Biology subjects

Nonoyama, S.

Publications and source records attributed to Nonoyama, S..

4 recordsLinked to original sources

bioRxiv2026

Horizontal gene transfer drives the emergence of nitrogen fixation in a unicellular Synechocystis lineage

Nitrogen fixation plays a central role in primary productivity and nitrogen cycling in aquatic ecosystems, yet its distribution among cyanobacterial lineages remains incompletely understood. Biological nitrogen fixation is energetically costly and highly oxygen-sensitive, imposing constraints in oxygenic phototrophs. The unicellular cyanobacterial genus Synechocystis has long been regarded as strictly non-diazotrophic. Here, we report that Synechocystis sp. LKSZ1 possesses a functional nitrogen fixation system. Comparative genomics revealed that LKSZ1 is distinct from other Synechocystis strains and uniquely harbors a complete nif gene. Phylogenetic and structural analyses indicate acquisition via horizontal gene transfer from filamentous cyanobacteria. Physiological assays demonstrated photoautotrophic growth under nitrogen-depleted conditions and nitrogenase activity under microoxic to anaerobic conditions. Disruption of nifK abolished both growth and activity. These findings show that ecological nitrogen limitation and host compatibility can enable functional integration of horizontally acquired nitrogen fixation.

microbiology↗

bioRxiv2025

NADPH phosphatase activity of Mesh1 controls sleep in Drosophila

Recent findings have shown that metazoans accumulate the bacterial second messenger guanosine tetraphosphate (ppGpp) and possess Mesh1, a gene encoding a ppGpp hydrolase domain. Mesh1 deficiency affects sleep behavior and eclosion under starvation in Drosopila, and ferroptosis in human cells. However, human Mesh1 also exhibits NADPH/NADP+ phosphatase activity in vitro, making it unclear whether these phenotypes result from loss of ppGpp hydrolysis, NADPH/NADP+ dephosphorylation, or both. To address this, we performed biochemical and genetic analysis of Drosophila Mesh1. We first found that Drosophila Mesh1 dephosphorylates NADPH, but not NADP+, in vitro. We subsequently sought to generate Drosophila Mesh1 point mutants specifically impaired in NADPH phosphatase activity. Based on structural data, we mutated W138 and R142, residues that are predicted to interact with NADPH but not ppGpp. W138 was replaced with phenylalanine results in complete loss of NADPH phosphatase activity with retained ppGpp hydrolase activity. Flies carrying the W138F mutation, introduced via genome editing, exhibited shortened total sleep and increased sleep fragmentation in behavioral assays, without changes in intracellular ppGpp levels. These results indicate that the NADPH phosphatase activity of Mesh1, and specifically the W138 residue, is essential for normal sleep regulation in Drosophila.

molecular biology↗

bioRxiv2024

Evolution of Tn4371 family ICE; traR mediated coordination of cargo gene upregulation and horizontal transfer

ICEKKS102Tn4677, which has been shown to transfer horizontally, carries bph operon for mineralization of PCBs/biphenyl and belongs to an ICE Tn4371 family. In this study we investigated the role of traR gene encoding a LysR-type transcriptional regulator, which is conserved in sequence, positioning, and directional orientation among Tn4371 family ICEs. The traR belonged to bph operon and its overexpression on solid medium resulted in modest upregulation of traG (3-fold) and marked upregulation of xis (80-fold), and enhanced ICE excision, and notably ICE transfer frequency. We propose the evolutional roles of traR, which upon insertion to the current position, connected the cargo gene activation and ICE-transfer. This property of ICE, transferring under environmental conditions that lead to cargo gene activation, would give fitness advantages to the host bacteria, thereby resulting in efficient dissemination of the Tn4371 family ICEs. SignificanceOnly ICEKKS102Tn4677 is proven to transfer among the widely disseminating Tn4371 family ICEs from {beta} and {gamma}-proteobacteria. We showed that the traR gene in ICEKKS102Tn4677 conserved in the ICE family with fixed location and direction is co-transcribed with the cargo gene and activates ICE transfer. We propose that capturing of traR by an ancestral ICE to the current position established ICE Tn4371 family ICEs. Our findings provide insights into the evolutionary processes that led to the widespread distribution of the Tn4371 family of ICEs across bacterial species.

molecular biology↗

bioRxiv2023

qMaLioffG: A single green fluorescent protein FLIM indicator enabling quantitative imaging of endogenous ATP

The widespread use of fluorescence lifetime imaging microscopy (FLIM) for quantitative imaging is hindered by the limited availability of a FLIM-based genetically encoded indicator using a conventional 488 nm laser. Here, we present qMaLioffG, a single green fluorescent protein FLIM indicator showing a fluorescence lifetime change in ATP concentration within the physiological range. This allows quantitative imaging of endogenous ATP to investigate cellular energy status of different cell types.

biophysics↗