Splicing factor Nova regulates the splice variants in exons 3 and 6 of GABA receptor subunit RDL from Chilo suppressalis Walker (Lepidoptera: Crambidae).

The insect ionotropic γ-aminobutyric acid (GABA) receptor is an important insecticide target, and alternative splicing (AS) among exons 3a, 3b, 6a, and 6b of its RDL subunit is ubiquitous in insects; however, the AS factors and mechanisms remain unclear. While the neuro-oncological ventral antigen (Nova) is known to regulate AS of the γ2 subunit of mammalian GABA receptors, its role in insects remains unexplored. Two CsNova isoforms, CsNova-X1 and CsNova-X3, were identified by BLAST in the third-generation transcriptome of Chilo suppressalis. These isoforms exhibited conserved KH domains with the open reading frames of CsNova-X1 and CsNova-X3 measuring 1638 bp and 1572 bp, respectively. Compared with CsNova-X1, CsNova-X3 lacks 22 amino acid residues in the N-terminal region. Developmental expression profiling revealed peak mRNA levels during the pupal stage. RNA interference (RNAi)-mediated knockdown of CsNova significantly reduced CsRDL-3a/3b/6a transcript levels after 72 h. Molecular docking simulations revealed that the UCAUCAC motif in the downstream of exon 2 of CsRDL could interact with CsNova-X1, while the UCAU and UCAC motifs in exon 6b and its flanking regions could interact with CsNova-X3. In conclusion, Nova was cloned from the Lepidoptera insect for the first time and could regulate the AS process of exon 3 and exon 6 of CsRDL, laying a foundation for in-depth studies on the regulatory mechanism of AS for RDL and the development of RNAi-based pesticides targeting these interactions.