Biology subjects

Koizumi, N.

Publications and source records attributed to Koizumi, N..

7 recordsLinked to original sources

bioRxiv2026

Simultaneous quantification of dynamic bacterial deformation and motility by machine learning

We developed a convolutional neural network-based machine learning technique to simultaneously analyze the morphology and motility of spirochetal bacteria swimming with continuous cellular deformation. Matching probabilities between experimental images and learned models realizes quantification of cell morphology and association with motility. This method can be applied to diverse transformable cells, offering critical biophysical insights into microbial dynamics.

microbiology↗

bioRxiv2026

A novel periplasmic layer formed by an outer membrane lipo-protein governs the cell-envelope integrity and stiffness of Leptospira interrogans

The structural integrity and mechanical properties of the cell envelope are crucial for bacterial physiology and dynamics; however, how specific molecular components govern these properties remains poorly understood. Here, we report the novel structural and mechanical functions of LipL32, the most abundant outer-membrane (OM) lipoprotein in the pathogenic spirochete Leptospira interrogans. LipL32 accounts for approximately 75% of the total OM proteins, yet its functional role has remained enigmatic. Cryo-electron microscopy revealed that the highly dense LipL32 forms a hitherto unappreciated thin layer in the periplasmic space, positioned adjacent to the peptidoglycan (PG) layer. The structural analysis also demonstrates that the disruption of lipL32 by transposon insertion results in irregular deformation of OM and spatial variability in the width of the periplasmic space. Quantitative measurements by optical tweezers confirmed that the lipL32::Tn mutant exhibited a significant reduction in whole-cell stiffness. Consistent with this mechanical impairment, the lipL32::Tn mutant displayed a diminished ability to penetrate a heterogeneous agar mesh model that mimics the hosts extracellular matrix, suggesting an important role for cell rigidity in initial infection via damaged skin. These findings define LipL32 as a critical mechanical stabilizer that maintains the structural integrity of the cell envelope. This work provides a new paradigm for understanding how specialized lipoproteins contribute to bacterial cell mechanics, offering insights into pathogenic invasiveness.

microbiology↗

bioRxiv2023

Machine-learning-based motion tracking revealed the inverse correlation between adhesivity and surface motility of the leptospirosis spirochete

Bacterial motility is generally a critical virulence factor for pathogenic species, and thus studies on bacterial motility are significant given that they elucidate the mechanisms of infection and disease. Although fluorescent labeling has been the mainstream approach to detecting individual bacteria in a population or in host tissues, it contains problems related to protein expression stability and interference with bacterial physiology. Here, we applied machine learning to microscopic image analysis to achieve label-free motion tracking of the zoonotic bacterium Leptospira interrogans on cultured animal cells. The label-free method allowed us to measure various leptospiral strains isolated from human and animal patients, and natural reservoirs, showing that fast mobility on kidney cells tends to result in severe symptom. We also analyzed the surface locomotion of mutant strains lacking outer membrane proteins (OMPs) and revealed that the loss of OMPs reduced adherence and facilitated motility on cultured kidney cells. The behavior of clinical isolates and OMP-deficient mutants on cultured cells showed the inverse correlation between adhesion and mobility, which could affect infection outcomes. Thus, our computer vision technique eliminated the restriction on available bacterial strains and provided information that could help in understanding the mechanisms underlying motility-dependent bacterial pathogenicity.

biophysics↗

bioRxiv2021

Light-dependent synthesis of a nucleotide second messenger controls bacterial motility

Nucleotide second messengers are universally crucial factors for the signal transduction of various organisms. In prokaryotes, cyclic nucleotide messengers are involved in the bacterial life cycle and function, such as virulence, biofilm formation, and others mainly via gene regulation. Here we show that the swimming motility of a soil bacterium is rapidly modulated by cyclic adenosine monophosphate (cAMP) synthesized upon light exposure. Analysis of a loss-of-photoresponsivity mutant obtained by transposon random mutagenesis determined the novel sensory gene, and its expression in Escherichia coli through codon optimization revealed the light-dependent synthesis of cAMP. GFP labeling showed the localization of the photoresponsive enzyme at the cell poles where flagellar motors reside. The present findings highlight the new role of cAMP that rapidly controls the flagella-dependent bacterial motility and the global distribution of the discovered photoactivated cyclase among diverse microbial species.

microbiology↗

bioRxiv2020

Adhesivity and motility of a zoonotic spirochete: Implications in host-dependent pathogenicity

Bacterial motility is crucial for many pathogenic species in the process of invasion and/or dissemination. The spirochete bacteria Leptospira spp. cause symptoms, such as hemorrhage, jaundice, and nephritis, in diverse mammals including humans. Although loss-of-motility attenuate the spirochete, the mechanism of the motility-dependent pathogenicity is unknown. Here, focusing on that Leptospira spp. swim in liquid and crawl on solid surfaces, we investigated the spirochetal dynamics on the host tissues by infecting cultured kidney cells from various species with pathogenic and nonpathogenic leptospires. We found that, in the case of the pathogenic leptospires, a larger fraction of bacteria attached to the host cells and persistently traveled long distances using the crawling mechanism. Our results associate the kinetics and kinematic features of the spirochetal pathogens with their virulence. One Sentence SummaryAdhesivity and crawling motility over host tissue surfaces are closely related to the pathogenicity of a zoonotic spirochete.

microbiology↗

bioRxiv2019

Establishing BARA: Biological Nitrogen Fixation for Future Agriculture

The extensive use of nitrogen (N) fertilizers implicates a paradox. While fertilizers ensure the supply of a large amount of food, they cause negative environmental externalities including reduced biodiversity, eutrophic streams, and lakes. Moreover, such fertilizers may also result in a major public health hazard: increased antibiotic resistance. This Perspective discusses a critical role of perturbations in N cycle caused by excessive use of fertilizers and resulting implications as they relate to resistance genes and biodiversity in the biosphere. While there are solutions such as cover crops, these solutions are expensive and inconvenient for farmers. We advocate the use of biological fixation for staple crops--microbiome mediated natural supply of fixed N. This would involve engineering a microbiome that can be grown cheaply and at scale (less expensive than Haber-Bosch fertilizers). We also propose a practical framework of where and how research investments should be directed to make such a solution practical. We make three recommendations for decision makers to facilitate a successful trajectory for this solution. First, that future agricultural science seek to understand how biological fixation might be employed as a practical and efficient strategy. This effort would require that industries and government partner to establish a pre-competitive research laboratory equipped with the latest state-of-the-art technologies that conduct metagenomic experiments to reveal signature microbiomes. Second, the Department of Agriculture and state governments provide research and development (R & D) tax credits to biotech companies specifically geared towards R&D investments aimed at increasing the viability of biological fixation and microbiome engineering. Third, governments and the UN Food and Agriculture Organization (FAO) coordinate Biological Advanced Research in Agriculture (BARA)--a global agricultural innovation initiative for investments and research in biological fixation and ethical, legal, and social implications of such innovation.

microbiology↗

bioRxiv2019

Unfolded protein-independent IRE1 activation contributes to multifaceted developmental processes in Arabidopsis

As an initial step for the unfolded protein response (UPR) pathway, the luminal domain of inositol requiring enzyme 1 (IRE1) senses unfolded proteins in the endoplasmic reticulum (ER). Recent findings in yeast and metazoans suggest alternative IRE1 activation without the sensor domain, although its mechanism and physiological significance remain to be elucidated. In Arabidopsis, the IRE1A and IRE1B double mutant (ire1a/b) is unable to activate cytoplasmic splicing of bZIP60 mRNA and regulated IRE1-dependent decay (RIDD) under ER stress, while the mutant does not exhibit severe developmental defects and is fertile under non-stress conditions. In this study, we focused on a third Arabidopsis IRE1 gene, designated as IRE1C, whose product lacks a sensor domain. We found that even though ire1c and ire1a/c mutants did not exhibit defective bZIP60 splicing and RIDD under ER stress, the ire1a/b/c triple mutant is lethal. Heterozygous IRE1C (ire1c/+) mutation in the ire1a/b mutants resulted in growth defects and reduction of the number of pollen grains. Genetic analysis revealed that IRE1C is required for male gametophyte development in the ire1a/b mutant background. Expression of a mutant form of IRE1B that lacks the luminal sensor domain ({Delta}LD) in the ire1a/b mutant did not complement defects in ER stress-dependent bZIP60 splicing and RIDD. Nevertheless, expression of {Delta}LD complemented a developmental defect in the male gametophyte in ire1a/b/c haplotype. In vivo, the {Delta}LD protein was activated by glycerol treatment that increases the composition of saturated lipid and was able to activate RIDD but not bZIP60 splicing. Phenotypes of IRE1B mutants lacking the sensor domain produced by CRISPR/Cas9-mediated gene editing in the ire1a/c mutant background were essentially same as those of {Delta}LD-expressing ire1a/b mutant. These observations suggest that IRE1 contributes to plant development, especially male gametogenesis, using an alternative activation mechanism that bypasses the unfolded protein-sensing luminal domain.

plant biology↗