Keisuke Shoji

Wolbachia infection causes male-specific death in Ostrinia furnacalis , but its removal from infected strains results in female-specific death instead of restoring 1:1 sex ratio, suggesting that cytoplasmic Wolbachia , not the host genome, primarily determines femaleness in infected strains. This phenomenon is a striking example of the evolutionary outcome of cytoplasmic sex determination, potentially arising from prolonged host-symbiont co-evolution. Although we recently identified Oscar, the Wolbachia -encoded male-killing effector targeting the host masculinizing factor OfMasc in Ostrinia moths, inactivation or loss of the host’s endogenous feminizer remains unknown. Here we identify a W-linked primary feminizer, OfFem piRNA, which targets an mRNA encoding an OfMasc-interacting protein Ofznf-2. We demonstrate that Ofznf-2 is essential for both masculinization and dosage compensation. We also show that OfFem piRNA is entirely absent in the Wolbachia -infected lineage, providing molecular evidence that a male-killing Wolbachia hijacks the host feminizing piRNA function by acquiring the Oscar protein during prolonged endosymbiosis.

Secondary siRNA biogenesis amplifies small RNA signals from target transcripts and plays a pivotal role in plant development and defense responses. The RNA-binding protein SGS3 is essential for this pathway, recruiting RNA-dependent RNA polymerase 6 (RDR6) to Argonaute-small RNA-bound targets. The N-terminal intrinsically disordered region (IDR) of SGS3, which contains a prion-like domain (PrLD), has been reported to drive liquid-liquid phase separation, forming siRNA bodies, and to be required for secondary siRNA production. However, the molecular mechanism by which the N-terminal IDR contributes to secondary siRNA production remains unclear. Here, using in vitro reconstitution and in planta assays, we show that the N-terminal IDR comprises two functional modules: the PrLD and a negatively charged region (NCR). The PrLD is required for phase separation and siRNA body formation but is dispensable for secondary siRNA production. In contrast, mutations in the NCR caused SGS3 to form abnormally large cytoplasmic assemblies and markedly impaired secondary siRNA production. These results suggest that the N-terminal IDR helps maintain SGS3 in a functional, soluble state that supports efficient secondary siRNA biogenesis.

The WZ sex determination system is found in a diverse range of animals, including lepidopteran insects. In the silkworm Bombyx mori , a lepidopteran model insect, females carry the W chromosome with the feminizing gene Feminizer ( Fem ), which is the source of a female-specific PIWI-interacting RNA (piRNA). The Fem piRNA–PIWI complex cleaves an mRNA encoding the masculinizing protein Masculinizer (BmMasc), resulting in the production of the female-type splice variant of Bombyx mori doublesex ( Bmdsx ), which is the master genetic switch of B. mori sex differentiation. In contrast, in males, BmMasc induces the production of the male-type Bmdsx splice variant ( Bmdsx ^M ). However, the molecular mechanism through which BmMasc transduces the masculinizing signal to the male-specific Bmdsx splicing event remains unknown. In this study, we showed that BmMasc physically interacts with Bombyx mori P-element somatic inhibitor (BmPSI), that is a RNA binding protein required for Bmdsx ^M expression. BmMasc overexpression resulted in the production of Bmdsx ^M in B. mori ovary-derived BmN-4 cells, but this induction was severely inhibited in BmPSI -knocked down cells, indicating that BmPSI is essential for the masculinizing activity of BmMasc. We also identified that BmMasc-containing protein complex was associated with a region of Bmdsx pre-mRNA spanning introns 2 to 4, particularly around the junctions of intron 2 with exon 3 and intron 3 with exon 4. Exons 3 and 4 of Bmdsx are female-specific units and are skipped in Bmdsx ^M . Together with a previous report of the binding of BmPSI to the CE1 sequence located in exon 4 of Bmdsx , the current results strongly suggest that the BmMasc–BmPSI complex is required for male-specific exon skipping in Bmdsx pre-mRNA through its binding to the female-specific Bmdsx introns and exons.

SUMMARY: PIWI-interacting RNAs (piRNAs) are crucial for silencing transposable elements (TEs). In many species, piRNAs are generated via a complex process known as the ping-pong pathway, which couples TE cleavage with new piRNA amplification. However, the biological significance of this complexity and its impact on the piRNA sequence repertoire remain unclear. Here, we systematically compared piRNA production patterns in two closely related silkworm cell lines and found significant changes in their piRNA sequence repertoire. Importantly, the changeability of this repertoire showed a strong negative correlation with the efficiency of piRNA biogenesis. This can be explained by competition between adjacent ping-pong sites, as supported by our mathematical modeling. Moreover, this competition can rationalize how piRNAs autonomously avoid deleterious mismatches to target TEs. These findings unveil the intrinsic plasticity and adaptability of the piRNA system to combat diverse TE sequences and highlight the universal power of competition and self-amplification to drive autonomous optimization.

The PIWI-interacting RNA (piRNA) pathway plays a crucial role in silencing transposons in the germline. piRNA-guided target cleavage by PIWI proteins triggers the biogenesis of new piRNAs from the cleaved RNA fragments. This process, known as the ping-pong cycle, is mediated by the two PIWI proteins, Siwi and BmAgo3, in silkworms. However, the detailed molecular mechanism of the ping-pong cycle remains largely unclear. Here, we show that Spindle-E (Spn-E), a putative ATP-dependent RNA helicase, is essential for BmAgo3-dependent production of Siwi-bound piRNAs in the ping-pong cycle and that this function of Spn-E requires its ATPase activity. Moreover, Spn-E acts to suppress homotypic Siwi–Siwi ping-pong, but this function of Spn-E is independent of its ATPase activity. These results highlight the dual role of Spn-E in facilitating proper heterotypic ping-pong in silkworms.

PIWI-interacting RNAs (piRNAs) are small RNAs that play a critical role in repressing transposons in the germline by guiding PIWI proteins to complementary target sequences. It is well known that the 5’ ends of piRNAs are typically defined through cleavage by PIWI proteins or by the endonuclease Zucchini, and piRNAs are amplified via reciprocal cleavage of sense and antisense transcripts by PIWI proteins. Here, we show that low levels of sense-stranded piRNAs are produced from the whole transcriptome in silkworms, flies, and mice, in a manner independent from the known biogenesis pathways. Notably, this mechanism is utilized in silkworm cultured cells for the production of piRNAs derived from the extremely abundant sub-genomic RNAs of Bombyx mori latent virus, which have been suggested to play a role in suppressing viral replication. We propose that this inefficient and non-specific piRNA-production pathway acts as a primitive sensor for aberrantly abundant transcripts in the germline, potentially seeding piRNA sequence repertoire for more efficient and established biogenesis pathways.

The PIWI-interacting RNA (piRNA) pathway plays a crucial role in silencing transposons in the germline. piRNA-guided target cleavage by PIWI proteins triggers biogenesis of new piRNAs from the cleaved RNA fragments. This process, known as the ping-pong cycle, is mediated by the two PIWI proteins, Siwi and BmAgo3, in silkworms. However, the detailed molecular mechanism of the ping-pong cycle remains largely unclear. Here, we show that Spindle-E (Spn-E), a putative ATP-dependent RNA helicase, is essential for BmAgo3-dependent production of Siwi-bound piRNAs in the ping-pong cycle and that this function of Spn-E requires its ATPase activity. Moreover, Spn-E acts to suppress homotypic Siwi-Siwi ping-pong, but this function of Spn-E is independent of its ATPase activity. These results highlight the dual role of Spn-E in facilitating proper heterotypic ping-pong in silkworms.

PIWI-interacting RNAs (piRNAs) guide PIWI proteins to target transposons in germline cells, thereby suppressing transposon activity to preserve genome integrity in metazoans’ gonadal tissues. Piwi, one of three Drosophila PIWI proteins, is expressed in the nucleus and suppresses transposon activity by forming heterochromatin in an RNA cleavage-independent manner. Recently, Piwi was reported to control cell metabolism in Drosophila fat body, providing an example of piRNAs acting in non-gonadal somatic tissues. However, mutant flies of the other two PIWI proteins, Aubergine (Aub) and Argonaute3 (Ago3), show no apparent phenotype except for infertility, blurring the importance of the piRNA pathway in non-gonadal somatic tissues. The silkworm, Bombyx mori, possesses two PIWI proteins, Siwi (Aub homolog) and BmAgo3 (Ago3 homolog), whereas B. mori does not have a Piwi homolog. Siwi and BmAgo3 are mainly expressed in gonadal tissues and play a role in repressing transposon activity by cleaving transposon RNA in the cytoplasm. Here, we generated Siwi and BmAgo3 loss-of-function mutants of B. mori and found that they both showed delayed larval growth and failed to become adult moths. They also exhibited defects in wing development and sexual differentiation. Transcriptome analysis revealed that loss of somatic piRNA biogenesis pathways results in abnormal expression of not only transposons but also host genes, presumably causing severe growth defects. Our results highlight the roles of non-gonadal somatic piRNAs in B. mori development.