Synthetic translational regulation by an L7Ae-kink-turn RNP switch.

The regulation of cell signaling pathways and the reconstruction of genetic circuits are important aspects of bioengineering research. Both of these goals require molecular devices to transmit information from an input biomacromolecule to the desired outputs. Here, we show that an RNA-protein (RNP)-containing L7Ae-kink-turn interaction can be used to construct translational regulators under control of an input protein that regulates the expression of desired output proteins. We built a system in which L7Ae, an archaeal ribosomal protein, regulates the translation of a designed mRNA in vitro and in human cells. The translational regulator composed of the RNP might provide new therapeutic strategies based on the detection, repair or rewiring of intrinsic cellular defects, and it may also serve as an invaluable tool for the dissection of the behavior of complex, higher-order circuits in the cell.

[1]  篠原 隆司,et al.  Induction of pluripotent stem cell cells from germ cells , 2012 .

[2]  Shana Topp,et al.  Riboswitches in unexpected places--a synthetic riboswitch in a protein coding region. , 2008, RNA.

[3]  Priscilla E. M. Purnick,et al.  The second wave of synthetic biology: from modules to systems , 2009, Nature Reviews Molecular Cell Biology.

[4]  K. Martin,et al.  Synapse- and Stimulus-Specific Local Translation During Long-Term Neuronal Plasticity , 2009, Science.

[5]  Engineering of synthetic mammalian gene networks , 2005 .

[6]  Daniel F Tardiff,et al.  Binds the Nascent RPL 30 Transcript to Repress U 2 snRNP Recruitment , 2022 .

[7]  D. St Johnston Moving messages: the intracellular localization of mRNAs , 2005, Nature reviews. Molecular cell biology.

[8]  M. O. Fenley,et al.  Molecular basis of box C/D RNA-protein interactions; cocrystal structure of archaeal L7Ae and a box C/D RNA. , 2004, Structure.

[9]  Yohei Yokobayashi,et al.  Engineering complex riboswitch regulation by dual genetic selection. , 2008, Journal of the American Chemical Society.

[10]  D. Bartel,et al.  Synthesizing life , 2001, Nature.

[11]  J. Gallivan Toward reprogramming bacteria with small molecules and RNA. , 2007, Current opinion in chemical biology.

[12]  D. Bartel MicroRNAs: Target Recognition and Regulatory Functions , 2009, Cell.

[13]  D. Endy Foundations for engineering biology , 2005, Nature.

[14]  S. Atsumi,et al.  Design and development of a catalytic ribonucleoprotein , 2001, The EMBO journal.

[15]  Markus Wieland,et al.  Improved aptazyme design and in vivo screening enable riboswitching in bacteria. , 2008, Angewandte Chemie.

[16]  Tan Inoue,et al.  RNA and RNP as new molecular parts in synthetic biology. , 2007, Journal of biotechnology.

[17]  A. Ferré-D’Amaré,et al.  Structure of protein L7Ae bound to a K-turn derived from an archaeal box H/ACA sRNA at 1.8 A resolution. , 2004, Structure.

[18]  T. Katoh,et al.  Specific residues at every third position of siRNA shape its efficient RNAi activity , 2007, Nucleic acids research.

[19]  Wade C Winkler,et al.  Riboswitches and the role of noncoding RNAs in bacterial metabolic control. , 2005, Current opinion in chemical biology.

[20]  L. Chavatte,et al.  Ribosomal protein L30 is a component of the UGA-selenocysteine recoding machinery in eukaryotes , 2005, Nature Structural &Molecular Biology.

[21]  M. Hatzoglou,et al.  A stress-responsive RNA switch regulates VEGF expression , 2008, Nature.

[22]  Gabriele Varani,et al.  The structure and function of small nucleolar ribonucleoproteins , 2007, Nucleic acids research.

[23]  Kai Sundmacher,et al.  Designing Biological Systems: Systems Engineering meets Synthetic Biology , 2012 .

[24]  Wendell A Lim,et al.  Rewiring cell signaling: the logic and plasticity of eukaryotic protein circuitry. , 2004, Current opinion in structural biology.

[25]  A. J. Carpousis,et al.  The K-loop, a general feature of the Pyrococcus C/D guide RNAs, is an RNA structural motif related to the K-turn , 2005, Nucleic acids research.

[26]  S. Yamanaka,et al.  Induction of Pluripotent Stem Cells from Mouse Embryonic and Adult Fibroblast Cultures by Defined Factors , 2006, Cell.

[27]  M. Win,et al.  Higher-Order Cellular Information Processing with Synthetic RNA Devices , 2008, Science.

[28]  R D Klausner,et al.  Identification of the iron-responsive element for the translational regulation of human ferritin mRNA. , 1987, Science.

[29]  Daniel F Tardiff,et al.  L30 binds the nascent RPL30 transcript to repress U2 snRNP recruitment. , 2008, Molecular cell.

[30]  Tan Inoue,et al.  Biochemical characterization of the kink-turn RNA motif. , 2003, Nucleic acids research.

[31]  M. Hentze,et al.  A translational repression assay procedure (TRAP) for RNA-protein interactions in vivo. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[32]  J. Miyazaki,et al.  Quantitative expression of Oct-3/4 defines differentiation, dedifferentiation or self-renewal of ES cells , 2000, Nature Genetics.

[33]  T. Steitz,et al.  The kink‐turn: a new RNA secondary structure motif , 2001, The EMBO journal.

[34]  S. Gottesman The small RNA regulators of Escherichia coli: roles and mechanisms*. , 2004, Annual review of microbiology.

[35]  Hirohide Saito,et al.  Time‐Resolved Tracking of a Minimum Gene Expression System Reconstituted in Giant Liposomes , 2009, Chembiochem : a European journal of chemical biology.

[36]  Takuya Ueda,et al.  Cell-free translation reconstituted with purified components , 2001, Nature Biotechnology.

[37]  Ben Turner,et al.  Induced fit of RNA on binding the L7Ae protein to the kink-turn motif. , 2005, RNA.

[38]  B. Suess,et al.  Engineered riboswitches: Overview, problems and trends , 2008, RNA biology.

[39]  P. Babitzke,et al.  Regulation of translation initiation by RNA binding proteins. , 2009, Annual review of microbiology.

[40]  M. Hentze,et al.  Bacteriophage and spliceosomal proteins function as position-dependent cis/trans repressors of mRNA translation in vitro. , 1992, Nucleic acids research.

[41]  A. Hüttenhofer,et al.  Binding of L7Ae protein to the K-turn of archaeal snoRNAs: a shared RNA binding motif for C/D and H/ACA box snoRNAs in Archaea. , 2003, Nucleic acids research.

[42]  Farren J. Isaacs,et al.  RNA synthetic biology , 2006, Nature Biotechnology.

[43]  Minghua Nie,et al.  Different modes and potencies of translational repression by sequence-specific RNA–protein interaction at the 5′-UTR , 2006, Nucleic acids research.

[44]  Atsushi Ogawa,et al.  An Artificial Aptazyme‐Based Riboswitch and its Cascading System in E. coli , 2008, Chembiochem : a European journal of chemical biology.

[45]  Maung Nyan Win,et al.  Frameworks for programming biological function through RNA parts and devices. , 2009, Chemistry & biology.

[46]  Tan Inoue,et al.  Synthetic biology with RNA motifs. , 2009, The international journal of biochemistry & cell biology.

[47]  N. Sugimoto,et al.  Riboswitches for Enhancing Target Gene Expression in Eukaryotes , 2008, Chembiochem : a European journal of chemical biology.

[48]  M. Hentze,et al.  Molecular mechanisms of translational control , 2004, Nature Reviews Molecular Cell Biology.

[49]  D. Bartel,et al.  Synthesizing life : Paths to unforeseeable science & technology , 2001 .