Publications

2018

• Structural and functional insight into serine hydroxymethyltransferase from Helicobacter pylori
  
  • Sodolescu Andreea
  • Dian Cyril
  • Terradot Laurent
  • Bouzhir-Sima Latifa
  • Lestini Roxane
  • Myllykallio Hannu
  • Skouloubris Stéphane
  • Liebl Ursula
  PLoS ONE, Public Library of Science, 2018, 13 (12), pp.e0208850. Serine hydroxymethyltransferase (SHMT), encoded by the glyA gene, is a ubiquitous pyridoxal 5’-phosphate (PLP)-dependent enzyme that catalyzes the formation of glycine from serine. The thereby generated 5,10-methylene tetrahydrofolate (MTHF) is a major source of cellular one-carbon units and a key intermediate in thymidylate biosynthesis. While in virtually all eukaryotic and many bacterial systems thymidylate synthase ThyA, SHMT and dihydrofolate reductase (DHFR) are part of the thymidylate/folate cycle, the situation is different in organisms using flavin-dependent thymidylate synthase ThyX. Here the distinct catalytic reaction directly produces tetrahydrofolate (THF) and consequently in most ThyX-containing organisms, DHFR is absent. While the resulting influence on the folate metabolism of ThyX-containing bacteria is not fully understood, the presence of ThyX may provide growth benefits under conditions where the level of reduced folate derivatives is compromised. Interestingly, the third key enzyme implicated in generation of MTHF, serine hydroxymethyltransferase (SHMT), has a universal phylogenetic distribution, but remains understudied in ThyX-containg bacteria. To obtain functional insight into these ThyX-dependent thymidylate/folate cycles, we characterized the predicted SHMT from the ThyX-containing bacterium Helicobacter pylori. Serine hydroxymethyltransferase activity was confirmed by functional genetic complementation of a glyA-inactivated E. coli strain. A H. pylori ΔglyA strain was obtained, but exhibited markedly slowed growth and had lost the virulence factor CagA. Biochemical and spectroscopic evidence indicated formation of a characteristic enzyme-PLP-glycine-folate complex and revealed unexpectedly weak binding affinity of PLP. The three-dimensional structure of the H. pylori SHMT apoprotein was determined at 2.8Ǻ resolution, suggesting a structural basis for the low affinity of the enzyme for its cofactor. Stabilization of the proposed inactive configuration using small molecules has potential to provide a specific way for inhibiting HpSHMT. (10.1371/journal.pone.0208850)
  DOI : 10.1371/journal.pone.0208850
• Dynamique interne des flavoprotéines étudiée par spectroscopie femtoseconde
  
  • Nag Lipsa
  , 2018. Nature employs charge transfer reactions in many biological functions. Redox-active cofactors like flavins (FAD and FMN) are often implicated in such reactions. Charge transfer in proteins often proceeds via formation of radical intermediates. The amino acid radicals of tyrosine (TyrOH) and tryptophan are thought to play important roles as intermediates in intra- and interprotein charge transfer reactions. Tryptophanyl radicals (both protonated cation and deprotonated neutral forms), had been characterized before. However, tyrosyl radicals had only been characterized in the neutral form, and were thought to be formed by concerted electron extraction and deprotonation of tyrosine. Short-lived intermediates are often difficult to observe in biochemical reactions, but may be populated when they can be photochemically formed using short light pulses.In this work, we have characterized intermediates in non-functional charge transfer reactions in flavoproteins using femtosecond time-resolved fluorescence and absorption spectroscopy. Excited states and product states formed in the wild type and mutant forms of the methyltransferase flavoenzyme TrmFO from Thermus thermophilus were investigated. In the TrmFO active site, a tyrosine (Tyr343), is closely stacked on the FAD isoalloxazine ring and a cysteine (Cys51) can form a highly fluorescent adduct with the FAD. In the mutant C51A, FADox fluorescence is strongly quenched by electron transfer from the Tyr343 in ~1ps. The resulting product state displayed a distinct spectral feature- a strong absorption band at ~490 nm unlike any previously characterized radical species. It was assigned to the radical cation of tyrosine (TyrOH•+) which had never been observed before. The FAD•-TyrOH•+ intermediate, is very short-lived as it decays in ~3ps, through charge recombination. As a general conclusion, despite the very low pKa of TyrOH•+, electron transfer from tyrosine can occur without concomitant proton transfer.Using polarization photoselection experiments, we estimated the dipole moment direction for this new transition. The resultant angle between the excited FADox transition and the probed TyrOH•+ transition in C51A TrmFO was 31º±5º. This result sets the orientation of the dipole moment of the transition in the molecular frame of the phenol ring. The finding of distinct directions for the excited FAD transition band and the 490 nm transition confirms their origin in different molecular entities.Following the results from TrmFO, we reinvestigated the photochemistry in the model flavoprotein glucose oxidase (GOX). Here, both tryptophan and tyrosine residues are located in the vicinity of FAD and the photoproduct evolution on the picosecond timescale is more complex. Distinct phases of excited state decay with time constants of 1ps and ~4ps were observed, as well as phases of ~4ps, ~37 ps and a longer-lives phase for product state evolution. Consequently, a comprehensive model for the involvement of radicals of tyrosine and tryptophan and, the different FAD redox states, in the light-induced charge separation and recombination in GOX was made. Partial involvement of the TyrOH•+ radical cation, spectrally similar to C51A TrmFO, was required for the 4 ps and 37 ps phases to account for the ensemble of data. This result explains previous enigmatic features and indicates the involvement of TyrOH•+ in a variety of protein systems.So far, only the deprotonated tyrosyl radical TyrO• had been observed as a functional intermediate in several systems. The visualization of protonated TyrOH•+ radical in TrmFO C51A and GOX suggests the possibility of its intermediate formation as a precursor of TyrO• in functional biochemical reactions.Finally, in TrmFO the construction of specific variants with site-directed mutagenesis was initiated to study active-site flexibility using electron transfer rates as conformational markers. Further experimental and modeling work is required to pursue this goal.
• Author Correction: A mechanism for CO regulation of ion channels
  
  • Kapetanaki Sofia
  • Burton Mark
  • Basran Jaswir
  • Uragami Chiasa
  • Moody Peter
  • Mitcheson John
  • Schmid Ralf
  • Davies Noel
  • Dorlet Pierre
  • Vos Marten H.
  • Storey Nina
  • Raven Emma
  Nature Communications, Nature Publishing Group, 2018, 9, pp.3354. The originally published version of this article contained an error in the subheading ‘Heme is required for CO-dependent channel activation’, which was incorrectly given as ‘Hame is required for CO-dependent channel activation’. This has now been corrected in both the PDF and HTML versions of the Article (10.1038/s41467-018-05622-6)
  DOI : 10.1038/s41467-018-05622-6
• Color Imaging with Multimodal Three-Photon Microscopy
  
  • Abdeladim Lamiae
  • Mahou Pierre
  • Supatto Willy
  • Beaurepaire Emmanuel
  • Guesmi Khmaies
  • Jurkus Karolis
  • Rigaud Philippe
  • Georges Patrick
  • Hanna Marc
  • Druon Frédéric
  • Tozer Samuel
  • Kumamoto Takuma
  • Loulier Karine
  • Livet Jean
  • Dray Nicolas
  Optics and photonics news, Optical Society of America - OSA Publishing, 2018.
• Advances and challenges in drug design against tuberculosis: application of in silico approaches
  
  • Aleksandrov Alexey
  • Myllykallio Hannu
  Expert Opinion on Drug Discovery, Informa Healthcare, 2018, pp.1 - 12. (10.1080/17460441.2019.1550482)
  DOI : 10.1080/17460441.2019.1550482
• Archaea-guided identification of an elusive human rRNA m6A methyltransferase enzyme
  
  • van Tran Nhan
  • Muller Leslie
  • van Fassen Ernst
  • Lestini Roxane
  • Létoquart Juliette
  • de Crecy-Lagard Valerie
  • Lafontaine Denis L. J.
  • Cianferani Sarah
  • Graille Marc
  , 2018.
• Chiral Cilia Orientation in the Left-Right Organizer
  
  • Ferreira Rita
  • Pakula Guillaume
  • Klaeyle Lhéanna
  • Fukui Hajime
  • Vilfan Andrej
  • Supatto Willy
  • Vermot Julien
  Cell Reports, Elsevier Inc, 2018, 25 (8), pp.2008-2016.e4. (10.1016/j.celrep.2018.10.069)
  DOI : 10.1016/j.celrep.2018.10.069
• Large volume multicolor nonlinear microscopy of neural tissues
  
  • Abdeladim Lamiae
  , 2018. Multiphoton microscopy has transformed neurobiology since the 1990s by enabling 3D imaging of thick tissues at subcellular resolution. However the depths provided by multiphoton microscopy are limited to a few hundreds of micrometers inside scattering tissues such as the brain. In the recent years, several strategies have emerged to overcome this depth limitation and to access larger volumes of tissue. Although these novel approaches are transforming brain imaging, they currently lack efficient multicolor and multicontrast modalities. This work aims at developing large-scale and deep-tissue multiphoton imaging modalities with augmented contrast capabilities. In a first chapter, we present the challenges of high-content large-volume brain imaging, with a particular emphasis on powerful multicolor labeling strategies which have so far been restricted to limited scales. We then introduce chromatic serial multiphoton (Chrom-SMP) microscopy, a method which combines automated histology with multicolor two-photon excitation through wavelength-mixing to access multiple nonlinear contrasts across large volumes, from several mm3 to whole brains, with submicron resolution and intrinsic channel registration. In a third chapter, we explore the potential of this novel approach to open novel experimental paradigms in neurobiological studies. In particular, we demonstrate multicolor volumetric histology of several mm3 of Brainbow-labeled tissues with preserved diffraction-limited resolution and illustrate the strengths of this method through color-based tridimensional analysis of astrocyte morphology, interactions and lineage in the mouse cerebral cortex. We further illustrate the potential of the method through multiplexed whole-brain mapping of axonal projections labeled with distinct tracers. Finally, we develop multimodal three-photon microscopy as a method to access larger depths in live settings.
• Snapshots of archaeal DNA replication and repair in living cells using super-resolution imaging
  
  • Delpech Floriane
  • Collien Yoann
  • Mahou Pierre
  • Beaurepaire Emmanuel
  • Myllykallio Hannu
  • Lestini Roxane
  Nucleic Acids Research, Oxford University Press, 2018. (10.1093/nar/gky829)
  DOI : 10.1093/nar/gky829
• Neural Cell Segmentation in Large-Scale 3D Color Fluorescence Microscopy Images for Developemental Neuroscience
  
  • Nourbakhsh Farshad
  • Abdeladim Lamiae
  • Clavreul Solène
  • Loulier Karine
  • Beaurepaire Emmanuel
  • Livet Jean
  • Chessel Anatole
  , 2018, pp.3828-3832. The cells composing brain tissue, neurons, and glia, form extraordinarily complex networks that support cognitive functions. Understanding the organization and development of these networks requires quantitative data resolved at the single cell level. To this aim, we apply novel large-scale 3D multicolor microscopy methodologies in combination with “Brainbow”, a transgenic approach enabling to label neural cells with diverse combinations of spectrally distinct fluorescent proteins. In this paper, we present a pipeline based on Convolutional Neural Network (CNN) to detect and segment individual astrocytes, the main type of glial cells of the brain, and map the domains occupied by their fine processes. This bioimage analysis approach successfully handles the challenging variety of astrocyte shape, color, size and their overlap with background elements. Our method shows significant improvement compared with classical techniques, opening the way to varied biological inquiries. (10.1109/ICIP.2018.8451702)
  DOI : 10.1109/ICIP.2018.8451702
• Combining the polarizable Drude force field with a continuum electrostatic Poisson-Boltzmann implicit solvation model
  
  • Aleksandrov Alexey
  • Lin Fang-Yu
  • Roux Benoît
  • Mackerell Alexander
  Journal of Computational Chemistry, Wiley, 2018, 39 (22), pp.1707-1719. (10.1002/jcc.25345)
  DOI : 10.1002/jcc.25345
• Resonant broadband stimulated Raman scattering in myoglobin
  
  • Ferrante C.
  • Batignani G.
  • Fumero G.
  • Pontecorvo E.
  • Virga A.
  • Montemiglio L.
  • Cerullo G.
  • Vos Marten H.
  • Scopigno T.
  Journal of Raman Spectroscopy, Wiley, 2018, 49 (6), pp.913-920. (10.1002/jrs.5323)
  DOI : 10.1002/jrs.5323
• Activation of the mismatch-specific endonuclease EndoMS/NucS by the replication clamp is required for high fidelity DNA replication
  
  • Ishino Sonoko
  • Skouloubris Stéphane
  • Kudo Hanae
  • L’hermitte-Stead Caroline
  • Es-Sadik Asmae
  • Lambry Jean-Christophe
  • Ishino Yoshizumi
  • Myllykallio Hannu
  Nucleic Acids Research, Oxford University Press, 2018. The mismatch repair (MMR) system, exemplified by the MutS/MutL proteins, is widespread in Bacteria and Eukarya. However, molecular mechanisms how numerous archaea and bacteria lacking the mutS/mutL genes maintain high replication fidelity and genome stability have remained elusive. EndoMS is a recently discovered hyperthermophilic mismatch-specific endonuclease encoded by nucS in Thermococcales. We deleted the nucS from the actinobacterium Corynebacterium glutamicum and demonstrated a drastic increase of spontaneous transition mutations in the nucS deletion strain. The observed spectra of these mutations were consistent with the enzymatic properties of EndoMS in vitro. The robust mismatch-specific endonuclease activity was detected with the purified C. glutamicum EndoMS protein but only in the presence of the β-clamp (DnaN). Our biochemical and genetic data suggest that the frequently occurring G/T mismatch is efficiently repaired by the bacterial EndoMS-β−clamp complex formed via a carboxy-terminal sequence motif of EndoMS proteins. Our study thus has great implications for understanding how the activity of the novel MMR system is coordinated with the replisome and provides new mechanistic insight into genetic diversity and mutational patterns in industrially and clinically (e.g. Mycobacteria) important archaeal and bacterial phyla previously thought to be devoid of the MMR system. (10.1093/nar/gky460)
  DOI : 10.1093/nar/gky460
• Unique Features and Anti-microbial Targeting of Folate- and Flavin-Dependent Methyltransferases Required for Accurate Maintenance of Genetic Information
  
  • Myllykallio Hannu
  • Sournia Pierre
  • Héliou Alice
  • Liebl Ursula
  Frontiers in Microbiology, Frontiers Media, 2018, 9, pp.918. Comparative genome analyses have led to the discovery and characterization of novel flavin- and folate-dependent methyltransferases that mainly function in DNA precursor synthesis and post-transcriptional RNA modification by forming (ribo) thymidylate and its derivatives. Here we discuss the recent literature on the novel mechanistic features of these enzymes sometimes referred to as “uracil methyltransferases,” albeit we prefer to refer to them as (ribo) thymidylate synthases. These enzyme families attest to the convergent evolution of nucleic acid methylation. Special focus is given to describing the unique characteristics of these flavin- and folate-dependent enzymes that have emerged as new models for studying the non-canonical roles of reduced flavin cofactors (FADH2) in relaying carbon atoms between enzyme substrates. This ancient enzymatic methylation mechanism with a very wide phylogenetic distribution may be more commonly used for biological methylation reactions than previously anticipated. This notion is exemplified by the recent discovery of additional substrates for these enzymes. Moreover, similar reaction mechanisms can be reversed by demethylases, which remove methyl groups e.g., from human histones. Future work is now required to address whether the use of different methyl donors facilitates the regulation of distinct methylation reactions in the cell. It will also be of great interest to address whether the low activity flavin-dependent thymidylate synthases ThyX represent ancestral enzymes that were eventually replaced by the more active thymidylate synthases of the ThyA family to facilitate the maintenance of larger genomes in fast-growing microbes. Moreover, we discuss the recent efforts from several laboratories to identify selective anti-microbial compounds that target flavin-dependent thymidylate synthase ThyX. Altogether we underline how the discovery of the alternative flavoproteins required for methylation of DNA and/or RNA nucleotides, in addition to providing novel targets for antibiotics, has provided new insight into microbial physiology and virulence. (10.3389/fmicb.2018.00918)
  DOI : 10.3389/fmicb.2018.00918
• Stromal scattering mean-free path, as a quantitative measure of corneal transparency, derived from objective analysis of depth-resolved corneal images
  
  • Bocheux Romain
  • Borderie Vincent M.
  • Laroche Laurent
  • Plamann Karsten
  • Irsch Kristina
  , 2018, 59 (9), pp.5812. Purpose : To address the unmet need for an objective means to quantify corneal transparency, we propose using the scattering mean-free path derived from objective analysis of depth-resolved corneal images, and demonstrate the feasibility of this approach by means of full-field optical coherence tomographic microscopy (FF-OCT or FF-OCM). Methods : An algorithm and related software were developed in Matlab (Mathworks, Inc., USA) to derive the scattering mean-free path from depth-resolved corneal images. Specifically, mean amplitude depth profiles were generated to assess stromal light backscattering, that is, the mean amplitude value was calculated as a function of stromal depth. The resultant profiles were fitted to an exponential function A(z) ~ e-Bz, which allowed us to extract the scattering mean-free path, ls= 1/B, as a measure of transparency. As a proof-of-concept demonstration, this approach was applied to 3D-image stacks acquired of two corneas (one eye-bank cornea and one pathological cornea with compromised transparency, as per “gold-standard” subjective and qualitative image inspection; see Fig. 1) with ex-vivo FF-OCT (LLTech, France), after automatic 3D-image segmentation, flattening based on the epithelial surface, and extraction of the stroma. Results : A graphical representation of the results is shown in Fig. 2. Logarithmic amplitude profiles are depicted, representing the grey value averaged over the entire field-of-view of individual en-face stromal slices as a function of depth, and illustrating the robustness of the exponential fitting procedure (linear regression line in log space) and scattering mean-free path extraction, confirmed by the very small standard deviations: ls= 180 ± 1 µm and ls= 125 ± 0 µm for the eye-bank and pathological cornea respectively. Conclusions : We demonstrated the feasibility and robustness of deriving the scattering mean-free path, as a quantitative measure of corneal transparency, from objective analysis of stromal light backscattering with FF-OCT. This approach has the potential to supply the demand for an objective means to quantify corneal transparency in both the eye-bank and clinical setting, where such means are limited. While in-vivo development of FF-OCT is underway, the proposed analysis may already be implemented into existing depth-resolved corneal imaging methods (e.g., confocal microscopy).
• Stromal scattering mean-free path, as a quantitative measure of corneal transparency, derived from objective analysis of depth-resolved corneal images
  
  • Bocheux Romain
  • Borderie Vincent M
  • Laroche Laurent
  • Plamann Karsten
  • Irsch Kristina
  , 2018.
• Use of MPA-capped CdS quantum dots for sensitive detection and quantification of Co2+ ions in aqueous solution
  
  • Bel Haj Mohamed Naim
  • Ben Brahim Nassim
  • Mrad Randa
  • Haouari Mohamed
  • Ben Chaâbane Rafik
  • Négrerie Michel
  Analytica Chimica Acta, Elsevier Masson, 2018, 1028, pp.50 - 58. Water soluble CdS quantum dots (QDs) were synthesized by a simple aqueous chemical route using mercaptopropionic acid (MPA) as a stabilizer. These QDs had a fluorescence emission band maximum at 540 nm with a FWHM ∼130 nm and a quantum yield of ∼12%. Transmission electronic microscopy images were used to determine the QD diameter of 8.9 ± 0.4 nm. From this value we calculated the molecular mass M(QD) = 1.17 × 106 g mol-1 and the extinction coefficient at the band edge (450 nm) ε450 = 4.7 × 106 cm-1 M-1, which allowed to determine the true molar concentration of 17 nM for spectroscopic measurements in solution. The fluorescence intensity of MPA-CdS QDs was quenched only in the presence of Co2+ ions, but not in the presence of thirteen other metal cations. The fluorescence quenching of MPA-CdS QDs appeared proportional to the Co2+ concentration in the range 0.04-2 μM. Based on a fluorescence peak position and a lifetime both independent from Co2+ concentration, the quenching mechanism of MPA-CdS QDs appeared static. Because the strong electronic absorption of Co2+ overlaps the emission of QDs, our results can be explained by Förster energy transfer from QD to the bound Co2+ cations. (10.1016/j.aca.2018.04.041)
  DOI : 10.1016/j.aca.2018.04.041
• Density of Grafted Chains in Thioglycerol-Capped CdS Quantum Dots Determines Their Interaction with Aluminum(III) in Water
  
  • Ben Brahim Nassim
  • Poggi Mélanie
  • Lambry Jean-Christophe
  • Bel Haj Mohamed Naim
  • Ben Chaâbane Rafik
  • Négrerie Michel
  Inorganic Chemistry, American Chemical Society, 2018, 57, pp.4979 - 4988. We aimed to quantify the interaction of watersoluble-functionalized CdS quantum dots (QDs) with metal cations from their composition and physical properties. From the diameter of thioglycerol-capped nanoparticles (TG-CdS QDs) measured by electronic microscopy (D = 12.3 ± 0.3 nm), we calculated the molecular mass of the individual particle MA QD = (3 ± 0.5) × 10 6 g•mol-1 and its molar absorption coefficient ε 450 = 21 × 10 6 M-1 •cm-1. We built a three-dimensional model of the TG-CdS QDs in agreement with the structural data, which allowed us to quantify the number of thioglycerol grafted chains to ∼2000 per QD. This value fully matches the saturation binding curve of Al 3+ cations interacting with TG-CdS QDs. The reaction occurred with a slow association rate (k on = 2.1 × 10 3 M-1 •s-1), as expected for heavy QDs. The photophysical properties of the functionalized QDs were studied using an absolute QD concentration of 7 nM, which allowed us to investigate the interaction with 14 metallic cations in water. The fluorescence intensity of TG-CdS QDs could be quenched only in the presence of Al 3+ ions in the range 0.2-10 μM but not with other cations and was not observed with other kinds of grafting chains. (10.1021/acs.inorgchem.7b03254)
  DOI : 10.1021/acs.inorgchem.7b03254
• Dual-color Three-photon Microscopy for Deep Imaging of Neural Tissue
  
  • Abdeladim Lamiae
  • Guesmi Khmaies
  • Mahou Pierre
  • Tozer Samuel
  • Kumamoto Takuma
  • Ferrer-Ortas Jùlia
  • Dray Nicolas
  • Loulier Karine
  • Hanna Marc
  • Georges Patrick
  • Livet Jean
  • Supatto Willy
  • Druon Frédéric
  • Beaurepaire Emmanuel
  , 2018. We demonstrate dual-color three-photon imaging of red and green fluorescent proteins in neural tissue using a novel ultrafast laser design providing simultaneous excitation at 1300 and 1700 nm. (10.1364/TRANSLATIONAL.2018.JW3A.62)
  DOI : 10.1364/TRANSLATIONAL.2018.JW3A.62
• Isolation and identification of two extremely halophilic archaea from sebkhas in the Algerian Sahara
  
  • Khallef Sakina
  • Lestini Roxane
  • Myllykallio Hannu
  • Houali Karim
  Cellular and Molecular Biology, CMB Association, 2018, 64 (4), pp.83–91. (10.14715/cmb/2018.64.4.14)
  DOI : 10.14715/cmb/2018.64.4.14
• Analysis of In Vivo Cell Migration in Mosaic Zebrafish Embryos
  
  • Boutillon Arthur
  • Giger Florence
  • David Nicolas
  , 2018, pp.213-226. Being optically clear, the zebrafish embryo is a nice model system to analyse cell migration in vivo. This chapter describes a combination of injection and cell transplant procedures that allows creation of mosaic embryos, containing a few cells labelled differently from their neighbours. Rapid 5D confocal imaging of these embryos permits to simultaneously track and quantify the movement of large cell groups, as well as analyse the cellular or subcellular dynamics of transplanted cells during their migration. In addition, expression of a candidate gene can be modified in transplanted cells. Comparing behaviour of these cells to control or neighbouring cells allows determination of the role of the candidate gene in cell migration. We describe the procedure, focusing on one specific cell population during gastrulation, but it can easily be adapted to other cell populations and migrating events during early embryogenesis. (10.1007/978-1-4939-7701-7_16)
  DOI : 10.1007/978-1-4939-7701-7_16
• SiNOI and AlGaAs-on-SOI nonlinear circuits for continuum generation in Si photonics
  
  • Dirani Houssein El
  • Monat Christelle
  • Sciancalepore Corrado
  • Letartre Xavier
  • Brision Stéphane
  • Jany Christophe
  • Olivier Nicolas
  • Yvind Kresten
  • Semenova Elizaveta
  • Oxenløwe Leif Katsuo
  • Frandsen Lars Hagedorn
  • Pu Minhao
  • Girouard Peter D.
  , 2018, 10535, pp.1053508. (10.1117/12.2286862)
  DOI : 10.1117/12.2286862
• The Future of Multiplexed Eukaryotic Genome Engineering
  
  • Thompson David
  • Aboulhouda Soufiane
  • Hysolli Eriona
  • Smith Cory
  • Wang Stan
  • Castanon Oscar
  • Church George
  ACS Chemical Biology, American Chemical Society, 2018, 13 (2), pp.313 - 325. Multiplex genome editing is the simultaneous introduction of multiple distinct modifications to a given genome. Though in its infancy, maturation of this field will facilitate powerful new biomedical research approaches and will enable a host of far-reaching biological engineering applications, including new therapeutic modalities and industrial applications, as well as “genome writing” and de-extinction efforts. In this Perspective, we focus on multiplex editing of large eukaryotic genomes. We describe the current state of multiplexed genome editing, the current limits of our ability to multiplex edits, and provide perspective on the many applications that fully realized multiplex editing technologies would enable in higher eukaryotic genomes. We offer a broad look at future directions, covering emergent CRISPR-based technologies, advances in intracellular delivery, and new DNA assembly approaches that may enable future genome editing on a massively multiplexed scale. (10.1021/acschembio.7b00842)
  DOI : 10.1021/acschembio.7b00842
• Evolutionary insights into Trm112-methyltransferase holoenzymes involved in translation between archaea and eukaryotes
  
  • Van tran Nhan
  • Muller Leslie
  • Ross Robert L
  • Lestini Roxane
  • Létoquart Juliette
  • Ulryck Nathalie
  • Limbach Patrick A
  • De crécy-Lagard Valérie
  • Cianférani Sarah
  • Graille Marc
  Nucleic Acids Research, Oxford University Press, 2018, 46 (16), pp.8483 - 8499. Protein synthesis is a complex and highly coordinated process requiring many different protein factors as well as various types of nucleic acids. All translation machinery components require multiple maturation events to be functional. These include post-transcriptional and post-translational modification steps and methylations are the most frequent among these events. In eukaryotes, Trm112, a small protein (COG2835) conserved in all three domains of life, interacts and activates four methyltransferases (Bud23, Trm9, Trm11 and Mtq2) that target different components of the translation machinery (rRNA, tRNAs, release factors). To clarify the function of Trm112 in archaea, we have characterized functionally and structurally its interaction network using Haloferax volcanii as model system. This led us to unravel that methyltransferases are also privileged Trm112 partners in archaea and that this Trm112 network is much more complex than anticipated from eukaryotic studies. Interestingly, among the identified enzymes, some are functionally orthologous to eukaryotic Trm112 partners, emphasizing again the similarity between eukaryotic and archaeal translation machineries. Other partners display some similarities with bacterial methyltransferases, suggesting that Trm112 is a general partner for methyltransferases in all living organisms. (10.1093/nar/gky638)
  DOI : 10.1093/nar/gky638
• Cartographier l’altération des parchemins : l’émergence d’une nouvelle technique de microscopie
  
  • Robinet Laurianne
  • Latour Gaël
  , 2018, pp.119-136.