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Gwennaele Fichant - One of the best experts on this subject based on the ideXlab platform.
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rna processing machineries in archaea the 5 3 exoribonuclease arnase j of the β casp family is engaged specifically with the helicase ash ski2 and the 3 5 exoribonucleolytic rna exosome machinery
Nucleic Acids Research, 2020Co-Authors: Duy Khanh Phung, Clarisse Etienne, Manon Batista, Yann Moalic, Sébastien Laurent, Sophie Liuu, Violette Morales, Mohamed Jebbar, Petra Langendijkgenevaux, Gwennaele FichantAbstract:A network of RNA helicases, endoribonucleases and exoribonucleases regulates the quantity and quality of cellular RNAs. To date, mechanistic studies focussed on bacterial and eukaryal systems due to the challenge of identifying the main drivers of RNA decay and processing in Archaea. Here, our data support that aRNase J, a 5'-3' exoribonuclease of the β-CASP family conserved in Euryarchaeota, engages specifically with a Ski2-like helicase and the RNA exosome to potentially exert control over RNA surveillance, at the vicinity of the ribosome. Proteomic landscapes and direct protein-protein interaction analyses, strengthened by comprehensive phylogenomic studies demonstrated that aRNase J interplay with ASH-Ski2 and a cap exosome subunit. Finally, Thermococcus barophilus whole-cell extract fractionation experiments provide evidences that an aRNase J/ASH-Ski2 complex might exist in vivo and hint at an association of aRNase J with the ribosome that is emphasised in absence of ASH-Ski2. Whilst aRNase J homologues are found among bacteria, the RNA exosome and the Ski2-like RNA helicase have eukaryotic homologues, underlining the mosaic aspect of archaeal RNA machines. Altogether, these results suggest a fundamental role of β-CASP RNase/helicase complex in archaeal RNA metabolism.
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RNA processing machineries in Archaea: the 5′-3′ exoribonuclease aRNase J of the β-CASP family is engaged specifically with the helicase ASH-Ski2 and the 3′-5′ exoribonucleolytic RNA exosome machinery
Nucleic Acids Research, 2020Co-Authors: Duy Khanh Phung, Clarisse Etienne, Manon Batista, Petra Langendijk-genevaux, Yann Moalic, Sébastien Laurent, Sophie Liuu, Violette Morales, Mohamed Jebbar, Gwennaele FichantAbstract:A network of RNA helicases, endoribonucleases and exoribonucleases regulates the quantity and quality of cellular RNAs. To date, mechanistic studies focussed on bacterial and eukaryal systems due to the challenge of identifying the main drivers of RNA decay and processing in Archaea. Here, our data support that aRNase J, a 5'-3' exoribonuclease of the β-CASP family conserved in Euryarchaeota, engages specifically with a Ski2-like helicase and the RNA exosome to potentially exert control over RNA surveillance, at the vicinity of the ribosome. Proteomic landscapes and direct protein-protein interaction analyses, strengthened by comprehensive phylogenomic studies demonstrated that aRNase J interplay with ASH-Ski2 and a cap exosome subunit. Finally, Thermococcus barophilus whole-cell extract fractionation experiments provide evidences that an aRNase J/ASH-Ski2 complex might exist in vivo and hint at an association of aRNase J with the ribosome that is emphasised in absence of ASH-Ski2. Whilst aRNase J homologues are found among bacteria, the RNA exosome and the Ski2-like RNA helicase have eukaryotic homologues, underlining the mosaic aspect of archaeal RNA machines. Altogether, these results suggest a fundamental role of β-CASP RNase/helicase complex in archaeal RNA metabolism.
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rna processing machineries in archaea the 5 3 exoribonuclease arnase j of the β casp family is engaged specifically with the helicase ash ski2 and the 3 5 exoribonucleolytic rna exosome machinery
bioRxiv, 2019Co-Authors: Duy Khanh Phung, Clarisse Etienne, Manon Batista, Yann Moalic, Sébastien Laurent, Violette Morales, Mohamed Jebbar, Gwennaele Fichant, Petra Langendijkgenevaux, Marie BouvierAbstract:A network of RNA helicases, endoribonucleases, and exoribonucleases regulates the quantity and quality of cellular RNAs. To date, mechanistic studies focused on bacterial and eukaryal systems due to the challenge of identifying the main drivers of RNA decay and processing in Archaea. Here, our data support that aRNase J, a 5′-3′ exoribonuclease of the β-CASP family conserved in Euryarchaea, engages specifically with a Ski2-like helicase and the RNA exosome to potentially exert control over RNA surveillance, and that this occurs in the vicinity of the ribosome. Proteomic landscapes and direct protein-protein interaction analyses demonstrated that aRNase J interplay with ASH-Ski2 and the Csl4 cap exosome subunit. These in vitro data are strengthened by our phylogenomic studies showing a taxonomic co-distribution of aRNase J and ASH-Ski2 among the archaeal phylogeny. Finally, our T. barophilus whole-cell extract fractionation experiments provide evidences that an aRNase J/ASH-Ski2 complex might exist in vivo and hint at an association of aRNase J with the ribosome or polysomes that is stressed in absence of ASH-Ski2. While aRNase J homologues are found among bacteria, the RNA exosome and the Ski2-like RNA helicase have eukaryotic homologues, underlining the mosaic aspect of archaeal RNA machines. Altogether, these results suggest, for the first time, a fundamental role of β-CASP RNase/helicase complex in archaeal RNA metabolism. Finally, our results position aRNase J at the junction of RNA surveillance and translation processes, thus opening new perspectives and evolutionary scenario on RNA processing players in Archaea.
Alan R Fersht - One of the best experts on this subject based on the ideXlab platform.
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Physical-organic molecular biology: pathway and stability of protein folding
2014Co-Authors: Alan R Fersht, Mark Bycroft, Andreas Matouschek, James T Kellis, Luis SerranoAbstract:Abstract- Protein engineering, the design and synthesis of novel proteins by genetic engineering, allows complex problems in molecular biology to be studied by structure-activity relationships in an analogous manner to the application of physical-organic chemistry to simple organic molecules. This approach has been applied to study the folding pathway and stability of Barnase, the RNAse from Bacillus amyloliquefaciens. The strategy is two fold: i, Mutations are made which remove defined interactions that stabilise Barnase. The changes in stability on mutation are measured from the changes in free energy of unfolding of the protein. In this way a library of interaction energies is achieved. ii, Kinetic measurements are made on the folding and unfolding of wild-type and mutant proteins. Combination of kinetic and thermodynamic data enables the roles of side chains in the stabilization of the final, transition and intermediate states of the protein to be measured. This gives the order of events during protein folding. The protein engineering experiments are corroborated by N M R studies of hydrogen exchange during the folding process. The combined procedures show that the folding is a multiphasic process in which secondary structure is formed very early on. Formation of the hydrophobic core by docking helix and sheet is (partly) rate determining
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an irregular beta bulge common to a group of bacterial rnases is an important determinant of stability and function in Barnase
Journal of Molecular Biology, 1999Co-Authors: Douglas D Axe, Nicholas W Foster, Alan R FershtAbstract:Single amino acid residue substitutions rarely destroy the structural integrity of proteins. Substitution of glycine residues, however, is among the few sorts of alterations that can have such an effect. Here, we seek to understand what accounts for the extreme functional impairment of the bacterial ribonuclease Barnase upon substitution of Gly52 or Gly53. We find that inactivation is caused by overall disruption of the folded state that manifests itself in three ways: (1) dramatically reduced stability (by 5.2 to 8.4 kcal mol-1 for mutants showing inactivation in vivo); (2) progressive loss of folded-state activity with increasing temperature, indicating a less well formed fold; and (3) substantial proteolytic degradation of mutant enzymes in vivo. Examination of two deletion mutants, missing either Gly53 or Asp54, shows that the irregular beta-bulge formed by these two residues is of vital importance to the structural integrity of Barnase. The parallel behaviour of mutants carrying replacements of either of the two glycine residues therefore appears to arise from a common mechanism: disruption of local structure at the beta-bulge. The importance of this structural element to the function of Barnase raises the question of whether it may be present in other RNases. The Streptomyces enzymes RNase Sa and RNase St differ considerably from Barnase in both sequence and structure, yet both show significant sequence similarity to Barnase over a region beginning at Gly53. Structural comparison indicates that the Streptomyces enzymes do have the Barnase-like irregular beta-bulge, making this an important characteristic feature of a group of bacterial ribonucleases. The sensitivity of this feature demonstrates that detailed aspects of local structure may have a major role in determining the overall structural and functional properties of an enzyme, even where no explanation for this role is readily apparent. If this is a general characteristic of the structure-function relationship, it may pose a formidable obstacle to the de novo design of new enzymes.
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exploring the folding funnel of a polypeptide chain by biophysical studies on protein fragments
Journal of Molecular Biology, 1999Co-Authors: Jose L Neira, Alan R FershtAbstract:Abstract We are examining possible roles of native and non-native interactions in early events in protein folding by a systematic analysis of the structures of fragments of proteins whose folding pathways are well characterised. Seven fragments of the 110-residue protein Barnase, corresponding to the progressive elongation from its N terminus, have been characterised by a battery of biophysical and spectroscopic methods. Barnase is a multi-modular protein that folds via an intermediate in which the C-terminal region of its major α-helix (α-helix1, residues Thr6-His18) is substantially formed as is also its anti-parallel β-sheet, centred around a β-hairpin (residues Ser92-Leu95). Fragments up to, and including, residues 1-95 (fragment B95), appeared to be mainly disordered, although a small amount of helical secondary structure in each was inferred from far-UV CD experiments, and fluorescence studies indicated some native-like tertiary interactions in B95. The largest fragment (residues 1-105, B105) is compactly folded. The secondary structure in α-helix1 in the seven fragments was found by NMR to increase with increasing chain length faster than the build-up of tertiary interactions, indicating that α-helix1 is being stabilised by non-native interactions. This behaviour contrasts with that in fragments of the 64-residue chymotrypsin inhibitor 2 (CI2), in which tertiary and secondary structures build up in parallel with increasing length. CI2 consists of a single module of structure that folds without a detectable intermediate. The largest fragment of Barnase, B105, has interactions that resemble its folding intermediate, whereas one of the largest fragments of CI2 (residues 1-60) resembles the folding transition state. The folding pathways of both proteins are consistent with a scheme in which there are low levels of native-like secondary structure in the denatured state that become stabilised by long-range interactions as folding proceeds. Neither protein forms a stable fold when lacking the last ten residues at the C terminus. Since at least 20 amino acid residues are bound to the ribosome during protein biosynthesis, these small proteins do not fold until they have left the ribosome, and so the studies of the folding of such proteins in vitro may be relevant to their folding in vivo, especially as the molecular chaperone GroEL binds only weakly to denatured CI2 and does not discernibly alter the folding mechanism of Barnase.
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combined molecular dynamics and φ value analysis of structure reactivity relationships in the transition state and unfolding pathway of Barnase structural basis of hammond and anti hammond effects
Journal of the American Chemical Society, 1998Co-Authors: Valerie Daggett, And Aijun Li, Alan R FershtAbstract:The folding/unfolding pathway of Barnase has been analyzed using a method similar to the classical Bronsted-β approach: Φ-value analysis. Kinetic and equilibrium measurements on the folding/unfolding of over 100 designed mutants have led to a residue-by-residue description of the transition state. The transition state responds to mutation and changes in solvent in a manner analogous to both classical Hammond and anti-Hammond behavior as the energy landscape is perturbed. Here, we compare the Φ-value analysis with an explicit structural analysis of the transition state by molecular dynamics simulations of thermal denaturation of wild-type and two mutant forms of Barnase. We look for similarities in the results of experiment and simulation to provide a detailed and reliable description of the folding reaction and for differences that could point to deficiencies in the methods. In general, there is excellent agreement between simulation and experiment, with a correlation coefficient of 0.93 between observed...
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thermodynamics of the interaction of Barnase and barstar changes in free energy versus changes in enthalpy on mutation
Journal of Molecular Biology, 1997Co-Authors: Christian Frisch, Gideon Schreiber, Christopher M Johnson, Alan R FershtAbstract:Abstract We have studied the thermodynamics of the interaction between the ribonuclease Barnase and its natural polypeptide inhibitor barstar. The contribution of specific residues and interactions within the Barnase-barstar interface to the enthalpy of binding has been examined using isothermal titration calorimetry and protein engineering. The enthalpy of association of the wild-type proteins is −18.9 (±0.1) kcal/mol at pH 8 and at 25°C. The enthalpy of binding remains favourable for 31 different combinations of mutations in the interface. The effects on the binding enthalpy upon replacing a side-chain involved in the interaction of Barnase and barstar are, however, always unfavourable and in most cases larger than the effects on the free energy of binding. Interaction enthalpies calculated by double mutant cycle analysis are in some cases much larger than the interaction free energies. The interaction enthalpies for complexes between different Barnase mutants with amino acid substitutions of the general base residue glutamic acid 73 and a barstar variant (D39A) vary by as much as 8.3 kcal/mol while the coupling free energies differ only by 1 kcal/mol. The use of enthalpies for the analysis of structure-activity relationships appears to be complicated by enthalpy-entropy compensation of weak intermolecular interactions. These tend to cancel out in measurements of free energy, which is thus the preferred quantity for simple analysis of interactions.
Duy Khanh Phung - One of the best experts on this subject based on the ideXlab platform.
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rna processing machineries in archaea the 5 3 exoribonuclease arnase j of the β casp family is engaged specifically with the helicase ash ski2 and the 3 5 exoribonucleolytic rna exosome machinery
Nucleic Acids Research, 2020Co-Authors: Duy Khanh Phung, Clarisse Etienne, Manon Batista, Yann Moalic, Sébastien Laurent, Sophie Liuu, Violette Morales, Mohamed Jebbar, Petra Langendijkgenevaux, Gwennaele FichantAbstract:A network of RNA helicases, endoribonucleases and exoribonucleases regulates the quantity and quality of cellular RNAs. To date, mechanistic studies focussed on bacterial and eukaryal systems due to the challenge of identifying the main drivers of RNA decay and processing in Archaea. Here, our data support that aRNase J, a 5'-3' exoribonuclease of the β-CASP family conserved in Euryarchaeota, engages specifically with a Ski2-like helicase and the RNA exosome to potentially exert control over RNA surveillance, at the vicinity of the ribosome. Proteomic landscapes and direct protein-protein interaction analyses, strengthened by comprehensive phylogenomic studies demonstrated that aRNase J interplay with ASH-Ski2 and a cap exosome subunit. Finally, Thermococcus barophilus whole-cell extract fractionation experiments provide evidences that an aRNase J/ASH-Ski2 complex might exist in vivo and hint at an association of aRNase J with the ribosome that is emphasised in absence of ASH-Ski2. Whilst aRNase J homologues are found among bacteria, the RNA exosome and the Ski2-like RNA helicase have eukaryotic homologues, underlining the mosaic aspect of archaeal RNA machines. Altogether, these results suggest a fundamental role of β-CASP RNase/helicase complex in archaeal RNA metabolism.
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RNA processing machineries in Archaea: the 5′-3′ exoribonuclease aRNase J of the β-CASP family is engaged specifically with the helicase ASH-Ski2 and the 3′-5′ exoribonucleolytic RNA exosome machinery
Nucleic Acids Research, 2020Co-Authors: Duy Khanh Phung, Clarisse Etienne, Manon Batista, Petra Langendijk-genevaux, Yann Moalic, Sébastien Laurent, Sophie Liuu, Violette Morales, Mohamed Jebbar, Gwennaele FichantAbstract:A network of RNA helicases, endoribonucleases and exoribonucleases regulates the quantity and quality of cellular RNAs. To date, mechanistic studies focussed on bacterial and eukaryal systems due to the challenge of identifying the main drivers of RNA decay and processing in Archaea. Here, our data support that aRNase J, a 5'-3' exoribonuclease of the β-CASP family conserved in Euryarchaeota, engages specifically with a Ski2-like helicase and the RNA exosome to potentially exert control over RNA surveillance, at the vicinity of the ribosome. Proteomic landscapes and direct protein-protein interaction analyses, strengthened by comprehensive phylogenomic studies demonstrated that aRNase J interplay with ASH-Ski2 and a cap exosome subunit. Finally, Thermococcus barophilus whole-cell extract fractionation experiments provide evidences that an aRNase J/ASH-Ski2 complex might exist in vivo and hint at an association of aRNase J with the ribosome that is emphasised in absence of ASH-Ski2. Whilst aRNase J homologues are found among bacteria, the RNA exosome and the Ski2-like RNA helicase have eukaryotic homologues, underlining the mosaic aspect of archaeal RNA machines. Altogether, these results suggest a fundamental role of β-CASP RNase/helicase complex in archaeal RNA metabolism.
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rna processing machineries in archaea the 5 3 exoribonuclease arnase j of the β casp family is engaged specifically with the helicase ash ski2 and the 3 5 exoribonucleolytic rna exosome machinery
bioRxiv, 2019Co-Authors: Duy Khanh Phung, Clarisse Etienne, Manon Batista, Yann Moalic, Sébastien Laurent, Violette Morales, Mohamed Jebbar, Gwennaele Fichant, Petra Langendijkgenevaux, Marie BouvierAbstract:A network of RNA helicases, endoribonucleases, and exoribonucleases regulates the quantity and quality of cellular RNAs. To date, mechanistic studies focused on bacterial and eukaryal systems due to the challenge of identifying the main drivers of RNA decay and processing in Archaea. Here, our data support that aRNase J, a 5′-3′ exoribonuclease of the β-CASP family conserved in Euryarchaea, engages specifically with a Ski2-like helicase and the RNA exosome to potentially exert control over RNA surveillance, and that this occurs in the vicinity of the ribosome. Proteomic landscapes and direct protein-protein interaction analyses demonstrated that aRNase J interplay with ASH-Ski2 and the Csl4 cap exosome subunit. These in vitro data are strengthened by our phylogenomic studies showing a taxonomic co-distribution of aRNase J and ASH-Ski2 among the archaeal phylogeny. Finally, our T. barophilus whole-cell extract fractionation experiments provide evidences that an aRNase J/ASH-Ski2 complex might exist in vivo and hint at an association of aRNase J with the ribosome or polysomes that is stressed in absence of ASH-Ski2. While aRNase J homologues are found among bacteria, the RNA exosome and the Ski2-like RNA helicase have eukaryotic homologues, underlining the mosaic aspect of archaeal RNA machines. Altogether, these results suggest, for the first time, a fundamental role of β-CASP RNase/helicase complex in archaeal RNA metabolism. Finally, our results position aRNase J at the junction of RNA surveillance and translation processes, thus opening new perspectives and evolutionary scenario on RNA processing players in Archaea.
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metabolisme de l arn chez les archees identification et caracterisation du complexe ribonuclease β casp helicase ski2 like de pyrococcus abyssi
2017Co-Authors: Duy Khanh PhungAbstract:Les ribonucleases et les helicases a ARN sont des acteurs cle du metabolisme des ARN et jouent donc des roles cruciaux pour la regulation de l'expression des genes. Peu de donnees sont connues concernant ce metabolisme chez les Archees, le troisieme domaine du vivant. L'equipe dans laquelle j'ai effectue mes travaux de these s'interesse au metabolisme de l'ARN chez les archees et plus particulierement aux ribonucleases s-CASP. Dans ce contexte, nous focalisons nos etudes sur la comprehension physiologique que pourrait jouer les ribonucleases s-CASP aCPSF1 et aRNase J, orthologue respectivement du facteur de terminaison de la transcription eucaryotes CPSF-73 et RNase J bacterienne. Par analogie avec CPSF-73 et RNase J, qui font partie de complexes multi-proteiques, des indices sur les fonctions des homologues archeens de ces ribonucleases pourraient provenir de l'identification des complexes autour de aCPSF1 et aRNase J. Utilisant des extraits de Pyrococcus abyssi et les proteines recombinantes aCPSF1 et aRNase J comme appâts, nous avons identifie que aRNase J fait partie d'un reseau d'interaction incluant une helicase de la famille des Ski2-like (ASH-Ski2). En parallele, des fractionnements d'extrait de P. abyssi sur gradient de saccharose par ultracentrifugation indiquent que aRNase J et ASH-Ski2 sont presentes toutes deux dans les fractions de haut poids moleculaires avec les sous-unites du ribosome et ceux de l'exosome. Nous avons aussi demontre une interaction stable entre aRNase J et ASH-Ski2 ainsi que des motifs impliquees dans cette interaction par des experiences de co- purification par chromatographie d'affinite. De plus, les caracterisations biochimiques de ASH-Ski2 indiquent que cette proteine possede une activite d'hydrolyse de l'ATP dependant de la presence d'acides nucleiques. ASH-Ski2 possede de plus la capacite d'hybridation et de deroulement de deux brins d'acides nucleiques en presence d'ATP. A notre connaissance, nos resultats sont les premiers a indiquer un complexe contenant une ribonuclease et d'une helicase a ARN Ski2-like chez les archees. De maniere intriguent, aRNase J est orthologue de la RNase J bacterienne et ASH-Ski2 des helicases Ski2-like des eucaryotes. Cela demontre que les Archees pourraient posseder un systeme composite implique dans le metabolisme des ARN partageant des caracteristiques bacteriens et eucaryotes. Ces resultats mettent en lumiere l'avantage de l'etude des Archees pour la comprehension des mecanismes moleculaires et evolutives des processus fondamentaux des trois domaines du vivant.
Violette Morales - One of the best experts on this subject based on the ideXlab platform.
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rna processing machineries in archaea the 5 3 exoribonuclease arnase j of the β casp family is engaged specifically with the helicase ash ski2 and the 3 5 exoribonucleolytic rna exosome machinery
Nucleic Acids Research, 2020Co-Authors: Duy Khanh Phung, Clarisse Etienne, Manon Batista, Yann Moalic, Sébastien Laurent, Sophie Liuu, Violette Morales, Mohamed Jebbar, Petra Langendijkgenevaux, Gwennaele FichantAbstract:A network of RNA helicases, endoribonucleases and exoribonucleases regulates the quantity and quality of cellular RNAs. To date, mechanistic studies focussed on bacterial and eukaryal systems due to the challenge of identifying the main drivers of RNA decay and processing in Archaea. Here, our data support that aRNase J, a 5'-3' exoribonuclease of the β-CASP family conserved in Euryarchaeota, engages specifically with a Ski2-like helicase and the RNA exosome to potentially exert control over RNA surveillance, at the vicinity of the ribosome. Proteomic landscapes and direct protein-protein interaction analyses, strengthened by comprehensive phylogenomic studies demonstrated that aRNase J interplay with ASH-Ski2 and a cap exosome subunit. Finally, Thermococcus barophilus whole-cell extract fractionation experiments provide evidences that an aRNase J/ASH-Ski2 complex might exist in vivo and hint at an association of aRNase J with the ribosome that is emphasised in absence of ASH-Ski2. Whilst aRNase J homologues are found among bacteria, the RNA exosome and the Ski2-like RNA helicase have eukaryotic homologues, underlining the mosaic aspect of archaeal RNA machines. Altogether, these results suggest a fundamental role of β-CASP RNase/helicase complex in archaeal RNA metabolism.
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RNA processing machineries in Archaea: the 5′-3′ exoribonuclease aRNase J of the β-CASP family is engaged specifically with the helicase ASH-Ski2 and the 3′-5′ exoribonucleolytic RNA exosome machinery
Nucleic Acids Research, 2020Co-Authors: Duy Khanh Phung, Clarisse Etienne, Manon Batista, Petra Langendijk-genevaux, Yann Moalic, Sébastien Laurent, Sophie Liuu, Violette Morales, Mohamed Jebbar, Gwennaele FichantAbstract:A network of RNA helicases, endoribonucleases and exoribonucleases regulates the quantity and quality of cellular RNAs. To date, mechanistic studies focussed on bacterial and eukaryal systems due to the challenge of identifying the main drivers of RNA decay and processing in Archaea. Here, our data support that aRNase J, a 5'-3' exoribonuclease of the β-CASP family conserved in Euryarchaeota, engages specifically with a Ski2-like helicase and the RNA exosome to potentially exert control over RNA surveillance, at the vicinity of the ribosome. Proteomic landscapes and direct protein-protein interaction analyses, strengthened by comprehensive phylogenomic studies demonstrated that aRNase J interplay with ASH-Ski2 and a cap exosome subunit. Finally, Thermococcus barophilus whole-cell extract fractionation experiments provide evidences that an aRNase J/ASH-Ski2 complex might exist in vivo and hint at an association of aRNase J with the ribosome that is emphasised in absence of ASH-Ski2. Whilst aRNase J homologues are found among bacteria, the RNA exosome and the Ski2-like RNA helicase have eukaryotic homologues, underlining the mosaic aspect of archaeal RNA machines. Altogether, these results suggest a fundamental role of β-CASP RNase/helicase complex in archaeal RNA metabolism.
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rna processing machineries in archaea the 5 3 exoribonuclease arnase j of the β casp family is engaged specifically with the helicase ash ski2 and the 3 5 exoribonucleolytic rna exosome machinery
bioRxiv, 2019Co-Authors: Duy Khanh Phung, Clarisse Etienne, Manon Batista, Yann Moalic, Sébastien Laurent, Violette Morales, Mohamed Jebbar, Gwennaele Fichant, Petra Langendijkgenevaux, Marie BouvierAbstract:A network of RNA helicases, endoribonucleases, and exoribonucleases regulates the quantity and quality of cellular RNAs. To date, mechanistic studies focused on bacterial and eukaryal systems due to the challenge of identifying the main drivers of RNA decay and processing in Archaea. Here, our data support that aRNase J, a 5′-3′ exoribonuclease of the β-CASP family conserved in Euryarchaea, engages specifically with a Ski2-like helicase and the RNA exosome to potentially exert control over RNA surveillance, and that this occurs in the vicinity of the ribosome. Proteomic landscapes and direct protein-protein interaction analyses demonstrated that aRNase J interplay with ASH-Ski2 and the Csl4 cap exosome subunit. These in vitro data are strengthened by our phylogenomic studies showing a taxonomic co-distribution of aRNase J and ASH-Ski2 among the archaeal phylogeny. Finally, our T. barophilus whole-cell extract fractionation experiments provide evidences that an aRNase J/ASH-Ski2 complex might exist in vivo and hint at an association of aRNase J with the ribosome or polysomes that is stressed in absence of ASH-Ski2. While aRNase J homologues are found among bacteria, the RNA exosome and the Ski2-like RNA helicase have eukaryotic homologues, underlining the mosaic aspect of archaeal RNA machines. Altogether, these results suggest, for the first time, a fundamental role of β-CASP RNase/helicase complex in archaeal RNA metabolism. Finally, our results position aRNase J at the junction of RNA surveillance and translation processes, thus opening new perspectives and evolutionary scenario on RNA processing players in Archaea.
Sébastien Laurent - One of the best experts on this subject based on the ideXlab platform.
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rna processing machineries in archaea the 5 3 exoribonuclease arnase j of the β casp family is engaged specifically with the helicase ash ski2 and the 3 5 exoribonucleolytic rna exosome machinery
Nucleic Acids Research, 2020Co-Authors: Duy Khanh Phung, Clarisse Etienne, Manon Batista, Yann Moalic, Sébastien Laurent, Sophie Liuu, Violette Morales, Mohamed Jebbar, Petra Langendijkgenevaux, Gwennaele FichantAbstract:A network of RNA helicases, endoribonucleases and exoribonucleases regulates the quantity and quality of cellular RNAs. To date, mechanistic studies focussed on bacterial and eukaryal systems due to the challenge of identifying the main drivers of RNA decay and processing in Archaea. Here, our data support that aRNase J, a 5'-3' exoribonuclease of the β-CASP family conserved in Euryarchaeota, engages specifically with a Ski2-like helicase and the RNA exosome to potentially exert control over RNA surveillance, at the vicinity of the ribosome. Proteomic landscapes and direct protein-protein interaction analyses, strengthened by comprehensive phylogenomic studies demonstrated that aRNase J interplay with ASH-Ski2 and a cap exosome subunit. Finally, Thermococcus barophilus whole-cell extract fractionation experiments provide evidences that an aRNase J/ASH-Ski2 complex might exist in vivo and hint at an association of aRNase J with the ribosome that is emphasised in absence of ASH-Ski2. Whilst aRNase J homologues are found among bacteria, the RNA exosome and the Ski2-like RNA helicase have eukaryotic homologues, underlining the mosaic aspect of archaeal RNA machines. Altogether, these results suggest a fundamental role of β-CASP RNase/helicase complex in archaeal RNA metabolism.
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RNA processing machineries in Archaea: the 5′-3′ exoribonuclease aRNase J of the β-CASP family is engaged specifically with the helicase ASH-Ski2 and the 3′-5′ exoribonucleolytic RNA exosome machinery
Nucleic Acids Research, 2020Co-Authors: Duy Khanh Phung, Clarisse Etienne, Manon Batista, Petra Langendijk-genevaux, Yann Moalic, Sébastien Laurent, Sophie Liuu, Violette Morales, Mohamed Jebbar, Gwennaele FichantAbstract:A network of RNA helicases, endoribonucleases and exoribonucleases regulates the quantity and quality of cellular RNAs. To date, mechanistic studies focussed on bacterial and eukaryal systems due to the challenge of identifying the main drivers of RNA decay and processing in Archaea. Here, our data support that aRNase J, a 5'-3' exoribonuclease of the β-CASP family conserved in Euryarchaeota, engages specifically with a Ski2-like helicase and the RNA exosome to potentially exert control over RNA surveillance, at the vicinity of the ribosome. Proteomic landscapes and direct protein-protein interaction analyses, strengthened by comprehensive phylogenomic studies demonstrated that aRNase J interplay with ASH-Ski2 and a cap exosome subunit. Finally, Thermococcus barophilus whole-cell extract fractionation experiments provide evidences that an aRNase J/ASH-Ski2 complex might exist in vivo and hint at an association of aRNase J with the ribosome that is emphasised in absence of ASH-Ski2. Whilst aRNase J homologues are found among bacteria, the RNA exosome and the Ski2-like RNA helicase have eukaryotic homologues, underlining the mosaic aspect of archaeal RNA machines. Altogether, these results suggest a fundamental role of β-CASP RNase/helicase complex in archaeal RNA metabolism.
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rna processing machineries in archaea the 5 3 exoribonuclease arnase j of the β casp family is engaged specifically with the helicase ash ski2 and the 3 5 exoribonucleolytic rna exosome machinery
bioRxiv, 2019Co-Authors: Duy Khanh Phung, Clarisse Etienne, Manon Batista, Yann Moalic, Sébastien Laurent, Violette Morales, Mohamed Jebbar, Gwennaele Fichant, Petra Langendijkgenevaux, Marie BouvierAbstract:A network of RNA helicases, endoribonucleases, and exoribonucleases regulates the quantity and quality of cellular RNAs. To date, mechanistic studies focused on bacterial and eukaryal systems due to the challenge of identifying the main drivers of RNA decay and processing in Archaea. Here, our data support that aRNase J, a 5′-3′ exoribonuclease of the β-CASP family conserved in Euryarchaea, engages specifically with a Ski2-like helicase and the RNA exosome to potentially exert control over RNA surveillance, and that this occurs in the vicinity of the ribosome. Proteomic landscapes and direct protein-protein interaction analyses demonstrated that aRNase J interplay with ASH-Ski2 and the Csl4 cap exosome subunit. These in vitro data are strengthened by our phylogenomic studies showing a taxonomic co-distribution of aRNase J and ASH-Ski2 among the archaeal phylogeny. Finally, our T. barophilus whole-cell extract fractionation experiments provide evidences that an aRNase J/ASH-Ski2 complex might exist in vivo and hint at an association of aRNase J with the ribosome or polysomes that is stressed in absence of ASH-Ski2. While aRNase J homologues are found among bacteria, the RNA exosome and the Ski2-like RNA helicase have eukaryotic homologues, underlining the mosaic aspect of archaeal RNA machines. Altogether, these results suggest, for the first time, a fundamental role of β-CASP RNase/helicase complex in archaeal RNA metabolism. Finally, our results position aRNase J at the junction of RNA surveillance and translation processes, thus opening new perspectives and evolutionary scenario on RNA processing players in Archaea.