SHARON SPIZZICHINO

PhD Graduate

PhD program:: XXXIV


supervisor: Giorgio Giardina
advisor: Francesca Cutruzzolà
co-supervisor: Francesca Cutruzzolà

Thesis title: One protein many functions: the non-canonical interactions of SHMT1. The structural and functional characterization of SHMT1 interactions with RNA and in the de novo thymidylate synthesis complex.

Several enzymes that were originally characterized to have one defined function in intermediatory metabolism, have now been found to participate in variety of other cellular processes (Castello, Hentze and Preiss, 2015; Huangyang and Simon, 2018). In fact, some metabolic enzymes, named moonlighting proteins, have been found to non-canonically interact with other proteins or nucleic acids. Interestingly, not all the newly found RNA binding proteins have been shown to regulate the nucleic acid’s function, identifying a novel process known as riboregulation. The catalytic activity of human serine hydroxymethyltransferase (SHMT1) has been found to be controlled by RNA (Guiducci et al., 2019). Moreover, it has been demonstrated that this enzyme takes part in the assembly of the de novo thymidylate synthesis complex (dTMP-SC) in the nucleus, together with thymidylate synthase (TYMS) and dihydrofolate reductase (DHFR) (Anderson, Quintero and Stover, 2011). Therefore, the aim of the present thesis is to investigate the details of the non-canonical functions of SHMT1, including the molecular mechanism at the basis of SHMT1 riboregulation. Here I will present the first 3D structure of a metabolic enzyme in complex with RNA, solved using cryo-election microscopy (cryo-EM), and the identification of the RNA features governing the interaction with SHMT1. In parallel, I will present a deep biochemical and molecular characterization of the dTMP-SC, providing the evidence that the complex can transiently form in vitro and in the cytosol as well. An observation that opens a novel scenario on its relevance in different processes. The present manuscript set the basis to fully understand how metabolic enzymes can be controlled by RNA and strengthen the idea that transient interactions might regulate the organization of biomolecular function in response to the cellular needs. Anderson, D., Quintero, C. and Stover, P. (2011) ‘Identification of a de novo thymidylate biosynthesis pathway in mammalian mitochondria’, Proceedings of the National Academy of Sciences of the United States of America. Proc Natl Acad Sci U S A, 108(37), pp. 15163–15168. doi: 10.1073/PNAS.1103623108. Castello, A., Hentze, M. W. and Preiss, T. (2015) ‘Metabolic Enzymes Enjoying New Partnerships as RNA-Binding Proteins’, Trends in Endocrinology and Metabolism. Elsevier Ltd, 26(12), pp. 746–757. doi: 10.1016/j.tem.2015.09.012. Guiducci, G. et al. (2019) ‘The moonlighting RNA-binding activity of cytosolic serine hydroxymethyltransferase contributes to control compartmentalization of serine metabolism’, Nucleic Acids Research, 47(8), pp. 4240–4254. doi: 10.1093/nar/gkz129. Huangyang, P. and Simon, M. C. (2018) ‘Hidden features: Exploring the non-canonical functions of metabolic enzymes’, DMM Disease Models and Mechanisms, 11(8). doi: 10.1242/dmm.033365.

Research products

11573/1707844 - 2024 - Combined delivery of miR-15/16 through humanized ferritin nanocages for the treatment of chronic lymphocytic leukemia
Liberati, Francesca Romana; Di Russo, Sara; Barolo, Lorenzo; Peruzzi, Giovanna; Farina, Maria Vittoria; Spizzichino, Sharon; Di Fonzo, Federica; Quaglio, Deborah; Pisano, Luca; Botta, Bruno; Giorgi, Alessandra; Boffi, Alberto; Cutruzzola, Francesca; Paone, Alessio; Baiocco, Paola - 01a Articolo in rivista
paper: PHARMACEUTICS (Basel: MDPI, 2009-) pp. - - issn: 1999-4923 - wos: WOS:001192904500001 (1) - scopus: 2-s2.0-85189008467 (1)

11573/1714195 - 2024 - Structure-based mechanism of riboregulation of the metabolic enzyme SHMT1
Spizzichino, Sharon; Di Fonzo, Federica; Marabelli, Chiara; Tramonti, Angela; Chaves-Sanjuan, Antonio; Parroni, Alessia; Boumis, Giovanna; Liberati, Francesca Romana; Paone, Alessio; Montemiglio, Linda Celeste; Ardini, Matteo; Jakobi, Arjen J.; Bharadwaj, Alok; Swuec, Paolo; Tartaglia, Gian Gaetano; Paiardini, Alessandro; Contestabile, Roberto; Mai, Antonello; Rotili, Dante; Fiorentino, Francesco; Macone, Alberto; Giorgi, Alessandra; Tria, Giancarlo; Rinaldo, Serena; Bolognesi, Martino; Giardina, Giorgio; Cutruzzola, Francesca - 01a Articolo in rivista
paper: MOLECULAR CELL (Cell Press:1100 Massachusetts Avenue:Cambridge, MA 02138:(617)661-7057, EMAIL: subs@cell.com, INTERNET: http://www.cellpress.com, Fax: (617)397-2850) pp. 2682-2697 - issn: 1097-2765 - wos: WOS:001281962900001 (0) - scopus: 2-s2.0-85198588581 (0)

11573/1575071 - 2022 - A conserved scaffold with heterogeneous metal ion binding site: the multifaceted example of HD-GYP proteins
Cutruzzolà, Francesca; Paiardini, Alessandro; Scribani Rossi, Chiara; Spizzichino, Sharon; Paone, Alessio; Giardina, Giorgio; Rinaldo, Serena - 01g Articolo di rassegna (Review)
paper: COORDINATION CHEMISTRY REVIEWS (Elsevier BV:PO Box 211, 1000 AE Amsterdam Netherlands:011 31 20 4853757, 011 31 20 4853642, 011 31 20 4853641, EMAIL: nlinfo-f@elsevier.nl, INTERNET: http://www.elsevier.nl, Fax: 011 31 20 4853598) pp. 214228- - issn: 0010-8545 - wos: WOS:000706196900003 (3) - scopus: 2-s2.0-85115933139 (3)

11573/1651824 - 2022 - Riboregulation as a new player in the control of cellular metabolism: clues from the cryo-EM structure of serine hydroxymethyltransferase-RNA complex
Giardina, Giorgio; Spizzichino, Sharon; Marabelli, Chiara; Di Fonzo, Federica; Tramonti, Angela; Parroni, Alessia; Contestabile, Roberto; Chaves, Antonio; Rinaldo, Serena; Bolognesi, Martino; Cutruzzola', Francesca - 04d Abstract in atti di convegno
conference: 17th SIBBM Seminar Frontiers in Molecular Biology - The RNA World 3.0 Abstracts (Roma)
book: Abstract Book - ()

11573/1584599 - 2022 - Cytosolic localization and in vitro assembly of human de novo thymidylate synthesis complex
Spizzichino, Sharon; Boi, Dalila; Boumis, Giovanna; Lucchi, Roberta; Liberati, Francesca Romana; Capelli, Davide; Montanari, Roberta; Pochetti, Giorgio; Piacentini, Roberta; Parisi, Giacomo; Paone, Alessio; Rinaldo, Serena; Contestabile, Roberto; Tramonti, Angela; Paiardini, Alessandro; Giardina, Giorgio; Cutruzzolà, Francesca - 01a Articolo in rivista
paper: THE FEBS JOURNAL (Blackwell Pub., Oxford, UK) pp. 1625-1649 - issn: 1742-464X - wos: WOS:000717476400001 (4) - scopus: 2-s2.0-85118844105 (5)

11573/1553790 - 2021 - The emerging role of amino acids of the brain microenvironment in the process of metastasis formation
Cutruzzola', Francesca; Bouzidi, Amani; Liberati, Francesca Romana; Spizzichino, Sharon; Boumis, Giovanna; Macone, Alberto; Rinaldo, Serena; Giardina, Giorgio; Paone, Alessio - 01g Articolo di rassegna (Review)
paper: CANCERS (Basel: MDPI) pp. - - issn: 2072-6694 - wos: WOS:000666104500001 (5) - scopus: 2-s2.0-85107408621 (5)

11573/1553985 - 2021 - Cytosolic localization and in vitro assembly of human de novo thymidylate synthesis complex
Spizzichino, Sharon; Boi, Dalila; Boumis, Giovanna; Tramonti, Angela; Paiardini, Alessandro; Contestabile, Roberto; Pochetti, Giorgio; Rinaldo, Serena; Paone, Alessio; Giardina, Giorgio; Cutruzzola', Francesca - 04d Abstract in atti di convegno
conference: 16th SIBBM Seminar Frontiers in Molecular Biology Frontiers in metabolic research (online)
book: 16th SIBBM Seminar Frontiers in Molecular Biology Frontiers in metabolic research Abstracts - ()

11573/1558518 - 2021 - Structural clues of Serine hidroxymethyltransferase (SHMT) riboregulation
Spizzichino, Sharon; Marabelli, Chiara; Chaves Sanjuan, Antonio; Swuec, Paolo; Montemiglio, Linda Celeste; Ardini, Matteo; Rinaldo, Serena; Paone, Alessio; Boumis, Giovanna; Giardina, Giorgio; Bolognesi, Martino; Cutruzzola', Francesca - 04d Abstract in atti di convegno
conference: 2nd Italian Crystallographic Association Biological MacroMolecules Group Meeting (online)
book: 2nd Italian Crystallographic Association Biological MacroMolecules Group Meeting - ()

11573/1568997 - 2021 - Crystal structure of Aspergillus fumigatus AroH, an aromatic amino acid aminotransferase
Spizzichino, Sharon; Pampalone, Gioena; Dindo, Mirco; Bruno, Agostino; Romani, Luigina; Cutruzzolà, Francesca; Zelante, Teresa; Pieroni, Marco; Cellini, Barbara; Giardina, Giorgio - 01a Articolo in rivista
paper: PROTEINS (John Wiley & Sons Incorporated:Customer Service, 111 River Street:Hoboken, NJ 07030:(800)225-5945, (201)748-6000, EMAIL: societyinfo@wiley.com, INTERNET: http://www.wiley.com, Fax: (212)748-6551) pp. - - issn: 0887-3585 - wos: WOS:000696151200001 (2) - scopus: 2-s2.0-85114905178 (2)

11573/1336446 - 2020 - Design, synthesis and discovery of novel N,N'-carbazoyl-aryl-urea inhibitors of Zika NS5 methyltransferase and virus replication.
Spizzichino, S; Mattedi, G; Lauder, K; Valle, C; Aouadi, W; Canard, B; Decroly, E; Kaptein, Sjf; Neyts, J; Graham, C; Sule, Z; Barlow, Dj; Silvestri, R; Castagnolo, D. - 01a Articolo in rivista
paper: CHEMMEDCHEM (Weinheim : Wiley-VCH-Verl..) pp. 385-390 - issn: 1860-7187 - wos: WOS:000505817500001 (14) - scopus: 2-s2.0-85078073812 (18)

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