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An 18.5-kb human DNA segment was selected from a human XCharon-4A library by hybridization to mammalian valine tRNAiAc and found to encompass a cluster of three tRNA genes. Two valine tRNA genes with anticodons of AAC and CAC, encoding the major and minor cytoplasmic valine tRNA isoacceptors, respectively, and a lysine tRNAcuu gene were identified by Southern blot hybridization and DNA sequence analysis of a 7.1-kb region of the human DNA insert. At least nine Alu family members were found interspersed throughout the human DNA fragment. The tRNA genes are accurately transcribed by RNA polymerase III in a HeLa cell extract, since the RNase Ti fingerprints of the mature-sized tRNA transcription products are consistent with the DNA sequences of the structural genes. Three members of the chimpanzee triosephosphate isomerase (TPI) gene family, the functional transcription unit and two processed pseudogenes, were characterized by genomic blotting and DNA sequence analysis. The bona fide TPI gene spans 3.5 kb with seven exons and six introns, and is the first complete hominoid TPI gene sequenced. The gene exhibits a very high identity with the human and rhesus TPI genes. In particular, the polypeptides of 248 amino acids encoded by the chimpanzee and human TPI genes are identical, although the two coding regions differ in the third codon wobble positions for five amino acids. An Alu member occurs upstream from one of the processed pseudogenes, whereas an isolated endogenous retroviral long terminal repeat (HERV-K) occurs within the structural region of the other processed pseudogene. The ages of the processed pseudogenes were estimated to be 2.6 and 10.4 million years, implying that one was inserted into the genome before the divergence of the chimpanzee and human lineages, and the other inserted into the chimpanzee genome after the divergence.

Tyrosine tRNA was isolated from bovine liver and its nucleotide sequence was determined using in vitro 32p_ labeling techniques. Several important structural features of the tRNA are: the presence of gal-Q in the first position of the anticodon, acp3U at position 20, and a pair of adjacent N,N-dimethylguanosines (residues 26 and 27). A human DNA fragment harbored in a lambda phage clone was isolated, and restriction enzyme analysis revealed the presence of three tRNA genes in a 6.0-kb BamHI subfragment. Portions of the 6.0-kb DNA fragment containing the tRNA genes were sequenced by the method of Maxam and Gilbert and analyzed for transcriptional activity in vitro using homologous cytoplasmic extracts. A threonine tRNAUGU gene exhibited high transcriptional activity dependent on its 5'- flanking sequence. The enhanced transcription is not completely inhibited by alpha-amanitin. The value of studying tRNA structure in concert with the cognate tRNA. genes is discussed.

Des mutations dans le génome mitochondrial donnent lieu à l’apparition de maladies neuro-dégénératives ou de myopathies. Pour développer des approches de thérapie génique pour prévenir de ces syndromes, nous devons mieux comprendre les mécanismes moléculaires d’import mitochondrial des ARN. Pour cela nous tentons de récapituler in vitro l’import des ARN à partir d’extraits cellulaires fractionnés par différentes méthodes telles que la chromatographie d’exclusion ou d’affinité à l’aide d’étiquettes d’ARN ou de protéines. Nos résultats affinent nos connaissances de ces mécanismes et permettent d’avancer l’idée que l’énolase, une enzyme de la glycolyse, n’agit pas seule lors de la première étape de l’import de l’ARNtLys avec anticodon CUU (tRK1). En effet nous avons montré que l’énolase ultra-purifiée ne se fixait plus à tRK1 in vitro, alors que des préparations de mitochondries de levure récapitulaient l’import lorsque diverses fractions ajoutées à l’énolase étaient testées. Les fractionnements d’extraits opérés permettent de cerner certaines protéines qui pourraient fonctionner de concert avec l’énolase pour véhiculer tRK1 vers la mitochondrie. / Mutations in the mitochondrial genome give rise to neurodegenerative diseases or myopathies. To develop gene therapy for preventing the appearance of these syndromes, we need to better understand the molecular mechanisms of mitochondrial RNA. For this purpose we try to recapitulate in vitro the import of RNA from cell extracts fractionated by different methods such as exclusion or affinity chromatography using tagged RNAs or proteins. Our results refine our knowledge of these mechanisms and allow to advance the idea that enolase, an enzyme of glycolysis, does not act alone during the first stage of import of tRNALys with anticodon CUU (tRK1). Indeed, we have shown that ultra-purified enolase no longer binds to tRK1 in vitro, while preparations of yeast mitochondria recapitulate the import when various fractions mixed with enolase were tested. The performed extracts fractionation make it possible to point to certain proteins which could work in concert with the enolase to convey tRK1 to mitochondria.

Background: Exosomes have great potential in regenerative medicine through the transfer of their bioactive cargos, such as RNA. tRF RNA and tiRNA are tRNAderived non-coding RNA. Here, we sought to identify the tRF/tiRNA profile in human mesenchymal stem cell (hMSC) exosomes. Methods: Bone marrow hMSCs were cultured with/without osteogenic differentiation medium and exosomes were harvested. RNA was extracted from: 1) control cells (Cell-NT); 2) control exosomes (EXO-NT); 3) differentiated cells (Cell-OM); 4) exosomes produced by differentiated cells (EXO-OM). RNA was sequenced to profile the small RNA with a focus on tRF/tiRNA. Results: tRF/tiRNA was highly enriched in hMSC exosomes. Less diversity was seen in the tRF/tiRNA profile in exosomes than that in parent cells. Selective tRF/tiRNA were packed into MSC exosomes and their profile is dependent on the cell maturation status. Conclusions: Our results suggest that tRF/tiRNA may play a role in mediating the function of exosomes in tissue regeneration.

Translation initiation factor 1 (IF1) has been shown to be an RNA chaperone. In order to find functional interactions that IF1 may have with rRNA, we have isolated second-site suppressors of a cold-sensitive IF1 mutant. Joining of the ribosomal subunit seems to be affected in the IF1 mutant strain and the suppressive effect is a consequence of decreasing the available pool of mature 50S subunits. The results serve as additional evidence that IF1 is an RNA chaperone and that final maturation of the ribosome takes place during translation initiation. In this study we have also investigated the effect of a cold-sensitive mutant IF1 or kasugamycin addition on gene expression using a 2D gel electrophoresis technique. The effect is much more dramatic when cells are treated with kasugamycin compared to mutant IF1. The ybgF gene is uniquely sensitive to the IF1 mutation as well as the addition of kasugamycin. This effect on the native gene could be connected with some property of the TIR sequence of ybgF and supports the notion that kasugamycin addition and the IF1 cold-sensitive mutation have a similar TIR-specific effect on mRNA translation. Finally we have isolated a suppressor of a temperature-sensitive mutation in ribosomal release factor 1 (RF1) to shed more light on the translation termination process. The suppressor mutation is linked to an IS10 insertion into the cysB gene and results in a Cys- phenotype. Our results suggest that suppression of the thermosensitive growth is a consequence of the mnm5s2U hypomodification of certain tRNA species. The ability of mnm5s2U hypomodified tRNA to induce frameshifting may be responsible for the suppression mechanism and it supports the hypothesis that modified nucleosides in the anticodon of tRNA act in part to prevent frameshifting by the ribosome. / At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 2: Manuscript.

The presence and synthesis of transfer RNA (tRNA) is highly conserved in all organisms and a lot of genetic material is dedicated to its synthesis. tRNA contains a large number of modified nucleosides and several diverse functions have been found but much about their function is still unknown. By using a novel frameshifting system to select for tRNA modification mutants, new mutations were isolated and subsequently analyzed. This thesis examines the synthesis and function of a subset of tRNA modifications that have a sulfur (thio) -group as part of the modification. The isc operon encodes for proteins synthesizing iron sulfur centers ([Fe-S]) that are a part of the active site of many key enzymes in the cell and the thiolated nucleosides are dependant on a functional iron sulfur gene (iscS) for their synthesis. By studying thiolated tRNA it is not only possible to learn more about the synthesis of the modifications themselves, but also about the synthesis of [Fe-S] clusters. Based on an analysis of mutations in three of the isc operon genes (iscS, iscU, and iscA), a two-model pathway is proposed for the synthesis of Salmonella enterica Serovar Typhimurium thiolated tRNA modifications. The interactions of IscS with other proteins in the tRNA modification thiolation pathways suggest a more complex sulfur relay than had previously been envisioned. Some of the specificities and the effect of an iscA mutant on the levels of tRNA modifications lead to an examination of the role of IscA in [Fe-S] formation and its importance for tRNA modifications.

tRNA genes have the fundamental role of translating the genetic code during protein synthesis. Beyond solely a passive decoding role, the tRNA pool exerts selection pressures on the codon usage of organisms and the viruses that infect them because processing codons read by rare tRNAs can be slow or even erroneous. To better understand the interactions of codons and anticodons in eukaryotic species, we first investigated whether tRNAs packaged into HIV-1 particles may relate to the poor codon usage of HIV-1 genes. By comparing the codon usage of HIV-1 genes with that of its human host, we found that tRNAs decoding poorly adapted codons are overrepresented in HIV-1 virions. Because the affinity of Gag-Pol for all tRNAs is non-specific, HIV packaging is most likely passive and reflects the tRNA pool at the time of viral particle formation. Moreover, differences that we found in the codon usage between early and late genes suggest alterations in the tRNA pool are induced late in viral infection. Next, we tested whether a reduced tRNA anticodon pattern, which was called into question by predicted tRNA datasets, is maintained across eukaryotes. tRNA prediction methods are prone to falsely identifying tRNA-derived repetitive sequences as functional tRNA genes. Thus, we proposed and tested a novel approach to identify falsely predicted tRNA genes using phylogenetics. Phylogenetic analysis removed nearly all the genes deviating from the anticodon pattern, therefore the anticodon pattern is reaffirmed across eukaryotes.

tRNA genes have the fundamental role of translating the genetic code during protein synthesis. Beyond solely a passive decoding role, the tRNA pool exerts selection pressures on the codon usage of organisms and the viruses that infect them because processing codons read by rare tRNAs can be slow or even erroneous. To better understand the interactions of codons and anticodons in eukaryotic species, we first investigated whether tRNAs packaged into HIV-1 particles may relate to the poor codon usage of HIV-1 genes. By comparing the codon usage of HIV-1 genes with that of its human host, we found that tRNAs decoding poorly adapted codons are overrepresented in HIV-1 virions. Because the affinity of Gag-Pol for all tRNAs is non-specific, HIV packaging is most likely passive and reflects the tRNA pool at the time of viral particle formation. Moreover, differences that we found in the codon usage between early and late genes suggest alterations in the tRNA pool are induced late in viral infection. Next, we tested whether a reduced tRNA anticodon pattern, which was called into question by predicted tRNA datasets, is maintained across eukaryotes. tRNA prediction methods are prone to falsely identifying tRNA-derived repetitive sequences as functional tRNA genes. Thus, we proposed and tested a novel approach to identify falsely predicted tRNA genes using phylogenetics. Phylogenetic analysis removed nearly all the genes deviating from the anticodon pattern, therefore the anticodon pattern is reaffirmed across eukaryotes.

Thèse de doctorat : Sciences du vivant : Strasbourg 1 : 2007. / Titre provenant de l'écran-titre. Bibliogr. p. 225-249.