Biology of tRNA and pathogenicity

@article{pmid37414209,

title = {RNA aptamers developed against tRip: A preliminary approach targeting tRNA entry in Plasmodium},

author = {Martina Pitolli and Marta Cela and Caroline Paulus and Joëlle Rudinger-Thirion and Magali Frugier},

doi = {10.1016/j.biochi.2023.06.011},

issn = {1638-6183},

year  = {2023},

date = {2023-07-01},

urldate = {2023-07-01},

journal = {Biochimie},

abstract = {Malaria is caused by Plasmodium parasites that multiply inside host cells and can be lethal when P. falciparum is involved. We identified tRip as a membrane protein that facilitates the import of exogenous transfer RNA (tRNA) into the parasite. tRip encompasses a tRNA binding domain exposed on the parasite surface. We used the SELEX approach to isolate high-affinity and specific tRip-binding RNA motifs from a library of random 25 nucleotide-long sequences. In five rounds of combined negative and positive selections, an enriched pool of aptamers was obtained; sequencing revealed that they were all different in their primary sequence; only by comparing their structure predictions did most of the selected aptamers reveal a conserved 5-nucleotide motif sequence. We showed that the integral motif is essential for tRip-binding while the rest of the molecule can be significantly reduced or mutated as long as the motif is presented in a single-stranded region. Such RNA aptamers bind in place of the original tRNA substrate and act as an efficient competitor, suggesting that they can block tRip function and slow parasite development.},

keywords = {FRUGIER, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{pmid36606712,

title = {Solution x-ray scattering highlights discrepancies in Plasmodium multi-aminoacyl-tRNA synthetase complexes},

author = {José R Jaramillo Ponce and Anne Théobald-Dietrich and Philippe Bénas and Caroline Paulus and Claude Sauter and Magali Frugier},

doi = {10.1002/pro.4564},

issn = {1469-896X},

year  = {2023},

date = {2023-01-01},

urldate = {2023-01-01},

journal = {Protein Sci},

pages = {e4564},

abstract = {tRip is a tRNA import protein specific to Plasmodium, the causative agent of malaria. In addition to its membrane localization and tRNA trafficking properties, tRip has the capacity to associate with three aminoacyl-tRNA synthetases (aaRS), the glutamyl- (ERS), glutaminyl- (QRS), and methionyl- (MRS) tRNA synthetases. In eukaryotes, such multi-aaRSs complexes (MSC) regulate the moonlighting activities of aaRSs. In Plasmodium, tRip and the three aaRSs all contain an N-terminal GST-like domain involved in the assembly of two independent complexes: the Q-complex (tRip:ERS:QRS) and the M-complex (tRip:ERS:MRS) with a 2:2:2 stoichiometry and in which the association of the GST-like domains of tRip and ERS (tRip-N:ERS-N) is central. In this study, the crystal structure of the N-terminal GST-like domain of ERS was solved and made possible further investigation of the solution architecture of the Q- and M-complexes by small-angle X-ray scattering (SAXS). This strategy relied on the engineering of a tRip-N-ERS-N chimeric protein to study the structural scaffold of both Plasmodium MSCs and confirm the unique homodimerization pattern of tRip in solution. The biological impact of these structural arrangements is discussed. This article is protected by copyright. All rights reserved.},

keywords = {FRUGIER, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{pmid36450801,

title = {LARS2 variants can present as premature ovarian insufficiency in the absence of overt hearing loss},

author = {Anne Sophie Neyroud and Joëlle Rudinger-Thirion and Magali Frugier and Lisa G Riley and Maud Bidet and Linda Akloul and Andrea Simpson and David Gilot and John Christodoulou and Célia Ravel and Andrew H Sinclair and Marc-Antoine Belaud-Rotureau and Elena J Tucker and Sylvie Jaillard},

doi = {10.1038/s41431-022-01252-1},

issn = {1476-5438},

year  = {2022},

date = {2022-12-01},

urldate = {2022-12-01},

journal = {Eur J Hum Genet},

volume = {31},

issue = {4},

pages = {453-460},

abstract = {Premature ovarian insufficiency (POI) affects 1 in 100 women and is a leading cause of female infertility. There are over 80 genes in which variants can cause POI, with these explaining only a minority of cases. Whole exome sequencing (WES) can be a useful tool for POI patient management, allowing clinical care to be personalized to underlying cause. We performed WES to investigate two French sisters, whose only clinical complaint was POI. Surprisingly, they shared one known and one novel likely pathogenic variant in the Perrault syndrome gene, LARS2. Using amino-acylation studies, we established that the novel missense variant significantly impairs LARS2 function. Perrault syndrome is characterized by sensorineural hearing loss in addition to POI. This molecular diagnosis alerted the sisters to the significance of their difficulty in following conversation. Subsequent audiology assessment revealed a mild bilateral hearing loss. We describe the first cases presenting with perceived isolated POI and causative variants in a Perrault syndrome gene. Our study expands the phenotypic spectrum associated with LARS2 variants and highlights the clinical benefit of having a genetic diagnosis, with prediction of potential co-morbidity and prompt and appropriate medical care, in this case by an audiologist for early detection of hearing loss.},

keywords = {FRUGIER, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {A case of QARS1 associated epileptic encephalopathy and review of epilepsy in aminoacyl-tRNA synthetase disorders},

author = {D. L. Chan and J. Rudinger-Thirion and M. Frugier and L. G. Riley and G. Ho and K. Kothur and S. S. Mohammad},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=34774383},

doi = {10.1016/j.braindev.2021.10.009},

isbn = {34774383},

year  = {2022},

date = {2022-01-01},

journal = {Brain Dev},

volume = {44},

number = {2},

pages = {142-147},

abstract = {INTRODUCTION: Mutations in QARS1, which encodes human glutaminyl-tRNA synthetase, have been associated with epilepsy, developmental regression, progressive microcephaly and cerebral atrophy. Epilepsy caused by variants in QARS1 is usually drug-resistant and intractable. Childhood onset epilepsy is also reported in various aminoacyl-tRNA synthetase disorders. We describe a case with a milder neurological phenotype than previously reported with QARS1 variants and review the seizure associations with aminoacyl-tRNA synthetase disorders. CASE REPORT: The patient is a 4-year-old girl presenting at 6 weeks of age with orofacial dyskinesia and hand stereotypies. She developed focal seizures at 7 months of age. Serial electroencephalograms showed shifting focality. Her seizures were controlled after introduction of carbamazepine. Progress MRI showed very mild cortical volume loss without myelination abnormalities or cerebellar atrophy. She was found to have novel compound heterozygous variants in QARS1 (NM_005051.2): c.[1132C > T];[1574G > A], p.[(Arg378Cys)];[(Arg525Gln)] originally classified as "variants of uncertain significance" and later upgraded to "likely pathogenic" based on functional testing and updated variant database review. Functional testing showed reduced solubility of the corresponding QARS1 mutants in vitro, but only mild two-fold loss in catalytic efficiency with the c.1132C > T variant and no noted change in tRNA(Gln) aminoacylation with the c.1574G > A variant. CONCLUSION: We describe two QARS1 variants associated with overall conserved tRNA aminoacylation activity but characterized by significantly reduced QARS protein solubility, resulting in a milder clinical phenotype. 86% of previous patients reported with QARS1 had epilepsy and 79% were pharmaco-resistant. We also summarise literature regarding epilepsy in aminoacyl-tRNA synthetase disorders, which is also often early onset, severe and drug-refractory.},

note = {1872-7131 (Electronic) 

0387-7604 (Linking) 

Case Reports},

keywords = {FRUGIER, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Discovery of two distinct aminoacyl-tRNA synthetase complexes anchored to the Plasmodium surface tRNA import protein},

author = {J. R. Jaramillo Ponce and D. Kapps and C. Paulus and J. Chicher and M. Frugier},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=35487244},

doi = {0.1016/j.jbc.2022.101987},

isbn = {35487244},

year  = {2022},

date = {2022-01-01},

urldate = {2022-01-01},

journal = {J Biol Chem},

volume = {298},

issue = {6},

pages = {101987},

abstract = {Aminoacyl-tRNA synthetases (aaRSs) attach amino acids to their cognate transfer RNAs. In eukaryotes, a subset of cytosolic aaRSs is organized into a multi-synthetase complex (MSC), along with specialized scaffolding proteins referred to as aaRS-interacting multifunctional proteins (AIMPs). In Plasmodium, the causative agent of malaria, the tRNA import protein (tRip), is a membrane protein that has been shown to participate in tRNA trafficking; here, we show that tRip also functions as an AIMP. We identified three aaRSs, namely the glutamyl- (ERS), glutaminyl- (QRS), and methionyl- (MRS) tRNA synthetases, which were specifically co-immunoprecipitated with tRip in P. berghei blood stage parasites. All four proteins contain an N-terminal GST-like domain that was demonstrated to be involved in MSC assembly. In contrast to previous studies, further dissection of GST-like interactions identified two exclusive heterotrimeric complexes: the Q-complex (tRip:ERS:QRS) and the M-complex (tRip:ERS:MRS). Gel filtration and light scattering suggest a 2:2:2 stoichiometry for both complexes but with distinct biophysical properties, and mutational analysis further revealed that the GST-like domains of QRS and MRS use different strategies to bind ERS. Taken together our results demonstrate that neither the singular homodimerization of tRip, nor its localization in the parasite plasma membrane prevents the formation of MSCs in Plasmodium. Besides, the extracellular localization of the tRNA-binding module of tRip is compensated by the presence of additional tRNA-binding modules fused to MRS and QRS, providing each MSC with two spatially distinct functions: aminoacylation of intraparasitic tRNAs and binding of extracellular tRNAs. This unique host-pathogen interaction is discussed.},

note = {1083-351X (Electronic) 

0021-9258 (Linking) 

Journal Article},

keywords = {FRUGIER, Labex, PPSE, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{deWijn2021,

title = {Crystallization and Structural Determination of an Enzyme:Substrate Complex by Serial Crystallography in a Versatile Microfluidic Chip},

author = {R de Wijn and K Rollet and V Olieric and O Hennig and N Thome and C Nous and C Paulus and B Lorber and H Betat and M Morl and C Sauter},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=33818565},

doi = {10.3791/61972},

isbn = {33818565},

year  = {2021},

date = {2021-01-01},

journal = {J Vis Exp},

number = {169},

abstract = {The preparation of well diffracting crystals and their handling before their X-ray analysis are two critical steps of biocrystallographic studies. We describe a versatile microfluidic chip that enables the production of crystals by the efficient method of counter-diffusion. The convection-free environment provided by the microfluidic channels is ideal for crystal growth and useful to diffuse a substrate into the active site of the crystalline enzyme. Here we applied this approach to the CCA-adding enzyme of the psychrophilic bacterium Planococcus halocryophilus in the presented example. After crystallization and substrate diffusion/soaking, the crystal structure of the enzyme:substrate complex was determined at room temperature by serial crystallography and the analysis of multiple crystals directly inside the chip. The whole procedure preserves the genuine diffraction properties of the samples because it requires no crystal handling.},

note = {1940-087X (Electronic) 

1940-087X (Linking) 

Journal Article 

Video-Audio Media},

keywords = {FRUGIER, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Identification of host tRNAs preferentially recognized by the Plasmodium surface protein tRip},

author = {M Cela and A Theobald-Dietrich and J Rudinger-Thirion and P Wolff and R Geslain and M Frugier},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=34530443},

doi = {10.1093/nar/gkab769},

isbn = {34530443},

year  = {2021},

date = {2021-01-01},

journal = {Nucleic Acids Res},

abstract = {Malaria is a life-threatening and devastating parasitic disease. Our previous work showed that parasite development requires the import of exogenous transfer RNAs (tRNAs), which represents a novel and unique form of host-pathogen interaction, as well as a potentially druggable target. This import is mediated by tRip (tRNA import protein), a membrane protein located on the parasite surface. tRip displays an extracellular domain homologous to the well-characterized OB-fold tRNA-binding domain, a structural motif known to indiscriminately interact with tRNAs. We used MIST (Microarray Identification of Shifted tRNAs), a previously established in vitro approach, to systematically assess the specificity of complexes between native Homo sapiens tRNAs and recombinant Plasmodium falciparum tRip. We demonstrate that tRip unexpectedly binds to host tRNAs with a wide range of affinities, suggesting that only a small subset of human tRNAs is preferentially imported into the parasite. In particular, we show with in vitro transcribed constructs that tRip does not bind specific tRNAs solely based on their primary sequence, hinting that post-transcriptional modifications modulate the formation of our host/parasite molecular complex. Finally, we discuss the potential utilization of the most efficient tRip ligands for the translation of the parasite's genetic information.},

note = {1362-4962 (Electronic) 

0305-1048 (Linking) 

Journal Article},

keywords = {ARN-MS, FRUGIER, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {CCA-addition in the cold: Structural characterization of the psychrophilic CCA-adding enzyme from the permafrost bacterium Planococcus halocryophilus},

author = {R. De Wijn and K. Rollet and F. G.M.Ernst and K. Wellner and H. Betat and M. Mörl and M. Sauter},

url = {https://www.sciencedirect.com/science/article/pii/S2001037021004402?via%3Dihub},

doi = {10.1016/j.csbj.2021.10.018},

isbn = {ISBN/2001-0370},

year  = {2021},

date = {2021-01-01},

journal = {Computational and Structural Biotechnology Journal},

volume = {19},

pages = {5845-5855},

abstract = {CCA-adding enzymes are highly specific RNA polymerases that add and maintain the sequence C-C-A at tRNA 3ﾑ-ends. Recently, we could reveal that cold adaptation of such a polymerase is not only achieved at the expense of enzyme stability, but also at the cost of polymerization fidelity. Enzymes from psychrophilic organisms usually show an increased structural flexibility to enable catalysis at low temperatures. Here, polymerases face a dilemma, as there is a discrepancy between the need for a tightly controlled flexibility during polymerization and an increased flexibility as strategy for cold adaptation. Based on structural and biochemical analyses, we contribute to clarify the cold adaptation strategy of the psychrophilic CCA-adding enzyme from Planococcus halocryophilus, a gram-positive bacterium thriving in the arctic permafrost at low temperatures down to −15 °C. A comparison with the closely related enzyme from the thermophilic bacterium Geobacillus stearothermophilus reveals several features of cold adaptation - a significantly reduced amount of alpha-helical elements in the C-terminal tRNA-binding region and a structural adaptation in one of the highly conserved catalytic core motifs located in the N-terminal catalytic core of the enzyme},

keywords = {CCA-adding enzyme, Cold adaptation, FRUGIER, Psychrophilic protein, Psychrophilic RNA polymerase, SAXS, tRNA, Unité ARN, X-ray crystallography},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {A case of QARS1 associated epileptic encephalopathy and review of epilepsy in aminoacyl-tRNA synthetase disorders},

author = {D. L. Chan and J. Rudinger-Thirion and M. Frugier and L. G. Riley and G. Ho and K. Kothur and S. S. Mohammad},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=34774383},

doi = {10.1016/j.braindev.2021.10.009},

isbn = {34774383},

year  = {2021},

date = {2021-01-01},

journal = {Brain Dev},

abstract = {INTRODUCTION: Mutations in QARS1, which encodes human glutaminyl-tRNA synthetase, have been associated with epilepsy, developmental regression, progressive microcephaly and cerebral atrophy. Epilepsy caused by variants in QARS1 is usually drug-resistant and intractable. Childhood onset epilepsy is also reported in various aminoacyl-tRNA synthetase disorders. We describe a case with a milder neurological phenotype than previously reported with QARS1 variants and review the seizure associations with aminoacyl-tRNA synthetase disorders. CASE REPORT: The patient is a 4-year-old girl presenting at 6 weeks of age with orofacial dyskinesia and hand stereotypies. She developed focal seizures at 7 months of age. Serial electroencephalograms showed shifting focality. Her seizures were controlled after introduction of carbamazepine. Progress MRI showed very mild cortical volume loss without myelination abnormalities or cerebellar atrophy. She was found to have novel compound heterozygous variants in QARS1 (NM_005051.2): c.[1132C > T];[1574G > A], p.[(Arg378Cys)];[(Arg525Gln)] originally classified as "variants of uncertain significance" and later upgraded to "likely pathogenic" based on functional testing and updated variant database review. Functional testing showed reduced solubility of the corresponding QARS1 mutants in vitro, but only mild two-fold loss in catalytic efficiency with the c.1132C > T variant and no noted change in tRNA(Gln) aminoacylation with the c.1574G > A variant. CONCLUSION: We describe two QARS1 variants associated with overall conserved tRNA aminoacylation activity but characterized by significantly reduced QARS protein solubility, resulting in a milder clinical phenotype. 86% of previous patients reported with QARS1 had epilepsy and 79% were pharmaco-resistant. We also summarise literature regarding epilepsy in aminoacyl-tRNA synthetase disorders, which is also often early onset, severe and drug-refractory.},

note = {1872-7131 (Electronic) 

0387-7604 (Linking) 

Case Reports},

keywords = {FRUGIER, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{12020,

title = {Adaptation of the Romanomermis culicivorax CCA-Adding Enzyme to Miniaturized Armless tRNA Substrates },

author = {O Hennig and S Philipp and S Bonin and K Rollet and T Kolberg and T Jühling and H Betat and C Sauter and M Mörl

},

url = {https://www.mdpi.com/1422-0067/21/23/9047},

doi = {10.3390/ijms21239047 },

year  = {2020},

date = {2020-11-28},

journal = {International Journal of Molecular Sciences},

volume = {21},

number = {23},

pages = {E9047},

abstract = {The mitochondrial genome of the nematode Romanomermis culicivorax encodes for miniaturized hairpin-like tRNA molecules that lack D- as well as T-arms, strongly deviating from the consensus cloverleaf. The single tRNA nucleotidyltransferase of this organism is fully active on armless tRNAs, while the human counterpart is not able to add a complete CCA-end. Transplanting single regions of the Romanomermis enzyme into the human counterpart, we identified a beta-turn element of the catalytic core that-when inserted into the human enzyme-confers full CCA-adding activity on armless tRNAs. This region, originally identified to position the 3'-end of the tRNA primer in the catalytic core, dramatically increases the enzyme's substrate affinity. While conventional tRNA substrates bind to the enzyme by interactions with the T-arm, this is not possible in the case of armless tRNAs, and the strong contribution of the beta-turn compensates for an otherwise too weak interaction required for the addition of a complete CCA-terminus. This compensation demonstrates the remarkable evolutionary plasticity of the catalytic core elements of this enzyme to adapt to unconventional tRNA substrates. },

keywords = {CCA-adding enzyme, co-evolution, evolutionary plasticity, FRUGIER, minimalized armless tRNAs, tRNA nucleotidyltransferase, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {The Expanding LARS2 Phenotypic Spectrum: HLASA, Perrault Syndrome With Leukodystrophy, and Mitochondrial Myopathy},

author = {L G Riley and J Rudinger-Thirion and M Frugier and M Wilson and M Luig and T I Alahakoon and C Y Nixon and E P Kirk and T Roscioli and S Lunke and Z Stark and K J Wierenga and S Palle and M Walsh and E Higgs and S Arbuckle and S Thirukeswaran and A G Compton and D R Thorburn and J Christodoulou},

url = {https://pubmed.ncbi.nlm.nih.gov/32442335/?dopt=Abstract},

doi = {doi: 10.1002/humu.24050},

isbn = {32442335},

year  = {2020},

date = {2020-01-01},

journal = {Hum Mutat},

volume = {41},

number = {8},

pages = {1425-1434},

abstract = {Perrault syndrome is a rare autosomal recessive disorder characterized by sensorineural hearing loss (SNHL) in both sexes and primary ovarian insufficiency in 46, XX karyotype females. Biallelic variants in five genes are reported to be causative: HSD17B4, HARS2, LARS2, CLPP and C10orf2. Here we present eight families affected by Perrault syndrome. In five families we identified novel or previously reported variants in HSD17B4, LARS2, CLPP and C10orf2. The proband from each family was whole exome sequenced and variants confirmed by Sanger sequencing. A female was compound heterozygous for a known, p.(Gly16Ser) and novel, p.(Val82Phe) variant in D-bifunctional protein (HSD17B4). A family was homozygous for mitochondrial leucyl aminocyl tRNA synthetase (mtLeuRS) (LARS2) p.(Thr522Asn), previously associated with Perrault syndrome. A further family was compound heterozygous for mtLeuRS, p.(Thr522Asn) and a novel variant, p.(Met117Ile). Affected individuals with LARS2 variants had low frequency SNHL, a feature previously described in Perrault syndrome. A female with significant neurological disability was compound heterozygous for p.(Arg323Gln) and p.(Asn399Ser) variants in Twinkle (C10orf2). A male was homozygous for a novel variant in CLPP, p.(Cys144Arg). In three families there were no putative pathogenic variants in these genes confirming additional disease-causing genes remain unidentified. We have expanded the spectrum of disease-causing variants associated with Perrault syndrome.},

keywords = {FRUGIER, Perrault syndrome low frequency hearing loss primary ovarian insufficiency sensorineural hearing loss, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Monitoring the Production of High Diffraction-Quality Crystals of Two Enzymes in Real Time Using In Situ Dynamic Light Scattering},

author = {R de Wijn and K Rollet and S Engilberge and A G McEwen and O Hennig and H Betat and M Mörl and F Riobé and O Maury and E Girard and P Bénas and B Lorber and C Sauter},

url = {https://www.mdpi.com/2073-4352/10/2/65},

doi = {10.3390/cryst10020065},

year  = {2020},

date = {2020-01-01},

journal = {Crystals},

volume = {10},

number = {2},

pages = {65},

abstract = {The reproducible preparation of well-diffracting crystals is a prerequisite for every structural study based on crystallography. An instrument called XtalController has recently been designed that allows the monitoring of crystallization assays using dynamic light scattering and microscopy, and integrates piezo pumps to alter the composition of the mother liquor during the experiment. We have applied this technology to study the crystallization of two enzymes, the CCA-adding enzyme of the psychrophilic bacterium Planococcus halocryophilus, and the lysozyme from hen egg white in the presence of a synthetic chemical nucleant. We were able to (i) detect early nucleation events and (ii) drive the crystallization system (through cycles of dissolution/crystallization) toward growth conditions yielding crystals with excellent diffraction properties. This technology opens a way to the rational production of samples for crystallography, ranging from nanocrystals for electron diffraction, microcrystals for serial or conventional X-ray diffraction, to larger crystals for neutron diffraction.},

keywords = {enzyme crystallization dynamic light scattering nucleation nucleant Tb-Xo4 crystallophore microcrystals nanocrystals X-ray diffraction XtalController, FRUGIER, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Structural Basis of Nanobody Recognition of Grapevine Fanleaf Virus and of Virus Resistance Loss},

author = {I Orlov and C Hemmer and L Ackerer and B Lorber and A Ghannam and V Poignavent and K Hleibieh and C Sauter and C Schmitt-Keichinger and L Belval and J M Hily and A Marmonier and V Komar and S Gersch and P Schellenberger and P Bron and E Vigne and S Muyldermans and O Lemaire and G Demangeat and C Ritzenthaler and B P Klaholz},

url = {https://www.ncbi.nlm.nih.gov/pubmed/32371486?dopt=Abstract},

doi = {10.1073/pnas.1913681117},

isbn = {32371486},

year  = {2020},

date = {2020-01-01},

journal = {Proc Natl Acad Sci U S A},

volume = {117},

number = {20},

pages = {10848-10855},

abstract = {Grapevine fanleaf virus (GFLV) is a picorna-like plant virus transmitted by nematodes that affects vineyards worldwide. Nanobody (Nb)-mediated resistance against GFLV has been created recently, and shown to be highly effective in plants, including grapevine, but the underlying mechanism is unknown. Here we present the high-resolution cryo electron microscopy structure of the GFLV-Nb23 complex, which provides the basis for molecular recognition by the Nb. The structure reveals a composite binding site bridging over three domains of one capsid protein (CP) monomer. The structure provides a precise mapping of the Nb23 epitope on the GFLV capsid in which the antigen loop is accommodated through an induced-fit mechanism. Moreover, we uncover and characterize several resistance-breaking GFLV isolates with amino acids mapping within this epitope, including C-terminal extensions of the CP, which would sterically interfere with Nb binding. Escape variants with such extended CP fail to be transmitted by nematodes linking Nb-mediated resistance to vector transmission. Together, these data provide insights into the molecular mechanism of Nb23-mediated recognition of GFLV and of virus resistance loss.},

keywords = {FRUGIER, GFLV nanobody structural biology virus, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Molecular basis for the differential interaction of plant mitochondrial VDAC proteins with tRNAs},

author = {T Salinas and S E Farouk-Ameqrane and E Ubrig and C Sauter and A M Duchêne and L Maréchal-Drouard},

url = {https://www.ncbi.nlm.nih.gov/pubmed/30517754?dopt=Abstract},

doi = {10.1093/nar/gky1247},

isbn = {30519697},

year  = {2019},

date = {2019-01-01},

journal = {Nucleic Acids Res},

volume = {47},

number = {2},

pages = {1048-1049},

keywords = {FRUGIER, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Biallelic variants in \textit{LARS2} and \textit{KARS} cause deafness and (ovario)leukodystrophy},

author = {M S van der Knaap and M Bugiani and M I Mendes and L G Riley and D E C Smith and J Rudinger-Thirion and M Frugier and M Breur and J Crawford and J van Gaalen and M Schouten and M Willems and Q Waisfisz and F T Mau-Them and R J Rodenburg and R J Taft and B Keren and J Christodoulou and C Depienne and C Simons and G S Salomons and F Mochel},

url = {https://www.ncbi.nlm.nih.gov/pubmed/30737337},

doi = {10.1212/WNL.0000000000007098},

isbn = {30737337},

year  = {2019},

date = {2019-01-01},

journal = {Neurology},

volume = {92},

number = {11},

pages = {e1225-e1237},

abstract = {OBJECTIVE: 

 

To describe the leukodystrophy caused by pathogenic variants in LARS2 and KARS, encoding mitochondrial leucyl transfer RNA (tRNA) synthase and mitochondrial and cytoplasmic lysyl tRNA synthase, respectively. 

METHODS: 

 

We composed a group of 5 patients with leukodystrophy, in whom whole-genome or whole-exome sequencing revealed pathogenic variants in LARS2 or KARS. Clinical information, brain MRIs, and postmortem brain autopsy data were collected. We assessed aminoacylation activities of purified mutant recombinant mitochondrial leucyl tRNA synthase and performed aminoacylation assays on patients' lymphoblasts and fibroblasts. 

RESULTS: 

 

Patients had a combination of early-onset deafness and later-onset neurologic deterioration caused by progressive brain white matter abnormalities on MRI. Female patients with LARS2 pathogenic variants had premature ovarian failure. In 2 patients, MRI showed additional signs of early-onset vascular abnormalities. In 2 other patients with LARS2 and KARS pathogenic variants, magnetic resonance spectroscopy revealed elevated white matter lactate, suggesting mitochondrial disease. Pathology in one patient with LARS2 pathogenic variants displayed evidence of primary disease of oligodendrocytes and astrocytes with lack of myelin and deficient astrogliosis. Aminoacylation activities of purified recombinant mutant leucyl tRNA synthase showed a 3-fold loss of catalytic efficiency. Aminoacylation assays on patients' lymphoblasts and fibroblasts showed about 50% reduction of enzyme activity. 

CONCLUSION: 

 

This study adds LARS2 and KARS pathogenic variants as gene defects that may underlie deafness, ovarian failure, and leukodystrophy with mitochondrial signature. We discuss the specific MRI characteristics shared by leukodystrophies caused by mitochondrial tRNA synthase defects. We propose to add aminoacylation assays as biochemical diagnostic tools for leukodystrophies.},

keywords = {FRUGIER, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {A simple and versatile microfluidic device for efficient biomacromolecule crystallization and structural analysis by serial crystallography},

author = {R de Wijn and O Hennig and J Roche and S Engilberge and K Rollet and P Fernandez-Millan and K Brillet and H Betat and M Mörl and A Roussel and E Girard and C Mueller-Dieckmann and G C Fox and V Olieric and J A Gavira and B Lorber and C Sauter},

url = {https://www.ncbi.nlm.nih.gov/pubmed/31098026?dopt=Abstract},

doi = {10.1107/S2052252519003622},

isbn = {31098026},

year  = {2019},

date = {2019-01-01},

journal = {IUCrJ},

volume = {6},

number = {Pt 3},

pages = {454-464},

abstract = {Determining optimal conditions for the production of well diffracting crystals is a key step in every biocrystallography project. Here, a microfluidic device is described that enables the production of crystals by counter-diffusion and their direct on-chip analysis by serial crystallography at room temperature. Nine 'non-model' and diverse biomacromolecules, including seven soluble proteins, a membrane protein and an RNA duplex, were crystallized and treated on-chip with a variety of standard techniques including micro-seeding, crystal soaking with ligands and crystal detection by fluorescence. Furthermore, the crystal structures of four proteins and an RNA were determined based on serial data collected on four synchrotron beamlines, demonstrating the general applicability of this multipurpose chip concept.},

keywords = {ChipX3 counter-diffusion crystallization ligand soaking macromolecule microfluidics protein structure room temperature seeding serial crystallography trace fluorescent labeling, ENNIFAR, FRUGIER, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Interaction of a Model Peptide on Gram Negative and Gram Positive Bacterial Sliding Clamps},

author = {C André and I Martiel and P Wolff and M Landolfo and B Lorber and C Silva da Veiga and A Dejaegere and P Dumas and G Guichard and V Olieric and J G Wagner and D Y Burnouf},

url = {https://www.ncbi.nlm.nih.gov/pubmed/30912430?dopt=Abstract},

doi = {10.1021/acsinfecdis.9b00089},

isbn = {30912430},

year  = {2019},

date = {2019-01-01},

urldate = {2019-01-01},

journal = {ACS Infect Dis},

volume = {5},

number = {6},

pages = {1022-1034},

abstract = {Bacterial sliding clamps control the access of DNA polymerases to the replication fork and are appealing targets for antibacterial drugs development. It is therefore essential to decipher the polymerase-clamp binding mode across various bacterial species. Here, two residues of the E. coli clamp binding pocket, EcS346 and EcM362, and their cognate residues in M. tuberculosis and B. subtilis clamps, were mutated. The effects of these mutations on the interaction of a model peptide with these variant clamps were evaluated by thermodynamic, molecular dynamics, X-rays crystallography and biochemical analyses. EcM362 and corresponding residues in Gram positive clamps occupy a strategic position where a mobile residue is essential for an efficient peptide interaction. EcS346 has a more subtle function that modulates the pocket folding dynamics, while the equivalent residue in B. subtilis is essential for polymerase activity and might therefore be a Gram positive specific molecular marker. Finally, the peptide binds through an induced-fit process to Gram negative and positive pockets but the complex stability varies according to a pocket specific network of interactions.},

keywords = {ARN-MS, ENNIFAR, FRUGIER, ITC ligand−target interaction new antibacterials development sliding clamp, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {The phenotypic spectrum of germline YARS2 variants: from isolated sideroblastic anemia to mitochondrial myopathy, lactic acidosis and sideroblastic anemia 2},

author = {L G Riley and M M Heeney and J Rudinger-Thirion and M Frugier and D R Campagna and R Zhou and G A Hale and L M Hilliard and J A Kaplan and J L Kwiatkowski and C A Sieff and D P Steensma and A J Rennings and A Simons and N Schaap and R J Roodenburg and T Kleefstra and L Arenillas and J Fita-Torró and R Ahmed and M Abboud and E Bechara and R Farah and R Y Tamminga and S S Bottomley and M Sanchez and D W Swinkels and J Christodoulou and M D Fleming},

url = {https://www.ncbi.nlm.nih.gov/pubmed/30026338},

doi = {10.3324/haematol.2017.182659},

isbn = {30026338},

year  = {2018},

date = {2018-01-01},

journal = {Haematologica},

volume = {103},

number = {12},

pages = {2008-2015},

abstract = {YARS2 variants have previously been described in patients with myopathy, lactic acidosis and sideroblastic anemia 2 (MLASA2). YARS2 encodes the mitochondrial tyrosyl-tRNA synthetase, which is responsible for conjugating tyrosine to its cognate mt-tRNA for mitochondrial protein synthesis. Here we describe 14 individuals from 11 families presenting with sideroblastic anemia and with YARS2 variants that we identified using a sideroblastic anemia gene panel or exome sequencing. The phenotype of these patients ranged from MLASA to isolated congenital sideroblastic anemia. As in previous cases, inter- and intra-familial phenotypic variability was observed, however this report includes the first cases with isolated sideroblastic anemia and patients with biallelic YARS2 variants that have no clinically ascertainable phenotype. We identified ten novel YARS2 variants and three previously reported variants. In vitro amino-acylation assays of three five novel missense variants showed they that three had less effect on the catalytic activity of YARS2 than the most commonly reported variant, p.(Phe52Leu), associated with MLASA2, which may explain the milder phenotypes in patients with these variants. However, the other two missense variants had a more severe effect on YARS2 catalytic efficiency. Several patients carried the common YARS2 c.572 G>T, p.(Gly191Val) variant (minor allele frequency = 0.1259) in trans with a rare deleterious YARS2 variant. We have previously shown that the p.(Gly191Val) variant reduces YARS2 catalytic activity. Consequently, we suggest that biallelic YARS2 variants, including severe loss-of-function alleles in trans of the common p.(Gly191Val) variant, should be considered as a cause of isolated congenital sideroblastic anemia, as well as the MLASA syndromic phenotype.},

keywords = {Congenital sideroblastic anemia MLASA YARS2 mitochondrial myopathy sideroblastic anemia, FRUGIER, Unité ARN},

pubstate = {published},

tppubtype = {article}

}