8 research outputs found
PAH chemistry at eV internal energies. 1. H-shifted isomers
The PAH family of organic compounds (polycyclic aromatic hydrocarbons),
involved in several fields of chemistry, has received particular attention in
astrochemistry, where their vibrational spectroscopy, thermodynamic, dynamic,
and fragmentation properties are now abundantly documented. This survey aims at
drawing trends for low spin-multiplicity surfaces of PAHs bearing internal
energies in the range 1-10 eV. It addresses some typical alternatives to the
ground-state regular structures of PAHs, making explicit possible
intramolecular rearrangements leading to high-lying minima. These
isomerisations should be taken into consideration when addressing PAH
processing in astrophysical conditions. The first part of this double-entry
study focuses on the hydrogen-shifted forms, which bear both a carbene center
and a saturated carbon. It rests upon DFT calculations mainly performed on two
emblematic PAH representatives, coronene and pyrene, in their neutral and mono
and multi-cationic states. Systematically searched for in neutral species,
these H-shifted minima are lying 4-5 eV above the regular all-conjugated forms,
and are separated by barriers of about one eV. General hydrogen-shifting is
found to be easier for cationic species as the relative energies of their
H-shifted minima are 1-1.5 eV lower than those for neutral species. As much as
possible, classical knowledge and concepts of organic chemistry such as
aromaticity and Clar's rules are invoked for result interpretation.Comment: 35 pages, accepted by Molecular Astrophysic
PAH chemistry at eV internal energies. 2. Ring alteration and dissociation
Recognized as important interstellar constituents, polycyclic aromatic
hydrocarbons (PAHs) have been intensively studied in astrochemistry and their
spectroscopy, thermodynamics, dynamics, and fragmentations are now amply
documented. There exists typical alternatives to the ground-state regular
planar structures of PAHs, as long as they bear internal energies in the range
1-10 eV. Resulting from intramolecular rearrangements, such high-lying minima
on the potential- energy surfaces should be taken into consideration in the
studies of PAH processing in astrophysical conditions. Resting upon DFT
calculations mainly performed on two emblematic PAH representatives, coronene
and pyrene, in their neutral and mono and multi-cationic states, this second
survey addresses the following alternatives: (1) opened forms containing
ethynyl or 2- butynyl groups, (2) vinylidene isomers, in which phenanthrene
patterns are reorganized into dibenzofulvene ones, (3) twisted forms, where
external CH=CH bonds can be partly twisted, and (4) bicyclobutane forms, in
which the latter are integrated in saturated bicyclic forms. A few scenarios
for elimination of fragments H, H2, C2H2 and C2H4 are explored. As far as
possible, familiar concepts of organic chemistry, such as aromaticity or Clar's
rules, are invoked for interpretations.Comment: 65 pages, accepted by Molecular Astrophysic
Transfer RNA Maturation Defects Lead to Inhibition of ribosomal RNA Processing via Synthesis of pppGpp
International audienc
RNAseq-dataset1_20230126
RNAseq raw data from Seqcenter (QUO1003393) Illumina sequencing.
Illumina adapter sequences have been trimmed off during the demultiplexing process
Couplage entre maturation des ARN de transfert et maturation de lâARN ribosomique chez B. subtilis
Cellular protein synthesis both requires functional ribosomes and mature transfer RNAs (tRNAs) as adapter molecules. The ribosomes are large essential ribonucleoprotein complexes whose biogenesis accounts for most of cellular transcription and consumes a major portion of the cellâs energy. Ribosome biogenesis is therefore tightly adjusted to the cellular needs and actively surveilled to rapidly degrade defective particles that could interfere with translation. Interestingly, tRNAs and ribosomal RNAs (rRNAs) are both transcribed from longer primary transcripts and universally require processing to become functional for translation. In this thesis, I have characterized a coupling mechanism between tRNA processing and ribosome biogenesis in the Gram-positive model organism Bacillus subtilis. Accumulation of immature tRNAs during tRNA maturase depletion, specifically abolishes 16S rRNA 3â processing by the endonuclease YqfG/YbeY, the last step in small ribosomal subunit formation. We showed that this maturation deficiency resulted from a late small subunit (30S) assembly defect coinciding with changes in expression of several key 30S assembly cofactors, mediated by both transcriptional and post-transcriptional effects. Interestingly, our results indicate that accumulation of immature tRNAs is sensed by the stringent factor RelA and triggers (p)ppGpp production. We showed that (p)ppGpp synthesis and the accompanying decrease in GTP levels inhibits 16S rRNA 3â processing, most likely by affecting GTPases involved in ribosome assembly. The inhibition of 16S rRNA 3â processing is thought to further lead to degradation of partially assembled particles by RNase R. Thus, we propose a model where RelA senses temporary slow-downs in tRNA maturation and this leads to an appropriate readjustment of ribosome biogenesis. This coupling mechanism would maintain the physiological balance between tRNAs and rRNAs, the two major components of the translation machinery.La synthĂšse des protĂ©ines cellulaires requiert Ă la fois des ribosomes fonctionnels et des ARN de transfert (ARNt) matures comme molĂ©cules adaptatrices. Les ribosomes sont de larges complexes ribonuclĂ©oprotĂ©iques dont la biogenĂšse reprĂ©sente la plupart de la transcription cellulaire et consomme une majeure partie de lâĂ©nergie de la cellule. Par consĂ©quent, la biogenĂšse des ribosomes fait lâobjet dâune rĂ©gulation importante afin dâajuster le nombre de ribosomes aux besoins de la cellule et de dĂ©grader efficacement les particules dĂ©fectueuses qui pourraient interfĂ©rer avec la traduction. Les ARNs ribosomiques (ARNr) et les ARNt sont tous deux transcrits sous formes de prĂ©curseurs et sont universellement maturĂ©s pour devenir fonctionnels pour la traduction. Ce travail de thĂšse a permis de mettre en Ă©vidence un couplage entre la maturation des ARNt et la biogenĂšse des ribosomes chez la bactĂ©rie modĂšle Ă Gram positif Bacillus subtilis. Ainsi, lâaccumulation dâARNt immatures lors dâune dĂ©plĂ©tion en enzymes de maturation, abolit spĂ©cifiquement la maturation en 3â de lâARNr 16S par lâendoribonuclĂ©ase YqfG/YbeY, derniĂšre Ă©tape dans la formation de la petite sous-unitĂ© ribosomique (30S). Nous avons mis en Ă©vidence que ce dĂ©faut de maturation rĂ©sultait dâun dĂ©faut dâassemblage tardif du 30S coĂŻncidant avec des changements dâexpression de plusieurs facteurs dâassemblage du ribosome. Nous avons montrĂ© que cette modulation dâexpression provenait dâeffets transcriptionel et post-transcriptionel. De façon inĂ©dite, nos rĂ©sultats indiquent que lâaccumulation dâARNt immatures est perçue par RelA (le facteur de la rĂ©ponse stringente), dĂ©clenchant la production de (p)ppGpp. Nous avons observĂ© que cette synthĂšse de (p)ppGpp et la baisse concomitante des niveaux de GTP cellulaire, inhibe la maturation de lâARNr 16S en 3â, probablement via un blocage des GTPases impliquĂ©es dans lâassemblage des ribosomes. Lâinhibition de la maturation de lâARNr 16S cĂŽtĂ© 3â est supposĂ©e conduire, par la suite, Ă une dĂ©gradation des particules partiellement assemblĂ©es par la RNase R. Ainsi, nos rĂ©sultats supportent un modĂšle oĂč RelA jouerait un rĂŽle central ; en percevant une dĂ©ficience de maturation des ARNt et en ajustant, en consĂ©quence, la biogenĂšse des ribosomes via la production de (p)ppGpp. Ce mĂ©canisme de couplage permettrait de maintenir un Ă©quilibre fonctionnel entre ARNt et ARNr, les deux composants majeurs de la machinerie de traduction
Dissociation of polycyclic aromatic hydrocarbons: molecular dynamics studies
17 pagesInternational audienc
Structures of B. subtilis Maturation RNases Captured on 50S Ribosome with Pre-rRNAs.
The pathways for ribosomal RNA (rRNA) maturation diverge greatly among the domains of life. In the Gram-positive model bacterium, Bacillus subtilis, the final maturation steps of the two large ribosomal subunit (50S) rRNAs, 23S and 5S pre-rRNAs, are catalyzed by the double-strand specific ribonucleases (RNases) Mini-RNase III and RNase M5, respectively. Here we present a protocol that allowed us to solve the 3.0 and 3.1Â Ă
resolution cryoelectron microscopy structures of these RNases poised to cleave their pre-rRNA substrates within the B. subtilis 50S particle. These data provide the first structural insights into rRNA maturation in bacteria by revealing how these RNases recognize and process double-stranded pre-rRNA. Our structures further uncover how specific ribosomal proteins act as chaperones to correctly fold the pre-rRNA substrates and, for Mini-III, anchor the RNase to the ribosome. These r-proteins thereby serve a quality-control function in the process from accurate ribosome assembly to rRNA processing