Biology subjects

Kai, T.

Publications and source records attributed to Kai, T..

5 recordsLinked to original sources

bioRxiv2024

HemK2 functions for sufficient protein synthesis and RNA stability through eRF1 methylation during Drosophila oogenesis

HemK2 is a highly conserved methyltransferase spanning from yeast to humans. Despite its conservation, the identification of its genuine substrates has been controversial, and its biological importance in higher organisms remains unclear. In this study, we elucidate the role of HemK2 in the methylation of eukaryotic Release Factor 1 (eRF1), a process essential for female germline development in Drosophila melanogaster. Knockdown of hemK2 in the germline cells (hemK2-GLKD) induces apoptosis in these cells, accompanied by a pronounced decrease in both eRF1 methylation and protein synthesis. The overexpression of a methylation-deficient eRF1 variant recapitulates the defects observed in hemK2-GLKD, suggesting that eRF1 is a primary methylation target of HemK2. Furthermore, hemK2-GLKD leads to significant reduction mRNA levels in germline cell. We demonstrate that these defects in oogenesis and protein synthesis can be partially restored by inhibiting the No-Go Decay pathway. In addition, hemK2 knockdown is associated with increased disome formation, suggesting that disruptions in eRF1 methylation may provoke ribosomal stalling, which subsequently activates translation-coupled mRNA surveillance mechanisms that degrade actively-translated mRNAs. We propose that HemK2-mediated methylation of eRF1 is critical for ensuring efficient protein production and mRNA stability, which are vital for the generation of high-quality eggs.

developmental biology↗

bioRxiv2022

Collective gradient sensing by swimming bacteria without clustering

We characterize the taxis enhancement of swimming bacteria by collective migration without apparent clustering. We confine dilute Salmonella suspension in a shallow channel and evaluate the thermotaxis response to local heating and diffusion. By combining cell tracking analysis and numerical simulation based on simple modeling, we show that the alignment interaction suppresses orientation fluctuation, strengthens migration bias, and also prevents the dispersion of accumulated population. The results show a prominent example of how a collective motion of active matter implements a biological function.

biophysics↗

bioRxiv2022

A pathway to produce non-coding piRNAs from endogenous protein-coding regions supports Drosophila spermatogenesis

PIWI-interacting (pi)RNA pathways control transposable elements (TEs) and endogenous genes in animal gonads, playing important roles in gamete formation. Here, we report a mechanism by which endogenous protein-coding regions, that normally provide their sequences for translation, serve as origins of non-coding piRNA biogenesis in Drosophila melanogaster testes. The products, namely endo-piRNAs, formed silencing complexes with Aubergine (Aub) in germ cells. Proximity proteome combined to functional analyses revealed a testis-specialized chaperone, Cyclophilin 40 (Cyp40), selectively increases endo-piRNA occupancy inside Aub-RISCs aside from other TE-related piRNAs. Moreover, Argonaute 2 (Ago2) activities were found critical for endo-piRNA production. We provide evidence that Ago2-bound short interfering (si)RNAs and micro(mi)RNAs specify precursors and direct endo-piRNA biogenesis. Consistently, Aub and Ago2 cooperate in spermatid differentiation and regulate endogenous genes via endo-piRNA-directed mRNA cleavage. Collectively, our data highlight that Drosophila testes employ a unique strategy to expand the diversity of germline piRNAs supporting late spermatogenesis. HeadlinesO_LIEndogenous protein-coding regions derive non-coding endo-piRNAs C_LIO_LIendo-piRNA and TE-piRNA are produced via distinct mechanisms C_LIO_LIsiRNA and miRNA activities direct secondary piRNA biogenesis C_LIO_LIendo-piRNA pathway controls chromatin and sperm formation C_LI

molecular biology↗

bioRxiv2022

Tejas functions as a core component of nuage assembly and precursor processing in Drosophila piRNA biogenesis

Piwi-interacting RNAs (piRNAs), a class of 23- to 29-nt gonad-specific small RNAs, function to combat transposons in gonads. piRNAs are thought to be processed and amplified in membrane-less granules called nuage in germline cells. In Drosophila, two PIWI family proteins, several Tudor-domain containing (Tdrd) proteins and RNA helicases are assembled at perinuclear region of germline cells, forming nuage to process into piRNAs. Among those, Tejas (Tej), a fly homolog of mouse Tdrd5, has been known as a robust nuage component required for piRNA biogenesis in germline cells, yet its molecular functions remained elusive. To understand its molecular basis on nuage assembly and functions for piRNA biogenesis, we investigated subcellular localization of fluorescent-tagged nuage proteins including Tej and monitored the behavior of piRNA precursors. Tej functions as a core component for assembly of Vasa and Spindle-E to nuage granules through distinct motifs, respectively. The loss of Tej function resulted in malformation of nuage and accumulation of piRNA precursors en route in processing, perturbing further piRNA biogenesis in germline cells. Our study also revealed that the low complexity region of Tej regulates the mobility of nuage by phase separation. Collectively, we propose that Tej plays a pivotal role in processing of piRNA precursors by assembling RNA helicases, Vasa and Spindle-E, to nuage, by controlling the dynamics of nuage components.

cell biology↗

bioRxiv2022

DNA binding domain undergoes dynamic and selective protein-protein interactions to facilitate CTCF insulation

CTCF is required for three-dimensional chromatin organization and a predominant insulator protein. However, its roles in insulating enhancers have not been fully explained in 3D nuclear organization. Here, we found that the CTCF DNA binding domain (DBD) forms dynamic self-interacting clusters. We next investigated the spatial relationships between these clusters and other transcription regulators with a light-induced imaging system. Strikingly, CTCF DBD clusters were found to incorporate other insulator proteins but are not coenriched with transcriptional activators in the nucleus. This property is not observed in other domains of CTCF or the DBDs of other transcription factors. Moreover, endogenous CTCF shows a phenotype consistent with the DBD by forming small protein clusters and interacts less transcriptional activators bound, CTCF motif arrays. Our results reveal an interesting phenomenon that CTCF DBD interacts with insulator proteins and selectively localizes to nuclear positions with lower concentrations of transcriptional activators, providing new insights into the insulation function of CTCF.

molecular biology↗