Publications

2017

• Trm112, a Protein Activator of Methyltransferases Modifying Actors of the Eukaryotic Translational Apparatus
  
  • Bourgeois Gabrielle
  • Létoquart Juliette
  • van Tran Nhan
  • Graille Marc
  Biomolecules, MDPI, 2017, 7 (1), pp.7. Post-transcriptional and post-translational modifications are very important for the control and optimal efficiency of messenger RNA (mRNA) translation. Among these, methylation is the most widespread modification, as it is found in all domains of life. These methyl groups can be grafted either on nucleic acids (transfer RNA (tRNA), ribosomal RNA (rRNA), mRNA, etc.) or on protein translation factors. This review focuses on Trm112, a small protein interacting with and activating at least four different eukaryotic methyltransferase (MTase) enzymes modifying factors involved in translation. The Trm112-Trm9 and Trm112-Trm11 complexes modify tRNAs, while the Trm112-Mtq2 complex targets translation termination factor eRF1, which is a tRNA mimic. The last complex formed between Trm112 and Bud23 proteins modifies 18S rRNA and participates in the 40S biogenesis pathway. In this review, we present the functions of these eukaryotic Trm112-MTase complexes, the molecular bases responsible for complex formation and substrate recognition, as well as their implications in human diseases. Moreover, as Trm112 orthologs are found in bacterial and archaeal genomes, the conservation of this Trm112 network beyond eukaryotic organisms is also discussed. (10.3390/biom7010007)
  DOI : 10.3390/biom7010007
• Structural Basis of Arp2/3 Complex Inhibition by GMF, Coronin, and Arpin
  
  • Sokolova Olga
  • Chemeris Angelina
  • Guo Siyang
  • Alioto Salvatore L
  • Gandhi Meghal
  • Padrick Shae
  • Pechnikova Evgeniya
  • David Violaine
  • Gautreau Alexis
  • Goode Bruce
  Journal of Molecular Biology, Elsevier, 2017, 429 (2), pp.237-248. The evolutionarily conserved Arp2/3 complex plays a central role in nucleating the branched actin filament arrays that drive cell migration, endocytosis, and other processes. To better understand Arp2/3 complex regulation, we used single particle electron microscopy to compare the structures of Arp2/3 complex bound to three different inhibitory ligands: GMF, Coronin, and Arpin. Although the three inhibitors have distinct binding sites on Arp2/3 complex, they each induced an ‘open’ nucleation-inactive conformation. Coronin promoted a standard (previously described) open conformation of Arp2/3 complex, with the N-terminal β-propeller domain of Coronin positioned near the p35/ARPC2 subunit of Arp2/3 complex. GMF induced two distinct open conformations of Arp2/3 complex, which correlated with two suggested binding sites for GMF. Further, GMF synergized with Coronin in inhibiting actin nucleation by Arp2/3 complex. Arpin, which uses VCA-related acidic (A) motifs to interact with the Arp2/3 complex, induced the standard open conformation, and two new masses appeared at positions near Arp2 and Arp3. Further, Arpin showed additive inhibitory effects on Arp2/3 complex with Coronin and GMF. Together, these data suggest that Arp2/3 complex conformation is highly polymorphic and that its activities can be controlled combinatorially by different inhibitory ligands. (10.1016/j.jmb.2016.11.030)
  DOI : 10.1016/j.jmb.2016.11.030
• Probing the stereospecificity of tyrosyl- and glutaminyl-tRNA synthetase with molecular dynamics
  
  • Druart Karen
  • Guennec Maeva Le
  • Palmai Zoltan
  • Simonson Thomas
  Journal of Molecular Graphics and Modelling, Elsevier, 2017, 71, pp.192-199. The stereospecificity of aminoacyl-tRNA synthetases helps exclude d-amino acids from protein synthesis and could perhaps be engineered to allow controlled d-amino acylation of tRNA. We use molecular dynamics simulations to probe the stereospecificity of the class I tyrosyl- and glutaminyl-tRNA synthetases (TyrRS, GlnRS), including wildtype enzymes and three point mutants suggested by three different protein design methods. l/d binding free energy differences are obtained by alchemically and reversibly transforming the ligand from L to D in simulations of the protein-ligand complex. The D81Q mutation in Escherichia coli TyrRS is homologous to the D81R mutant shown earlier to have inverted stereospecificity. D81Q is predicted to lead to a rotated ligand backbone and an increased, not a decreased l-Tyr preference. The E36Q mutation in Methanococcus jannaschii TyrRS has a predicted l/d binding free energy difference ΔΔG of just 0.5±0.9kcal/mol, compared to 3.1±0.8kcal/mol for the wildtype enzyme (favoring l-Tyr). The ligand ammonium position is preserved in the d-Tyr complex, while the carboxylate is shifted. Wildtype GlnRS has a similar preference for l-glutaminyl adenylate; the R260Q mutant has an increased preference, even though Arg260 makes a large contribution to the wildtype ΔΔG value. (10.1016/j.jmgm.2016.11.007)
  DOI : 10.1016/j.jmgm.2016.11.007
• Gradients of Rac1 Nanoclusters Support Spatial Patterns of Rac1 Signaling
  
  • Remorino Amanda
  • de Beco Simon
  • Cayrac Fanny
  • Di Federico Fahima
  • Cornilleau Gaetan
  • Gautreau Alexis
  • Parrini Maria Carla
  • Masson Jean-Baptiste
  • Dahan Maxime
  • Coppey Mathieu
  Cell Reports, Elsevier Inc, 2017, 21 (7), pp.1922-1935. Rac1 is a small RhoGTPase switch that orchestrates actin branching in space and time and protrusion/retraction cycles of the lamellipodia at the cell front during mesenchymal migration. Biosensor imaging has revealed a graded concentration of active GTP-loaded Rac1 in protruding regions of the cell. Here, using single-molecule imaging and super-resolution microscopy, we show an additional supramolecular organization of Rac1. We find that Rac1 partitions and is immobilized into nanoclusters of 50–100 molecules each. These nanoclusters assemble because of the interaction of the polybasic tail of Rac1 with the phosphoinositide lipids PIP2 and PIP3. The additional interactions with GEFs and possibly GAPs, downstream effectors, and other partners are responsible for an enrichment of Rac1 nanoclusters in protruding regions of the cell. Our results show that subcellular patterns of Rac1 activity are supported by gradients of signaling nanodomains of heterogeneous molecular composition, which presumably act as discrete signaling platforms. (10.1016/j.celrep.2017.10.069)
  DOI : 10.1016/j.celrep.2017.10.069
• β1 integrin dependent Rac/group I PAK signaling mediates YAP activation of Yes associated protein 1 (YAP1) via NF2/merlin.
  
  • Sabra Hiba
  • Brunner Molly
  • Mandati Vinay
  • Wehrle-Haller Bernhard
  • Lallemand Dominique
  • Ribba Anne-Sophie
  • Chevalier Genevieve
  • Guardiola Philippe
  • Block Marc R.
  • Bouvard Daniel
  Journal of Biological Chemistry, American Society for Biochemistry and Molecular Biology, 2017. Cell adhesion to the extracellular matrix or to surrounding cells plays a key role in cell proliferation and differentiation, and is critical for proper tissue homeostasis. An important pathway in adhesion-dependent cell proliferation is the Hippo signaling cascade, which is coregulated by the transcription factors Yes-associated protein 1 (YAP1) and transcriptional coactivator with PDZ-binding motif (TAZ). However, how cells integrate extracellular information at the molecular level to regulate YAP1's nuclear localization is still puzzling. Herein, we investigated the role of β1 integrins in regulating this process. We found that β1 integrin–dependent cell adhesion is critical for supporting cell proliferation in mesenchymal cells both in vivo and in vitro. β1 integrin– dependent cell adhesion relied on the relocation of YAP1 to the nucleus after the downregulation of its phosphorylated state mediated by large tumor suppressor gene 1 and 2 (LATS1/2). We also found that this phenotype relies on β1 integrin–dependent local activation of the small GTPase Rac1 at the plasma membrane to control the activity of P21 (RAC1)-activated kinase (PAK) of group 1. We further report that the regulatory protein merlin (neurofibromin 2, NF2) interacts with both YAP1 and LATS1/2 via its C-terminal moiety and FERM domain, respectively. PAK-mediated merlin phosphorylation on Ser-518 reduced merlin's interactions with both LATS1/2 and YAP1, resulting in YAP1 dephosphorylation and nuclear shuttling. Our results highlight Rac1/PAK1 as major players in YAP1 regulation triggered by cell adhesion. (10.1074/jbc.M117.808063)
  DOI : 10.1074/jbc.M117.808063
• Activation mode of the eukaryotic m2G10 tRNA methyltransferase Trm11 by its partner protein Trm112
  
  • Bourgeois Gabrielle
  • Marcoux Julien
  • Saliou Jean-Michel
  • Cianférani Sarah
  • Graille Marc
  Nucleic Acids Research, Oxford University Press, 2017, 45 (4), pp.1971–1982. Post-transcriptional and post-translational modifications of factors involved in translation are very important for the control and accuracy of protein biosynthesis. Among these factors, tRNAs harbor the largest variety of grafted chemical structures, which participate in tRNA stability or mRNA decoding. Here, we focused on Trm112 protein, which associates with four different eukaryotic methyltrans-ferases modifying tRNAs (Trm9 and Trm11) but also 18S-rRNA (Bud23) and translation termination factor eRF1 (Mtq2). In particular, we have investigated the role of Trm112 in the Trm11-Trm112 complex, which forms 2-methylguanosine at position 10 on several tRNAs and thereby is assumed to stabilize tRNA structure. We show that Trm112 is important for Trm11 enzymatic activity by influencing S-adenosyl-L-methionine binding and by contributing to tRNA binding. Using hydrogen-deuterium eXchange coupled to mass spectrometry, we obtained experimental evidences that the Trm11-Trm112 interaction relies on the same molecular bases as those described for other Trm112-methyltransferases complexes. Hence, all Trm112-dependent methyltrans-ferases compete to interact with this partner. (10.1093/nar/gkw1271)
  DOI : 10.1093/nar/gkw1271