guiana, France
| | - Philippe Minodier
- Department of Pediatric Emergency Medicine, North Hospital, Marseille, France
| | - Anicet Sika
- Department of Pediatric Surgery, Andrée Rosemon Hospital, French Guiana, Cayenne, France
| | - Thierry Basset
- Department of Pediatric Surgery, Andrée Rosemon Hospital, French Guiana, Cayenne, France
| | - Hervé Seligmann
- URMITE "Research Unit on Infectious and Emerging Diseases", Inserm 1095, CNRS 7278, IRD 198, UMR 63, Institut Hospitalo-Universitaire Méditerranée-Infection, APHM Public Hospitals, Aix-Marseille University, Marseille, France
| | - Anne Terraz
- Department of Public Health, Inserm CIC 1424, Andrée Rosemon Hospital, Cayenne, French Guiana, France
| | - Magalie Demar
- Department of Microbiology, Andrée Rosemon Hospital, Cayenne, French Guiana, France
| | - Jacques Pochard
- Department of Pediatrics, Centre Médico-chirurgical de Kourou, Kourou, French Guiana, France
| | - Jérôme Clouzeau
- Department of Pediatrics, Centre Hospitalier de l'Ouest Guyanais, Saint-Laurent du Maroni, French Guiana, France
| | - Pierre-Edouard Fournier
- URMITE "Research Unit on Infectious and Emerging Diseases", Inserm 1095, CNRS 7278, IRD 198, UMR 63, Institut Hospitalo-Universitaire Méditerranée-Infection, APHM Public Hospitals, Aix-Marseille University, Marseille, France
| | - Narcisse Elenga
- Department of Pediatrics, Andrée Rosemon Hospital, French Guiana, Cayenne, France
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Seligmann H, Warthi G. Genetic Code Optimization for Cotranslational Protein Folding: Codon Directional Asymmetry Correlates with Antiparallel Betasheets, tRNA Synthetase Classes. Comput Struct Biotechnol J 2017; 15:412-424. [PMID: 28924459 PMCID: PMC5591391 DOI: 10.1016/j.csbj.2017.08.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 07/20/2017] [Accepted: 08/05/2017] [Indexed: 12/14/2022] Open
Abstract
A new codon property, codon directional asymmetry in nucleotide content (CDA), reveals a biologically meaningful genetic code dimension: palindromic codons (first and last nucleotides identical, codon structure XZX) are symmetric (CDA = 0), codons with structures ZXX/XXZ are 5'/3' asymmetric (CDA = - 1/1; CDA = - 0.5/0.5 if Z and X are both purines or both pyrimidines, assigning negative/positive (-/+) signs is an arbitrary convention). Negative/positive CDAs associate with (a) Fujimoto's tetrahedral codon stereo-table; (b) tRNA synthetase class I/II (aminoacylate the 2'/3' hydroxyl group of the tRNA's last ribose, respectively); and (c) high/low antiparallel (not parallel) betasheet conformation parameters. Preliminary results suggest CDA-whole organism associations (body temperature, developmental stability, lifespan). Presumably, CDA impacts spatial kinetics of codon-anticodon interactions, affecting cotranslational protein folding. Some synonymous codons have opposite CDA sign (alanine, leucine, serine, and valine), putatively explaining how synonymous mutations sometimes affect protein function. Correlations between CDA and tRNA synthetase classes are weaker than between CDA and antiparallel betasheet conformation parameters. This effect is stronger for mitochondrial genetic codes, and potentially drives mitochondrial codon-amino acid reassignments. CDA reveals information ruling nucleotide-protein relations embedded in reversed (not reverse-complement) sequences (5'-ZXX-3'/5'-XXZ-3').
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Affiliation(s)
- Hervé Seligmann
- Aix-Marseille Univ, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS UMR7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, Postal code 13385, France
- Dept. Ecol Evol Behav, Alexander Silberman Inst Life Sci, The Hebrew University of Jerusalem, IL-91904 Jerusalem, Israel
| | - Ganesh Warthi
- Aix-Marseille Univ, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS UMR7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, Postal code 13385, France
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El Houmami N, Bakour S, Bzdrenga J, Rathored J, Seligmann H, Robert C, Armstrong N, Schrenzel J, Raoult D, Yagupsky P, Fournier PE. Isolation and characterization of Kingella negevensis sp. nov., a novel Kingella species detected in a healthy paediatric population. Int J Syst Evol Microbiol 2017; 67:2370-2376. [PMID: 28699877 DOI: 10.1099/ijsem.0.001957] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
We herein report the isolation and characterization of 21 Gram-stain-negative strains cultivated from the oropharynx of healthy children in Israel and Switzerland. Initially described as small colony variants of Kingella kingae, phenotypic analysis, biochemical analysis, phylogenetic analysis based on sequencing of the partial 16S rRNA gene and five housekeeping genes (abcZ, adk, G6PD, groEL and recA), and whole genome sequencing and comparison between members of the genera Kingella and Neisseria provided evidence for assigning them to the genus Kingella. Cellular fatty acids included important amounts of C12 : 0, C14 : 0, C16 : 0 and C16 : 1n7. Digital DNA-DNA hybridization between the isolates Sch538T and K. kingae ATCC 23330T revealed relatedness of 19.9 %. Comparative analysis of 16S rRNA gene sequences available in GenBank allowed matches to strains isolated in the USA, suggesting a wider geographical distribution. A novel species named Kingella negevensis sp. nov. is proposed, as most strains have been isolated in the Negev, a desert region of southern Israel. The type strain is Sch538T (=CCUG 69806T=CSUR P957).
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Affiliation(s)
- Nawal El Houmami
- Aix-Marseille University, UM63, CNRS 7278, IRD 198, Inserm 1095, URMITE, Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Sofiane Bakour
- Aix-Marseille University, UM63, CNRS 7278, IRD 198, Inserm 1095, URMITE, Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Janek Bzdrenga
- Aix-Marseille University, UM63, CNRS 7278, IRD 198, Inserm 1095, URMITE, Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Jaishiram Rathored
- Aix-Marseille University, UM63, CNRS 7278, IRD 198, Inserm 1095, URMITE, Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Hervé Seligmann
- Aix-Marseille University, UM63, CNRS 7278, IRD 198, Inserm 1095, URMITE, Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Catherine Robert
- Aix-Marseille University, UM63, CNRS 7278, IRD 198, Inserm 1095, URMITE, Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Nicholas Armstrong
- Aix-Marseille University, UM63, CNRS 7278, IRD 198, Inserm 1095, URMITE, Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Jacques Schrenzel
- Hôpitaux Universitaires de Genève, Service of Infectious Diseases and Service of Laboratory Medicine, Geneva, Switzerland
| | - Didier Raoult
- Aix-Marseille University, UM63, CNRS 7278, IRD 198, Inserm 1095, URMITE, Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Pablo Yagupsky
- Clinical Microbiology Laboratory, Soroka University Medical Center, Beer-Sheva, Israel
| | - Pierre-Edouard Fournier
- Aix-Marseille University, UM63, CNRS 7278, IRD 198, Inserm 1095, URMITE, Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
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Abstract
We present an evolutionary hypothesis assuming that signals marking nucleotide synthesis (DNA replication and RNA transcription) evolved from multi- to unidimensional structures, and were carried over from transcription to translation. This evolutionary scenario presumes that signals combining secondary and primary nucleotide structures are evolutionary transitions. Mitochondrial replication initiation fits this scenario. Some observations reported in the literature corroborate that several signals for nucleotide synthesis function in translation, and vice versa. (a) Polymerase-induced frameshift mutations occur preferentially at translational termination signals (nucleotide deletion is interpreted as termination of nucleotide polymerization, paralleling the role of stop codons in translation). (b) Stem-loop hairpin presence/absence modulates codon-amino acid assignments, showing that translational signals sometimes combine primary and secondary nucleotide structures (here codon and stem-loop). (c) Homopolymer nucleotide triplets (AAA, CCC, GGG, TTT) cause transcriptional and ribosomal frameshifts. Here we find in recently described human mitochondrial RNAs that systematically lack mono-, dinucleotides after each trinucleotide (delRNAs) that delRNA triplets include 2x more homopolymers than mitogenome regions not covered by delRNA. Further analyses of delRNAs show that the natural circular code X (a little-known group of 20 translational signals enabling ribosomal frame retrieval consisting of 20 codons {AAC, AAT, ACC, ATC, ATT, CAG, CTC, CTG, GAA, GAC, GAG, GAT, GCC, GGC, GGT, GTA, GTC, GTT, TAC, TTC} universally overrepresented in coding versus other frames of gene sequences), regulates frameshift in transcription and translation. This dual transcription and translation role confirms for X the hypothesis that translational signals were carried over from transcriptional signals.
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Affiliation(s)
- Nawal El Houmami
- URMITE, Aix Marseille Université UM63, CNRS 7278, IRD 198, INSERM 1095, IHU - Méditerranée Infection Marseille, France
| | - Hervé Seligmann
- URMITE, Aix Marseille Université UM63, CNRS 7278, IRD 198, INSERM 1095, IHU - Méditerranée Infection Marseille, France
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El Houmami N, Minodier P, Bouvier C, Seligmann H, Jouve JL, Raoult D, Fournier PE. Primary subacute epiphyseal osteomyelitis caused by Mycobacterium species in young children: a modern diagnostic approach. Eur J Clin Microbiol Infect Dis 2017; 36:771-777. [PMID: 28054229 DOI: 10.1007/s10096-016-2886-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 12/19/2016] [Indexed: 11/30/2022]
Abstract
Primary epiphyseal subacute osteomyelitis (PESAO) caused by Mycobacterium species in young children is poorly recognized. We aimed to define the spectrum of this uncommon condition and to propose a novel diagnostic approach. We performed a systematic review of the literature on the PubMed website by selecting all reports of isolated infantile PESAO caused by Mycobacterium species since 1975. We identified 350 citations, of which 174 were assessed for eligibility based on title and abstract. The full text of 81 eligible citations was screened, and relevant data of 15 children under 4 years of age with mycobacterial PESAO were extracted. These data were pooled with those from our Institution. Data from 16 children were reviewed. The median age was 16 ± 7 months and the male:female ratio 1.7. The knee was the most common infection site (94%). The diagnosis of mycobacterial disease was delayed in all cases (range, 2 weeks to 6 months), and initially presumed by histology in 15 children (94%). Microbiologically proven diagnosis was confirmed by bone cultures in 8 of the 15 children (53%), and by specific PCR in 2 of the 3 culture-negative bone specimens (67%). Three children experienced long-term orthopedic complications despite surgical drainage and prolonged antimycobacterial regimens. All recently reported cases came from high-burden tuberculosis areas. Mycobacterium species contribute to the burden of infantile PESAO in endemic tuberculosis areas and may cause growth disturbances. We argue in favor of the early recognition of mycobacterial disease by specific molecular assays in children with infantile PESAO living in high-burden areas.
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Affiliation(s)
- N El Houmami
- Research Unit on Infectious and Emerging Tropical Diseases (URMITE), Inserm U1095, UMR 63, CNRS 7278, IRD 198, University Hospital Institute Méditerranée Infection, Aix-Marseille University, Marseille, France. .,Department of Pediatric Orthopedics, University La Timone Children's Hospital, Aix-Marseille University, Marseille, France.
| | - P Minodier
- Department of Pediatric Emergency Medicine, University North Hospital, APHM Public Hospitals, Aix-Marseille University, Marseille, France
| | - C Bouvier
- Department of Pathology, University La Timone Hospital, APHM Public Hospitals, Aix-Marseille University, Marseille, France
| | - H Seligmann
- Research Unit on Infectious and Emerging Tropical Diseases (URMITE), Inserm U1095, UMR 63, CNRS 7278, IRD 198, University Hospital Institute Méditerranée Infection, Aix-Marseille University, Marseille, France
| | - J-L Jouve
- Department of Pediatric Orthopedics, University La Timone Children's Hospital, Aix-Marseille University, Marseille, France
| | - D Raoult
- Research Unit on Infectious and Emerging Tropical Diseases (URMITE), Inserm U1095, UMR 63, CNRS 7278, IRD 198, University Hospital Institute Méditerranée Infection, Aix-Marseille University, Marseille, France
| | - P-E Fournier
- Research Unit on Infectious and Emerging Tropical Diseases (URMITE), Inserm U1095, UMR 63, CNRS 7278, IRD 198, University Hospital Institute Méditerranée Infection, Aix-Marseille University, Marseille, France
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Seligmann H. Natural mitochondrial proteolysis confirms transcription systematically exchanging/deleting nucleotides, peptides coded by expanded codons. J Theor Biol 2016; 414:76-90. [PMID: 27899286 DOI: 10.1016/j.jtbi.2016.11.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 11/11/2016] [Accepted: 11/22/2016] [Indexed: 12/19/2022]
Abstract
Protein sequences have higher linguistic complexities than human languages. This indicates undeciphered multilayered, overprinted information/genetic codes. Some superimposed genetic information is revealed by detections of transcripts systematically (a) exchanging nucleotides (nine symmetric, e.g. A<->C, fourteen asymmetric, e.g. A->C->G->A, swinger RNAs) translated according to tri-, tetra- and pentacodons, and (b) deleting mono-, dinucleotides after each trinucleotide (delRNAs). Here analyses of two independent proteomic datasets considering natural proteolysis confirm independently translation of these non-canonical RNAs, also along tetra- and pentacodons, increasing coverage of putative, cryptically encoded proteins. Analyses assuming endoproteinase GluC and elastase digestions (cleavages after residues D, E, and A, L, I, V, respectively) detect additional peptides colocalizing with detected non-canonical RNAs. Analyses detect fewer peptides matching GluC-, elastase- than trypsin-digestions: artificial trypsin-digestion outweighs natural proteolysis. Results suggest occurrences of complete proteins entirely matching non-canonical, superimposed encoding(s). Protein-coding after bijective transformations could explain genetic code symmetries, such as along Rumer's transformation.
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Affiliation(s)
- Hervé Seligmann
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Émergentes, Faculté de Médecine, URMITE CNRS-IRD 198 UMER 6236, IHU (Institut Hospitalo-Universitaire), Aix-Marseille University, Marseille, France.
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Seligmann H. Natural chymotrypsin-like-cleaved human mitochondrial peptides confirm tetra-, pentacodon, non-canonical RNA translations. Biosystems 2016; 147:78-93. [PMID: 27477600 DOI: 10.1016/j.biosystems.2016.07.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Revised: 07/15/2016] [Accepted: 07/26/2016] [Indexed: 12/22/2022]
Abstract
Mass spectra of human mitochondrial peptides match non-canonical transcripts systematically (a) deleting mono/dinucleotides after trinucleotides (delRNA), (b) exchanging nucleotides (swinger RNA), translated according to tri, (c) tetra- and pentacodons (codons expanded by a 4th (and 5th) silent nucleotide(s)). Swinger transcriptions are 23 bijective transformations, nine symmetric (X<->Y, e.g. A<->C) and fourteen asymmetric exchanges (X->Y->Z->X, e.g. A->C->G->A). Here, proteomic analyses assuming cleavage after W,Y, F (chymotrypsin-like, for trypsinized samples) detect fewer chymotrypsinized than trypsinized peptides. Detected non-canonical peptides map preferentially on detected non-canonical RNAs for chymotrypsinized peptides, as previously found for trypsinized peptides. This suggests residual natural chymotrypsin-like digestion detectable within experimentally trypsinized peptide data. Some trypsinized peptides are detected twice, by analyses assuming trypsin, and those assuming chymotrypsin cleavages. They have higher spectra counts than peptides detected only once, meaning that abundant peptides are more frequently detected, but detection certainties resemble those for peptides detected only once. Analyses assuming 'incorrect' digestions are inadequate negative controls for digestion enzymes naturally active in biological samples. Chymotrypsin-analyses confirm non-canonical transcriptions/translations independently of results obtained assuming trypsinization, increase non-canonical peptidome coverage, indicating mitogenome-encoding of yet undetected proteins.
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Affiliation(s)
- Hervé Seligmann
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Émergentes, Faculté de Médecine, Université d'Aix-Marseille, URMITE CNRS-IRD 198 UMER 6236, Marseille, France.
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Barthélémy RM, Seligmann H. Cryptic tRNAs in chaetognath mitochondrial genomes. Comput Biol Chem 2016; 62:119-32. [DOI: 10.1016/j.compbiolchem.2016.04.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 04/11/2016] [Accepted: 04/14/2016] [Indexed: 12/14/2022]
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Seligmann H, Raoult D. Unifying view of stem–loop hairpin RNA as origin of current and ancient parasitic and non-parasitic RNAs, including in giant viruses. Curr Opin Microbiol 2016; 31:1-8. [DOI: 10.1016/j.mib.2015.11.004] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 11/19/2015] [Accepted: 11/25/2015] [Indexed: 12/20/2022]
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Seligmann H. Translation of mitochondrial swinger RNAs according to tri-, tetra- and pentacodons. Biosystems 2015; 140:38-48. [PMID: 26723232 DOI: 10.1016/j.biosystems.2015.11.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 11/08/2015] [Accepted: 11/23/2015] [Indexed: 10/22/2022]
Abstract
Transcriptomes and proteomes include RNA and protein fragments not matching regular transcription/translation. Some 'non-canonical' mitochondrial transcripts match mitogenomes after assuming one among 23 systematic exchanges between nucleotides, producing swinger RNAs (nine symmetric, X↔Y, example C↔T; 14 asymmetric, X→Y→Z→X, example A→T→G→A) in GenBank's EST database. Here, reanalyzes of (a) public human mitochondrial transcriptome data (Illumina: RNA-seq) allowed to detect mitochondrial swinger RNAs for all 23 exchanges and (b) independent public human mitochondrial trypsinized proteomic mass spectrometry data allowed to detect peptides predicted from translation of parts of swinger-transformed mitogenomes covered by detected swinger reads. RNA-seq and previous EST swinger transcript data converge. Swinger RNA translation frequently inserts various amino acids at stop codons. Swinger RNA-peptide associations exist also for peptides matching systematically frameshifting translation, peptides entirely coded by tetra- and pentacodons (regular codons expanded by silent mononucleotides at 4th, and silent dinucleotides at 4th and 5th position(s), respectively). Swinger peptides differ from regular mitochondrial proteins: not membrane embedded, reflect warmer, anaerobic, low resource conditions, reminding a free-living ancestor. Tetra- and pentacoded peptides associate with low, high GC contents, respectively, suggesting expanded codon translations associate with thermic stresses. Results confirm experimentally predicted swinger, tetra- and pentacoded mitochondrial peptides, increasing mitogenomic coding density.
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Affiliation(s)
- Hervé Seligmann
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Émergentes, Faculté de Médecine, URMITE CNRS-IRD 198 UMER 6236, Université de la Méditerranée, Marseille, France.
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Seligmann H. Codon expansion and systematic transcriptional deletions produce tetra-, pentacoded mitochondrial peptides. J Theor Biol 2015; 387:154-65. [PMID: 26456204 DOI: 10.1016/j.jtbi.2015.09.030] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 09/28/2015] [Accepted: 09/30/2015] [Indexed: 11/28/2022]
Abstract
Genes include occasionally isolated codons with a fourth (and fifth) silent nucleotide(s). Assuming tetracodons, translated hypothetical peptides align with regular GenBank proteins; predicted tetracodons coevolve with predicted tRNAs with expanded anticodons in each mammal, Drosophila and Lepidosauria mitogenomes, GC contents and with lepidosaurian body temperatures, suggesting that expanded codons are an adaptation of translation to high temperature. Hypothetically, continuous stretches of tetra- and pentacodons code for peptides. Both systematic nucleotide deletions during transcription, and translation by tRNAs with expanded anticodons could produce these peptides. Reanalyses of human nanoLc mass spectrometry peptidome data detect numerous tetra- and pentapeptides translated from the human mitogenome. These map preferentially on (BLAST-detected) human RNAs matching the human mitogenome, assuming systematic mono- and dinucleotide deletions after each third nucleotide (delRNAs). Translation by expanded anticodons is incompatible with silent nucleotides in the midst rather than at codon 3' extremity. More than 1/3 of detected tetra- and pentapeptides assume silent positions at codon extremity, suggesting that both mechanisms, regular translation of delRNAs and translation of regular RNAs by expanded anticodons, produce this peptide subgroup. Results show that systematically deleting polymerization occurs, and confirm serial translation of expanded codons. Non-canonical transcriptions and translations considerably expand the coding potential of DNA and RNA sequences.
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Affiliation(s)
- Hervé Seligmann
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Émergentes, Faculté de Médecine, URMITE CNRS-IRD 198 UMER 6236, Université de la Méditerranée, 13385 Marseille, France.
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Seligmann H. Systematic exchanges between nucleotides: Genomic swinger repeats and swinger transcription in human mitochondria. J Theor Biol 2015; 384:70-7. [PMID: 26297891 DOI: 10.1016/j.jtbi.2015.07.036] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 07/11/2015] [Accepted: 07/24/2015] [Indexed: 10/23/2022]
Abstract
Chargaff׳s second parity rule, quasi-equal single strand frequencies for complementary nucleotides, presumably results from insertion of repeats and inverted repeats during sequence genesis. Vertebrate mitogenomes escape this rule because repeats are counterselected: their hybridization produces loop bulges whose deletion is deleterious. Some DNA/RNA sequences match mitogenomes only after assuming one among 23 systematic nucleotide exchanges (swinger DNA/RNA: nine symmetric, e.g. A ↔ C; and 14 asymmetric, e.g. A → C → G → A). Swinger-transformed repeats do not hybridize, escaping selection against deletions due to bulge formation. Blast analyses of the human mitogenome detect swinger repeats for all 23 swinger types, more than in randomized sequences with identical length and nucleotide contents. Mean genomic swinger repeat lengths increase with observed human swinger RNA frequencies: swinger repeat and swinger RNA productions appear linked, perhaps by swinger RNA retrotranscription. Mean swinger repeat lengths are proportional to reading frame retrievability, post-swinger transformation, by the natural circular code. Genomic swinger repeats confirm at genomic level, independently of swinger RNA detection, occurrence of swinger polymerizations. They suggest that repeats, and swinger repeats in particular, contribute to genome genesis.
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Affiliation(s)
- Hervé Seligmann
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Émergentes, Faculté de Médecine, URMITE CNRS-IRD 198 UMER 6236, Université Aix-Marseille, Marseille, France.
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Seligmann H. Sharp switches between regular and swinger mitochondrial replication: 16S rDNA systematically exchanging nucleotides A<->T+C<->G in the mitogenome of Kamimuria wangi. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2440-6. [PMID: 25865623 DOI: 10.3109/19401736.2015.1033691] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Swinger DNAs are sequences whose homology with known sequences is detected only by assuming systematic exchanges between nucleotides. Nine symmetric (X<->Y, i.e. A<->C) and fourteen asymmetric (X->Y->Z, i.e. A->C->G) exchanges exist. All swinger DNA previously detected in GenBank follow the A<->T+C<->G exchange, while mitochondrial swinger RNAs distribute among different swinger types. Here different alignment criteria detect 87 additional swinger mitochondrial DNAs (86 from insects), including the first swinger gene embedded within a complete genome, corresponding to the mitochondrial 16S rDNA of the stonefly Kamimuria wangi. Other Kamimuria mt genome regions are "regular", stressing unanswered questions on (a) swinger polymerization regulation; (b) swinger 16S rDNA functions; and (c) specificity to rDNA, in particular 16S rDNA. Sharp switches between regular and swinger replication, together with previous observations on swinger transcription, suggest that swinger replication might be due to a switch in polymerization mode of regular polymerases and the possibility of swinger-encoded information, predicted in primordial genes such as rDNA.
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Affiliation(s)
- Hervé Seligmann
- a Unité de Recherche sur les Maladies Infectieuses et Tropicales Émergentes, Faculté de Médecine, URMITE CNRS-IRD 198 UMR 6236, Université d'Aix-Marseille , Marseille , France
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Seligmann H. Mitochondrial swinger replication: DNA replication systematically exchanging nucleotides and short 16S ribosomal DNA swinger inserts. Biosystems 2014; 125:22-31. [PMID: 25283331 DOI: 10.1016/j.biosystems.2014.09.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 09/08/2014] [Accepted: 09/29/2014] [Indexed: 11/27/2022]
Abstract
Assuming systematic exchanges between nucleotides (swinger RNAs) resolves genomic 'parenthood' of some orphan mitochondrial transcripts. Twenty-three different systematic nucleotide exchanges (bijective transformations) exist. Similarities between transcription and replication suggest occurrence of swinger DNA. GenBank searches for swinger DNA matching the 23 swinger versions of human and mouse mitogenomes detect only vertebrate mitochondrial swinger DNA for swinger type AT+CG (from five different studies, 149 sequences) matching three human and mouse mitochondrial genes: 12S and 16S ribosomal RNAs, and cytochrome oxidase subunit I. Exchange A<->T+C<->G conserves self-hybridization properties, putatively explaining swinger biases for rDNA, against protein coding genes. Twenty percent of the regular human mitochondrial 16S rDNA consists of short swinger repeats (from 13 exchanges). Swinger repeats could originate from recombinations between regular and swinger DNA: duplicated mitochondrial genes of the parthenogenetic gecko Heteronotia binoei include fewer short A<->T+C<->G swinger repeats than non-duplicated mitochondrial genomes of that species. Presumably, rare recombinations between female and male mitochondrial genes (and in parthenogenetic situations between duplicated genes), favors reverse-mutations of swinger repeat insertions, probably because most inserts affect negatively ribosomal function. Results show that swinger DNA exists, and indicate that swinger polymerization contributes to the genesis of genetic material and polymorphism.
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Affiliation(s)
- Hervé Seligmann
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Émergentes, Faculté de Médecine, URMITE CNRS-IRD 198 UMER 6236, Université de la Méditerranée, Marseille, France.
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Seligmann H. Species radiation by DNA replication that systematically exchanges nucleotides? J Theor Biol 2014; 363:216-22. [PMID: 25192628 DOI: 10.1016/j.jtbi.2014.08.036] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 08/14/2014] [Accepted: 08/19/2014] [Indexed: 11/28/2022]
Abstract
RNA and DNA syntheses share many properties. Therefore, the existence of 'swinger' RNAs, presumed 'orphan' transcripts matching genomic sequences only if transcription systematically exchanged nucleotides, suggests replication producing swinger DNA. Transcripts occur in many short-lived copies, the few cellular DNA molecules are long-lived. Hence pressures for functional swinger DNAs are greater than for swinger RNAs. Protein coding properties of swinger sequences differ from original sequences, suggesting rarity of corresponding swinger DNA. For genes producing structural RNAs, such as tRNAs and rRNAs, three exchanges (A<->T, C<->G and A<->T+C<->G) conserve self-hybridization properties. All nuclear eukaryote swinger DNA sequences detected in GenBank are for rRNA genes assuming A<->T+C<->G exchanges. In brachyuran crabs, 25 species had A<->T+C<->G swinger 18S rDNA, all matching the reverse-exchanged version of regular 18S rDNA of a related species. In this taxon, swinger replication of 18S rDNA apparently associated with, or even resulted in species radiation. A<->T+C<->G transformation doesn't invert sequence direction, differing from inverted repeats. Swinger repeats (detectable only assuming swinger transformations, A<->T+C<->G swinger repeats most frequent) within regular human rRNAs, independently confirm swinger polymerizations for most swinger types. Swinger replication might be an unsuspected molecular mechanism for ultrafast speciation.
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Affiliation(s)
- Hervé Seligmann
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Émergentes, Faculté de Médecine, URMITE CNRS-IRD 198 UMER 6236, Université de la Méditerranée, Marseille, France.
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Michel CJ, Seligmann H. Bijective transformation circular codes and nucleotide exchanging RNA transcription. Biosystems 2014; 118:39-50. [PMID: 24565870 DOI: 10.1016/j.biosystems.2014.02.002] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 02/06/2014] [Accepted: 02/12/2014] [Indexed: 10/25/2022]
Abstract
The C(3) self-complementary circular code X identified in genes of prokaryotes and eukaryotes is a set of 20 trinucleotides enabling reading frame retrieval and maintenance, i.e. a framing code (Arquès and Michel, 1996; Michel, 2012, 2013). Some mitochondrial RNAs correspond to DNA sequences when RNA transcription systematically exchanges between nucleotides (Seligmann, 2013a,b). We study here the 23 bijective transformation codes ΠX of X which may code nucleotide exchanging RNA transcription as suggested by this mitochondrial observation. The 23 bijective transformation codes ΠX are C(3) trinucleotide circular codes, seven of them are also self-complementary. Furthermore, several correlations are observed between the Reading Frame Retrieval (RFR) probability of bijective transformation codes ΠX and the different biological properties of ΠX related to their numbers of RNAs in GenBank's EST database, their polymerization rate, their number of amino acids and the chirality of amino acids they code. Results suggest that the circular code X with the functions of reading frame retrieval and maintenance in regular RNA transcription, may also have, through its bijective transformation codes ΠX, the same functions in nucleotide exchanging RNA transcription. Associations with properties such as amino acid chirality suggest that the RFR of X and its bijective transformations molded the origins of the genetic code's machinery.
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Affiliation(s)
- Christian J Michel
- Equipe de Bioinformatique Théorique, ICube, Université de Strasbourg, CNRS, 300 Boulevard Sébastien Brant, 67400 Illkirch, France.
| | - Hervé Seligmann
- National Natural History Museum Collections, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel; Department of Life Sciences, Ben Gurion University, 84105 Beer Sheva, Israel.
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Seligmann H, Labra A. Tetracoding increases with body temperature in Lepidosauria. Biosystems 2013; 114:155-63. [DOI: 10.1016/j.biosystems.2013.09.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 09/04/2013] [Accepted: 09/05/2013] [Indexed: 10/26/2022]
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