Biology subjects

Yorimoto, S.

Publications and source records attributed to Yorimoto, S..

3 recordsLinked to original sources

bioRxiv2025

EC-isHCR: a rapid method for in situ hybridization chain reaction in diverse animal samples

The in situ hybridization chain reaction (isHCR) visualizes RNA across multiple spatial scales, from organs to subcellular structures, in diverse samples. We previously proposed a rapid protocol, EC-isHCR, for Drosophila embryos and ovaries. Whether EC-isHCR retains the features of conventional isHCR, including wide-spatial-scale analyses in various samples, however, has remained unclear. Here, we show that EC-isHCR enables robust RNA detection in a broad range of samples, such as whole-mount fruit fly, parasitoid wasp, and aphid preparations; paraffin sections of trout; frozen mouse sections; and human cultured cells. Moreover, EC-isHCR enabled detection of subcellular RNA localization. EC-isHCR also visualized co-localization of RNA with phase-separated condensates in fruit fly embryos and detected the protrusion-enriched mRNA in HeLa cells. To broaden the applicability of EC-isHCR, we developed an automated probe design tool (https://github.com/ShuntaYorimoto/hcrkit). By combining this tool with EC-isHCR, we provide a fast and versatile framework to visualize mRNAs. This framework will help reduce the barrier to using fast isHCR and thereby facilitate research across diverse areas of the life sciences. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=77 SRC="FIGDIR/small/696653v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@1852584org.highwire.dtl.DTLVardef@621682org.highwire.dtl.DTLVardef@1b3bf5corg.highwire.dtl.DTLVardef@1d86841_HPS_FORMAT_FIGEXP M_FIG C_FIG Highlights- EC-isHCR enables rapid acquisition of high-contrast images. - EC-isHCR preserves features of conventional isHCR, including versatile sample compatibility and high-resolution imaging. - An automated probe design tool was developed for EC-isHCR. - EC-isHCR/probe tool framework will help reduce the barrier to using fast isHCR.

bioengineering↗

bioRxiv2025

Evolution of multi-partner symbiotic systems in the Cerataphidini tribe: genome reduction of Buchnera and frequent turnover of companion symbionts

How multi-partner symbiotic systems originate and diversify within a lineage remains poorly understood. To address this, we investigated the evolutionary dynamics of bacterial symbionts across eight species of the aphid subfamily Hormaphidinae, with detailed molecular, genomic, and microscopic analyses focused on two Cerataphidini species, Ceratovacuna nekoashi and Pseudoregma panicola. Our 16S ribosomal RNA gene amplicon sequencing analysis revealed that Cerataphidini species consistently harbor companion symbionts alongside Buchnera, whereas the examined Hormaphidini and Nipponaphidini species harbor only Buchnera. Notably, Arsenophonus in C. nekoashi and C. japonica have distinct phylogenetic origins, and P. panicola has acquired Symbiopectobacterium instead of Arsenophonus. Microscopic analyses demonstrated that these companion symbionts are maternally transmitted and occupy distinct cell types from those harboring Buchnera. Genome sequencing revealed extreme reduction in Buchnera genomes to [~]0.4 Mbp in both C. nekoashi and P. panicola, comparable to C. japonica but significantly smaller than Buchnera genomes of [~]0.6 Mbp in mono-symbioses. The companion symbiont genomes retain complete riboflavin biosynthesis pathways absent in Buchnera. Our findings suggest that Buchnera genome reduction and companion symbiont acquisition occurred in the common ancestor of Cerataphidini, followed by multiple companion symbiont replacements, demonstrating that ancient obligate symbionts can remain evolutionarily stable while companion symbionts undergo frequent turnover. ImportanceMany insects depend on multiple bacterial symbionts to survive on nutritionally limited diets, yet how such multi-partner symbiotic systems originate and change over evolutionary time is poorly understood. By examining the aphid subfamily Hormaphidinae, particularly Ceratovacuna nekoashi and Pseudoregma panicola, we show that a dramatic reduction in the genome of the ancient symbiont Buchnera and the acquisition of a companion symbiont occurred together in the common ancestor of the tribe Cerataphidini. Strikingly, while Buchnera has been stably maintained across all examined species, the companion symbiont has been repeatedly replaced by phylogenetically diverse bacteria, even among closely related species. These findings reveal an evolutionary asymmetry between ancient and recently acquired symbionts and suggest that companion symbiont turnover is a common consequence in insects harboring genomically degraded obligate symbionts.

microbiology↗

bioRxiv2022

Complex host/symbiont integration of a multi-partner symbiotic system in the eusocial aphid Ceratovacuna japonica

Some hemipteran insects rely on multiple endosymbionts for essential nutrients. However, the evolution of multi-partner symbiotic systems is not well-established. Here, we report a co-obligate symbiosis in the eusocial aphid, Ceratovacuna japonica. 16S rRNA amplicon sequencing unveiled co-infection with a novel Arsenophonus sp. symbiont and Buchnera aphidicola, a common obligate endosymbiont in aphids. Both symbionts were housed within distinct bacteriocytes and were maternally transmitted. The Buchnera and Arsenophonus symbionts had streamlined genomes of 432,286 bp and 853,149 bp, respectively, and exhibited metabolic complementarity in riboflavin and peptidoglycan synthesis pathways. These anatomical and genomic properties were similar to those of independently evolved multi-partner symbiotic systems, such as Buchnera-Serratia in Lachninae and Periphyllus aphids, representing remarkable parallelism. Furthermore, symbiont populations and bacteriome morphology differed between reproductive and soldier castes. Our study provides the first example of co-obligate symbiosis in Hormaphidinae and gives insight into the evolutionary genetics of this complex system.

evolutionary biology↗