Publications

2018

• 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
• 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
• Multiscale conformational dynamics probed by time-resolved circular dichroism.
  
  • Schmid Marco
  • Changenet Pascale
  • Hache François
  Proceedings of SPIE, the International Society for Optical Engineering, SPIE, The International Society for Optical Engineering, 2018.
• Dual-color deep-tissue three-photon microscopy with a multiband infrared laser
  
  • Guesmi Khmaies
  • Abdeladim Lamiae
  • Tozer Samuel
  • Mahou Pierre
  • Kumamoto Takuma
  • Jurkus Karolis
  • Rigaud Philippe
  • Loulier Karine
  • Dray Nicolas
  • Georges Patrick
  • Hanna Marc
  • Livet Jean
  • Supatto Willy
  • Beaurepaire Emmanuel
  • Druon Frédéric
  Light: Science and Applications, Nature Publishing Group, 2018, 7 (1), pp.12. Multiphoton microscopy combined with genetically encoded fluorescent indicators is a central tool in biology. Three-photon (3P) microscopy with excitation in the short-wavelength infrared (SWIR) water transparency bands at 1.3 and 1.7 µm opens up new opportunities for deep-tissue imaging. However, novel strategies are needed to enable in-depth multicolor fluorescence imaging and fully develop such an imaging approach. Here, we report on a novel multiband SWIR source that simultaneously emits ultrashort pulses at 1.3 and 1.7 µm that has characteristics optimized for 3P microscopy: sub-70 fs duration, 1.25 MHz repetition rate, and µJ-range pulse energy. In turn, we achieve simultaneous 3P excitation of green fluorescent protein (GFP) and red fluorescent proteins (mRFP, mCherry, tdTomato) along with third-harmonic generation. We demonstrate in-depth dual-color 3P imaging in a fixed mouse brain, chick embryo spinal cord, and live adult zebrafish brain, with an improved signal-to-background ratio compared to multicolor two-photon imaging. This development opens the way towards multiparametric imaging deep within scattering tissues. (10.1038/s41377-018-0012-2)
  DOI : 10.1038/s41377-018-0012-2
• A mechanism for CO regulation of ion channels
  
  • Kapetanaki Sofia M.
  • Burton Mark J.
  • Basran Jaswir
  • Uragami Chiasa
  • Moody Peter C. E.
  • Mitcheson John S.
  • Schmid Ralf
  • Davies Noel W.
  • Dorlet Pierre
  • Vos Marten H.
  • Storey Nina M.
  • Raven Emma
  Nature Communications, Nature Publishing Group, 2018, 9, pp.907. Despite being highly toxic, carbon monoxide (CO) is also an essential intracellular signalling molecule. The mechanisms of CO-dependent cell signalling are poorly defined, but are likely to involve interactions with heme proteins. One such role for CO is in ion channel regulation. Here, we examine the interaction of CO with K$_{ATP}$ channels. We find that CO activates K$_{ATP}$ channels and that heme binding to a CXXHX$_{16}$H motif on the SUR2A receptor is required for the CO-dependent increase in channel activity. Spectroscopic and kinetic data were used to quantify the interaction of CO with the ferrous heme-SUR2A complex. The results are significant because they directly connect CO-dependent regulation to a heme-binding event on the channel. We use this information to present molecular-level insight into the dynamic processes that control the interactions of CO with a heme-regulated channel protein, and we present a structural framework for understanding the complex interplay between heme and CO in ion channel regulation. (10.1038/s41467-018-03291-z)
  DOI : 10.1038/s41467-018-03291-z