Reconstruction of a Comprehensive Interactome and Experimental Data Analysis of FRA10AC1 May Provide Insights into Its Biological Role in Health and Disease

Theologia Sarafidou; Eleni Galliopoulou; Despina Apostolopoulou; Georgios A Fragkiadakis; Nicholas K Moschonas

doi:10.3390/genes14030568

Reconstruction of a Comprehensive Interactome and Experimental Data Analysis of FRA10AC1 May Provide Insights into Its Biological Role in Health and Disease

Genes (Basel). 2023 Feb 24;14(3):568. doi: 10.3390/genes14030568.

Authors

Theologia Sarafidou¹, Eleni Galliopoulou¹, Despina Apostolopoulou², Georgios A Fragkiadakis³, Nicholas K Moschonas^{4

5}

Affiliations

¹ Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis, 41500 Larissa, Greece.
² Department of Biology, University of Crete, 71500 Heraklion, Greece.
³ Department of Nutrition and Dietetics Sciences, Hellenic Mediterranean University, Tripitos, 72300 Siteia, Greece.
⁴ School of Medicine, University of Patras, 26500 Patras, Greece.
⁵ Institute of Chemical Engineering Sciences, Foundation for Research and Technology Hellas (FORTH/ICE-HT), 26504 Patras, Greece.

Abstract

FRA10AC1, the causative gene for the manifestation of the FRA10A fragile site, encodes a well-conserved nuclear protein characterized as a non-core spliceosomal component. Pre-mRNA splicing perturbations have been linked with neurodevelopmental diseases. FRA10AC1 variants have been, recently, causally linked with severe neuropathological and growth retardation phenotypes. To further elucidate the participation of FRA10AC1 in spliceosomal multiprotein complexes and its involvement in neurological phenotypes related to splicing, we exploited protein-protein interaction experimental data and explored network information and information deduced from transcriptomics. We confirmed the direct interaction of FRA10AC1with ESS2, a non-core spliceosomal protein, mapped their interacting domains, and documented their tissue co-localization and physical interaction at the level of intracellular protein stoichiometries. Although FRA10AC1 and SF3B2, a major core spliceosomal protein, were shown to interact under in vitro conditions, the endogenous proteins failed to co-immunoprecipitate. A reconstruction of a comprehensive, strictly binary, protein-protein interaction network of FRA10AC1 revealed dense interconnectivity with many disease-associated spliceosomal components and several non-spliceosomal regulatory proteins. The topological neighborhood of FRA10AC1 depicts an interactome associated with multiple severe monogenic and multifactorial neurodevelopmental diseases mainly referring to spliceosomopathies. Our results suggest that FRA10AC1 involvement in pre-mRNA processing might be strengthened by interconnecting splicing with transcription and mRNA export, and they propose the broader role(s) of FRA10AC1 in cell pathophysiology.

Keywords: RNA in situ hybridization; disease-protein network; expression profile; protein interactions methods; protein interactome; spliceosome.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Chromosome Fragile Sites
Data Analysis
Nuclear Proteins / genetics
RNA Precursors* / genetics
RNA Splicing / genetics
Spliceosomes* / chemistry
Spliceosomes* / genetics
Spliceosomes* / metabolism

Substances

Nuclear Proteins
RNA Precursors
FRA10AC1 protein, human

Grants and funding

This work was supported by the “FRA-SYS”, research grant No. 4072, Funder: General Secretariat for Research and Technology (GSRT-GR) “Excellence II” Action funded by the European Social Fund (ESF) and National Resources of Greece under the operational program “Education and Lifelong Learning” (E.P.E.D.V.M.) to N.M. We also acknowledge the support provided by the internal funds of the U. of Thessaly postgraduate programs “Biotechnology-Quality Assessment in Nutrition and the Environment” (grand No. 5864) and “Molecular Biology and Genetics Applications—Diagnostic Markers” (grand No. 5838) to T.S.