Biophysics of Molecular Recognition

Summary

Most cellular functions come as a result of the interplay between a huge number of interactions between macromolecules and ligands, which define what has been termed the “interactome”. Our group studies the structural determinants of specific recognition between macromolecules (protein-protein or protein-nucleic acid) and between macromolecules and small ligands. We are currently working on the formation of the miRNA processing complex in plants. We make use of NMR spectroscopy for the site-specific structural characterization, together with other biophysical techniques (such as CD, Fluorescence, EPR, chromatography and fast kinetics) to get a comprehensive view of the systems under study. Furthermore, structural information obtained from our model system is combined with functional studies in plants as an integrative approach to elucidate how miRNAs control relevant biological processes. In our laboratory we use skotomorphogenesis -the development of seedlings in darkness- as a biological model, which is crucial to ensure survival of plant species, and that is strongly influenced by components of the microprocessor in Arabidopsis.

Research Lines

Structural aspects of plant miRNA processing.

Small RNA molecules have emerged as a major mechanism of gene regulation in higher eukaryotes. Among them, microRNAs single out as they originate on endogenous transcripts which are processed to yield a product ca. 22 nt long. At present there is little information on the mechanistic details of the processing which result in the precise excision of the precursors in plants. Our group studies the maturation of miRNA in plants from a structural point of view. We work on two of the proteins which form the miRNA processing complex, DCL1 and HYL1 from Arabidopsis thaliana. Using biophysical methods, mainly NMR and optical spectroscopies, we try to understand how the different domains of these proteins co-operate to recognize the precursor and place the catalytic site of DCL1 at the right position. Knowledge of the structural motifs recognized in the precursor and their relative position within its structure will improve the prediction of miRNA sequences and help the optimization of artificial precursors with potential biotechnological and therapeutic use.

Regulation of early development in Arabidopsis by the miRNAs processing machinery

A number of relevant biological processes, such as leaf and flower development, phytohormone signaling or developmental timing in plants are tightly regulated by key master regulators and their counterparts, target-specific miRNAs. However, an exhaustive place and time-of-action of these regulatory modules is still unknown and, thus, many other biologically relevant processes might be controlled by miRNAs and their targets. Results from our laboratory indicate this is taking place during early development of seedlings in darkness, termed skotomorphogenesis. Seedlings emerging from the seeds -normally buried in the soil- should display a particular developmental program and administer resources in order to seek the light, change to a photoautotrophic growth and ensure its survival. Mutant plants in several components of microprocessor complex display defects in skotomorphogenic growth. The aim of our lab is to understand how these proteins control skotomorphogenesis in Arabidopsis, using a combination of physiological, molecular, cellular, biochemical and structural approaches.

Selected Publications

  • Mascali, F. C., Ching, H. Y., Rasia, R. M., Un, S., & Tabares, L. C. (2016). Using Genetically Encodable Self‐Assembling GdIII Spin Labels To Make In‐Cell Nanometric Distance Measurements. Angewandte Chemie, 128(37), 11207-11209.
  • Drusin, S. I., Suarez, I. P., Gauto, D. F., Rasia, R. M., & Moreno, D. M. (2016). dsRNA-protein interactions studied by molecular dynamics techniques. Unravelling dsRNA recognition by DCL1. Archives of biochemistry and biophysics, 596, 118-125.
  • Suarez, I. P., Burdisso, P., Benoit, M. P., Boisbouvier, J., & Rasia, R. M. (2015). Induced folding in RNA recognition by Arabidopsis thaliana DCL1. Nucleic acids research, 43(13), 6607-6619.
  • Aguirre, A., Cabruja, M., Cabrera, R., Eberhardt, F., Peirú, S., Menzella, H. G., & Rasia, R. M. (2015). A fluorometric enzymatic assay for quantification of steryl glucosides in biodiesel. Journal of the American Oil Chemists' Society, 92(1), 47-53.
  • Burdisso, P., Milia, F., Schapire, A. L., Bologna, N. G., Palatnik, J. F., & Rasia, R. M. (2014). Structural Determinants of Arabidopsis thaliana Hyponastic Leaves 1 Function In Vivo. PloS one, 9(11), e113243.
  • Burdisso, P., Suarez, I. P., Bologna, N. G., Palatnik, J. F., Bersch, B., & Rasia, R. M. (2012). Second double-stranded RNA binding domain of dicer-like ribonuclease 1: structural and biochemical characterization. Biochemistry, 51(51), 10159-10166.

Collaborators

  • Dr. Jerome Boisbouvier (Biomolecular Nuclear Magnetic Resonance Group, Institut de Biologie Structurale Jean-Pierre Ebel, Grenoble, France).
  • Dr. Claudia Höbartner (Nucleic Acid Chemistry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Alemania).
  • Dr. Leandro Tabares (Institut de Biologie Intégrative de la Cellule (I2BC), IBITECS, CEA, CNRS, Univ. Paris Sud, Université Paris-Saclay, F-91198, Gif-sur-Yvette, France).

Grants

  • Subsidio para Proyecto de Investigación (PICT-2016-4124). Institución otorgante: Agencia Nacional de Promoción Científica y Tecnológica. Tema: "Optimización de glucosidasas para reacción en interfases y medios no acuosos aplicadas al refinamiento de biodiesel".
  • Subsidio para Proyecto de Investigación (PICT-2016-0314). Institución otorgante: Agencia Nacional de Promoción Científica y Tecnológica. Tema: "Papel funcional de HYL1 durante el desarrollo escotomorfogénico en Arabidopsis thaliana".
  • Subsidio para Proyecto de Investigación (PICT-2013-3281, Max Planck). Institución otorgante: Agencia Nacional de Promoción Científica y Tecnológica. Tema: "Complex formation and precursor processing in plant miRNA biogenesis".
  • Subsidio de Cooperación Internacional ECOS-Sud (A14B02). Institución otorgante: MinCyT- ECOS. Tema: "Bases estructurales del procesamiento de miARNs en plantas". 2015-2017. Una misión por año Argentina-Francia y dos misiones por año Francia-Argentina. Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT).

Director

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Rasia, Rodolfo M.
Core CCT
Email: rasia@ibr-conicet.gov.ar
Phone: +54 341 4237070
Office Extension: 644
Laboratory Extension: 615

Researchers

  • Nahuel González Schain

Postdoctoral fellows

  • Marco Miotto
  • Paula Burdisso

Doctoral fellows

  • Salvador Drusin
  • Florencia C. Mascali
  • Roberta Crespo

Undergraduate Students

Juan Manuel Sacnun