RNA Cell Biology

Graciela L. Boccaccio - Fundación Instituto Leloir


We work on translational regulation. An innovative concept that emerged several years ago is that mRNA repression is linked to the formation of supramolecular aggregates of messenger ribonucleoproteins (mRNPs). The Processing Bodies (PBs), which are involved in mRNA silencing and decay, and the Stress Granules (SGs), which are induced upon acute cellular stress, are the founding members of this novel family of cytosolic bodies. Their formation is directed by aggregation motifs present in their protein components, and both SGs and PBs dynamically release transcripts allowing their translation. These bodies behave as liquid droplets and the assembly and dissolution of SGs and PBs can be conceptualized as regulated phase-separation processes.
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Our laboratory contributed early to the field, and we have identified a number of SGs components and investigated their functional relevance (Thomas et al. MBoC, 2005; Thomas et al., JCS, 2009). Later on, we speculated that the condensation of these discrete bodies in the cytosol involves the action of molecular motors and found that a balance between anterograde and retrograde microtubule-dependent transport govern the transient formation of SGs, and similarly affects PBs (Loschi et al. JCS 2009).
More recently, we wondered whether related bodies are involved in translational regulation in neuros, specifically at the post-synapse, where thousands of mRNAs are localized and presumably regulated by synaptic stimulation thus helping synapse plasticity. We found that a specific translational repressor termed Smaug1/Samd4a form RNA bodies at hippocampal synapses that respond to neuronal activity releasing key messenger RNAs (Baez & Boccaccio JBC 2005; Baez et al., J Cell Biol, 2011).

1- Signaling pathways that regulate SG formation
Work from our lab and others indicate that SG formation is bidirectionally influenced by factors that affect translation initiation; polysome stability; subcellular transport; autophagy; chaperone and proteosome activities, as well as by the presence of anomalous RNAs or proteins –several of them linked to neurodegeneration- (reviewed in Thomas et al., 2011). More recently, in collaboration with the Drosophila RNAi Screen Center (DRSC, Harvard), we have performed an RNAi-based screen inDrosophila S2R+ cells to identify kinases and phosphatases that affect SG formation. We developed a MATLAB algorithm for the automatic analysis of the numerous micrographs (Perez-Pepe et al., 2012). We are currently investigating how these signaling networks regulate SG assembly and dissolution and and will explore the consequences of dysregulated SG formation in translation and cell survival.
2- RNA-silencing bodies in regulated translation at the post-synapse
The translational repressor mSmaug1/Samd4a form RNA silencing bodies at the post-synapse, that we termed S-foci. The S-foci rapidly respond to the stimulation of NMDAR and release CamKII-alpha mRNA and likely several other unknown transcripts. As expected for a molecule involved in synaptic translation, the KD of Smaug1 seriously affects synapse morphology and function in hippocampal neurons (Baez et al., 2011; Pascual et al., 2012). In addition, we found that the exoribonuclease XRN1 form a distinct type of bodies located at the post-synapse, that are distinct from S-foci and PBs, and that we termed Synaptic Xrn1 (SX)-bodies (Luchelli et al., 2015). The SX-bodies respond to synaptic stimulation with a distinct pattern, and they slowly grow upon NMDAR activation whereas the S-foci dissolve. Supporting a role for the SX-bodies in translational regulation, we found that XRN1 KD affects the global translational silencing triggered by NMDAR activation. In addition to this response to NMDA, SX-body dynamics is affected by the stimulation of metabotropic receptors. We found that both S-foci and SX-bodies dissolve with different time courses upon mGluR activation. In turn, RNA granules containing Fragile X Mental Retardation Protein (FMRP) display yet another response pattern. We found that FMRP granules do not respond to NMDA and rapidly dissolve upon mGluR stimulation. The regulated assembly of S-foci, SX-bodies and FMRP granules directly controls which mRNA species are available to enter translation, thus providing a mechanism for the control of the local transcriptome upon specific synapse stimuli (Thomas et al., 2014; Pimentel and Boccaccio, 2014).
We focused on two types of specific mRNA-silencing bodies that we have identified at the synapse, containing the mRNA repressor Smaug1/Samd4a and the exoribonuclease XRN1, respectively (Baez et al., JCB 2011; Luchelli et al., JCS 2015). We are currently investigating how synaptic activity influences their formation and integrity and which specific mRNAs are affected by the controlled assembly and dissolution of different bodies.
Anne Plessis, Institute Jack Monod, Paris.
Elisa Izaurralde, MaxPlanck- Tuebingen.
Hernán Greco, Dptm of Physics, FCEyN-University of Buenos Aires..
Anabella Srebrow, IFIBYNE-FCEyN, UBA.

Perez-Pepe, M., Fernández-Alvarez, A.J.,  Boccaccio, G.L. Life and work of Stress Granules and Processing Bodies: New insights into their formation and function. Biochemistry. 2018 May 1;57(17):2488-2498.  Pubmed Cover article

Scarpin, M.R., Sigaut, L., Temprana, S.G., Boccaccio, G.L., Pietrasanta, L.I., Muschietti, J.P. Two Arabidopsis late pollen transcripts are detected in cytoplasmic granules. Plant Direct 1(4): e00012.

Fernández-Alvarez, A.J., Pascual, M.L., Boccaccio, G.L., Thomas, M.G. Smaug variants in neural and non-neuronal cells. Commun Integr Biol. (2016) Feb 18;9(2). Pubmed

Thomas, M.G., Boccaccio, G.L. Nobel mRNA-silencing bodies at the synapse: A never-ending story. Commun Integr Biol. (2016) Feb 2;9(2). Pubmed

Luchelli, L., Thomas, M.G., Boccaccio, G.L. Synaptic control of mRNA translation by reversible assembly of XRN1 bodies. J Cell Sci. (2015) 128(8):1542-54. Pubmed Cover article

Pimentel, J., Boccaccio, G.L. Translation and silencing in RNA granules: a tale of sand grains. Front Mol Neurosci. (2014) 7: 68. PubMed

Katz, M.J., Acevedo, J.M., Loenarz, C., Galagovsky, D., Liu-Yi, P., Pérez-Pepe, M., Thalhammer, A., Sekirnik, R., Ge, W., Melani, M., Thomas, M.G., Simonetta, S., Boccaccio, G.L., Schofield, C.J., Cockman, M.E., Ratcliffe, P.J., Wappner, P. Sudestada1, a Drosophila ribosomal prolyl-hydroxylase required for mRNA translation, cell homeostasis, and organ growth. Proc Natl Acad Sci U S A. (2014) 111:4025-4030. PubMed

Thomas, M.G., Pascual, M., Maschi, D., Luchelli, L., Boccaccio, G.L. Synaptic control of local translation: the plot thickens with multiple characters. Cellular and Molecular Life Sciences. (2013) 12:2219-39. PubMed

Perez-Pepe, M., Slomiansky, V., Loschi, M., Luchelli, L., Neme, M., Thomas, M.G., Boccaccio, G.L. BUHO: a MATLAB script for the study of stress granules and processing bodies by high-throughput image analysis. PLoS One. 2012;7(12):e51495. PubMed

Thomas, M.G., Luchelli, L., Pascual, M., Gottifredi, V., Boccaccio, G.L. A monoclonal antibody against p53 cross-reacts with processing bodies. PLoS One. 2012;7(5):e36447. PubMed

Pascual, M.L., Luchelli, L., Habif, M., Boccaccio, G.L. Synaptic activity regulated mRNA-silencing foci for the fine tuning of local protein synthesis at the synapse. Commun Integr Biol. (2012) 5(4):388-392. PubMed

Martínez Tosar, L.J., Thomas, M.G., Baez, M.V., Ibañez, I.L.,Chernomoretz, A., Boccaccio,G.L. The double-stranded RNA binding protein Staufen: from embryo polarity to the stress response and neurodegeneration. Front Biosci. (En prensa).

Thomas M.G., Loschi M., Desbats M.A., Boccaccio G.L. RNA granules: the good, the bad and the ugly. Cell Signal. 23:324-334 (2011). PubMed

Dekanty, A., Romero, N.M., Bertolin, A.P., Thomas, M.G., Leishman, C.C., Perez-Perri, J.I., Boccaccio, G.L.,Wappner, P. Drosophila genome-wide RNAi screen identifies multiple regulators of HIF-dependent transcription in hypoxia. PLoS Genet. 6: 1000994 (2010). PubMed

Abrahamyan, L.G., Chatel-Chaix, L., Ajamian, L., Milev, M.P., Monette, A., Clément, J.F., Song, R., Lehmann, M., DesGroseillers, L., Laughrea, M., Boccaccio, G., Mouland, A.J. Novel Staufen1 ribonucleoproteins prevent formation of stress granules but favour encapsidation of HIV-1 genomic RNA. J Cell Sci. 123: 369-383 (2010).    PubMed

Loschi, M., Leishman, C.C., Berardone, N., Boccaccio, G.L. Dynein and kinesin regulate stress-granule and P-body dynamics. J Cell Sci. 122: 3973-3982 (2009).     PubMed

Thomas, M.G., Martínez Tosar, L.J., Desbats, M.A., Leishman, C.C., Boccaccio, G.L. Mammalian Staufen 1 is recruited to stress granules and impairs their assembly. J Cell Sci. 122: 563-573 (2009).     PubMed

Báez, M.V., Boccaccio, G.L. Mammalian Smaug is a translational repressor that forms cytoplasmic foci similar to stress granules. J Biol Chem. 280: 43131-4340 (2005).     PubMed

Craig, P.O., Berguer, P.M., Ainciart, N., Zylberman, V., Thomas, M.G., Martínez Tosar, L.J., Bulloj, A., Boccaccio, G.L., Goldbaum, F.A. Multiple display of a protein domain on a bacterial polymeric scaffold. Proteins. 61: 1089-1100 (2005).     PubMed

Thomas, M.G., Martínez Tosar, L.J., Loschi, M., Pasquini, J.M., Correale, J., Kindler, S., Boccaccio, G.L. Staufen recruitment into stress granules does not affect early mRNA transport in oligodendrocytes. Mol Biol Cell. 16: 405-420 (2005).     PubMed

Graciela L. Boccaccio
Head of Laboratory - gboccaccio@leloir.org.ar

María Gabriela Thomas
Associate Researcher

Ana Julia Fernández Álvarez
Associate Researcher

Marcelo Pérez-Pepe
Postdoctoral Fellow CONICET

Pablo La Spina

Natalia Contreras

Jerónimo Pimentel

Leticia Larotonda
Predoctoral Fellow

Carolina Lizarazo
Master student

Karol Arizaca Maquera
Master student

David Mancilla
External collaborator