Biology subjects

MASUDA, S.

Publications and source records attributed to MASUDA, S..

5 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↗

bioRxiv2024

Sulfide-responsive transcription control in Escherichia coli

To elucidate the mechanism of large-scale transcriptional changes dependent on sulfide in Escherichia coli, a large scale RNA-sequencing analysis was performed on wild-type and sulfide-responsive transcription factor YgaV deletion mutants grown under three conditions: aerobic, semi-aerobic, and semi-aerobic with sulfide. The resulting dataset from these six conditions was subjected to principal component analysis, which categorized the data into five principal components. Estimation of the typical gene expression regulatory mechanisms in each category suggested the presence of mechanisms that are dependent on sulfide but independent of YgaV, as well as those that depend on YgaV but not on sulfide. In YgaV-dependent transcriptional regulation, YgaV was found to function as both a repressor and an activator. These results support the previous hypothesis that YgaV acts as a global regulator responsible for redox homeostasis.

microbiology↗

bioRxiv2023

Bacterial Pathogen Infection Triggers Magic Spot Nucleotide Signaling in Arabidopsis thaliana Chloroplasts Through Specific RelA/SpoT Homologs

Magic spot nucleotides (p)ppGpp are important signaling molecules in bacteria and plants. In the latter, RSH enzymes are responsible for (p)ppGpp turnover. Profiling of (p)ppGpp is more difficult in plants than in bacteria due to lower concentrations and more severe matrix effects. Here, we report that capillary electrophoresis mass spectrometry (CE-MS) can be deployed to study (p)ppGpp abundance and identity in Arabidopsis thaliana. This goal is achieved by combining a titanium dioxide extraction protocol and pre-spiking with chemically synthesized stable isotope labeled internal reference compounds. The high sensitivity and separation efficiency of CE-MS enables monitoring of changes in (p)ppGpp levels in A. thaliana upon infection with the pathogen Pseudomonas syringae pv. tomato (PstDC3000). We observed a significant increase of ppGpp post infection that is also stimulated by the flagellin peptide flg22 only. This increase depends on functional flg22 receptor FLS2 and its interacting kinase BAK1 indicating that pathogen-associated molecular pattern (PAMP) receptor-mediated signaling controls ppGpp levels. Transcript analyses showed an upregulation of RSH2 upon flg22 treatment and both RSH2 and RSH3 after PstDC3000 infection. A. thaliana mutants deficient in RSH2 and RSH3 activity display no ppGpp accumulation upon infection and flg22 treatment, supporting involvement of these synthases in PAMP-triggered innate immunity responses to pathogens within the chloroplast.

biochemistry↗

bioRxiv2019

Plastidial (p)ppGpp synthesis by the Ca2+-dependent RelA-SpoT homolog regulates the adaptation of chloroplast gene expression to darkness in Arabidopsis

In bacteria, the hyper-phosphorylated nucleotides, guanosine 5-diphosphate 3-diphosphate (ppGpp) and guanosine 5-triphosphate 3-diphosphate (pppGpp), function as secondary messengers in the regulation of various metabolic processes of the cell, including transcription, translation, and enzymatic activities, especially under nutrient deficiency. The activity carried out by these nucleotide messengers is known as the stringent response. (p)ppGpp levels are controlled by two distinct enzymes, namely, RelA and SpoT, in Escherichia coli. RelA-SpoT homologs (RSHs) are also conserved in plants and algae where they function in the plastids. The model plant Arabidopsis thaliana contains four RSHs: RSH1, RSH2, RSH3, and Ca2+-dependent RSH (CRSH). Genetic characterizations of RSH1, RSH2, and RSH3 were undertaken, which showed that the (p)ppGpp-dependent plastidial stringent response significantly influences plant growth and stress acclimation. However, the physiological significance of CRSH-dependent (p)ppGpp synthesis remains unclear, as no crsh-null mutant has been available. Here to investigate the function of CRSH, a crsh-knockout mutant of Arabidopsis was constructed using a site-specific gene-editing technique, and its phenotype was characterized. A transient increase of ppGpp was observed for 30 min in the wild type (WT) after light-to-dark transition, but this increase was not observed in the crsh mutant. Similar analyzes were performed with the rsh2rsh3 double and rsh1rsh2rsh3 triple mutants of Arabidopsis and showed that the transient increments of ppGpp in the mutants were higher than those in the WT. The increase of (p)ppGpp in the WT and rsh2rsh3 accompanied decrements in the mRNA levels of psbD transcribed by the plastid-encoded plastid RNA polymerase. These results indicated that the transient increase of intracellular ppGpp at night is due to CRSH-dependent ppGpp synthesis and the (p)ppGpp level is maintained by the hydrolytic activities of RSH1, RSH2, and RSH3 to accustom plastidial gene expression to darkness.

plant biology↗

bioRxiv2019

DLDG1, the Arabidopsis Homolog of the Cyanobacterial H+-Extrusion Protein, Regulates Non-Photochemical Quenching in Chloroplasts

Plants convert solar energy into chemical energy through photosynthesis, which supports almost all life activities on earth. Because the intensity and quality of sunlight can change dramatically throughout the day, various regulatory mechanisms help plants adjust their photosynthetic output accordingly, including the regulation of light energy accumulation to prevent the generation of damaging reactive oxygen species. Non-photochemical quenching (NPQ) is a regulatory mechanism that dissipates excess light energy, but how it is regulated is not fully elucidated. Herein, we report a new NPQ-regulatory protein named Day-Length-dependent Delayed-Greening1 (DLDG1). The Arabidopsis DLDG1 associates with the chloroplast envelope membrane, and the dldg1 mutant had a large NPQ value compared with wild type. The mutant also had a pale-green phenotype in developing leaves but only under continuous light; this phenotype was not observed when dldg1 was cultured in the dark for [≥]8 h per day. DLDG1 is a homolog of the plasma-membrane-localizing cyanobacterial proton-extrusion-protein A that is required for light-induced H+ extrusion, and also shows similarity in its amino-acid sequence to that of Ycf10 encoded in the plastid genome. Arabidopsis DLDG1 enhances the growth-retardation phenotype of the Escherichia coli K+/H+ antiporter mutant, and the everted membrane vesicles of the E. coli expressing DLDG1 show the K+/H+ antiport activity. Our findings suggest that DLDG1 functionally interacts with Ycf10 to control H+ homeostasis in chloroplasts, which is important for the light-acclimation response, by optimizing the extent of NPQ.

plant biology↗