Biology subjects

Sugimoto, S.

Publications and source records attributed to Sugimoto, S..

7 recordsLinked to original sources

bioRxiv2025

Lysyl-phosphatidylglycerol promotes cell-to-cell interaction and biofilm formation of Staphylococcus aureus as a biofilm matrix component

Biofilms formed by Staphylococcus aureus contribute significantly to persistent infections and antibiotic resistance, driven by the unique composition of their extracellular matrix. While previous studies highlighted extracellular DNA, proteins, and polysaccharides as key components, the role of phospholipids in biofilm architecture remains underexplored. This study identifies extracellular phospholipids, including lysyl-phosphatidylglycerol (Lys-PG), phosphatidylglycerol, and cardiolipin (CL), as critical structural elements in S. aureus biofilms. Bacterial phospholipase A1 (PLA1) that cleaves the acyl ester bond at the sn-1 position of phospholipids effectively dispersed pre-formed biofilms and prevented new biofilm formation by hydrolyzing extracellular phospholipids, without affecting bacterial growth or exhibiting cytotoxicity. Microscopy analyses confirmed that PLA1 disrupts membranous nanostructures, including extracellular vesicles and nanofilaments, integral to biofilm stability. Lipidomic analysis revealed an enrichment of Lys-PG and CL in the biofilm matrix. Lys-PG promotes bacterial aggregation by acting as a molecular glue, mediated through electrostatic and hydrophobic interactions. Deletion of the mprF gene, responsible for Lys-PG synthesis, significantly impaired biofilm formation, confirming its essential role. These findings reveal a "moonlighting" function of phospholipids in biofilm architecture, providing insights into biofilm biology and presenting PLA1 as a promising tool for biofilm control. SignificanceBiofilms, dense bacterial communities, pose significant challenges across medical, industrial, and daily life contexts. Understanding their formation mechanisms is crucial for developing effective strategies against them. We investigated biofilm matrix components in S. aureus biofilms, focusing on phospholipids. Our study reveals the presence and significance of Lys-PG in the biofilm matrix, acting as a crucial factor in biofilm formation and maintenance. Through biochemical, lipidomic, and genetic analyses, we demonstrate the role of Lys-PG in facilitating cell-to-cell contacts, contributing to the robustness and thickness of S. aureus biofilms. These findings shed light on the physiological function of extracellular phospholipids in bacterial biofilms and suggest targeting Lys-PG and its synthetic mechanism as a promising strategy for biofilm control.

microbiology↗

bioRxiv2025

A multimodal dataset linking wide-field calcium imaging to behavior changes in mice during an operant lever-pull task

The BraiDyn-BC (Brain Dynamics underlying emergence of Behavioral Change) Database offers an extensive, multimodal dataset that links wide-field calcium imaging of the mouse neocortex to comprehensive behavioral measurements during a behavioral task. As one of the contents in this database, we newly provide a dataset that includes 15 sessions spanning two weeks of motor skill learning, in which 25 mice were trained to pull a lever to obtain water rewards. Simultaneous high-speed videography captures body, facial, and eye movements, and environmental parameters are monitored. The dataset also features resting-state cortical activity and sensory-evoked responses, enhancing its utility for both learning-related and sensory-driven neural dynamics studies. Data are formatted in accordance with the Neurodata Without Borders (NWB) standard, ensuring compatibility with existing analysis tools and adherence to the FAIR principles. This resource enables in-depth investigations into the neural mechanisms underlying behavior and learning. The platform encourages collaborative research, supporting the exploration of rapid within-session learning effects, long-term behavioral adaptations, and neural circuit dynamics.

neuroscience↗

bioRxiv2024

Periplasmic serine protease Prc is responsible for amyloid subunit CsgA degradation and proteostasis in Escherichia coli

Escherichia coli synthesizes curli amyloid fibers extracellularly during biofilm formation and host colonization. The proteostasis network regulates the major curli subunit, CsgA, to prevent intracellular amyloid aggregation, yet the degradation mechanism remains elusive. Here, through a comprehensive investigation employing genetically engineered E. coli, multi-copy-suppressor screening, and biochemical analyses, we identify periplasmic serine protease Prc as a key player in CsgA degradation. Prc directly degrades CsgA through internal cleavage, differing from canonical tail-specific proteases. Although the bacterial HtrA homologs DegP and DegQ exhibit limited CsgA degradation activity in vitro in the presence of the suicide activator YjfN, deletion of these proteases did not affect native CsgA degradation in vivo. Instead, Prc, in coordination with the periplasmic chaperone CsgC, prevents the periplasmic accumulation of CsgA amyloid-like aggregates. Additionally, disruptions in secretion efficiency and proteolytic systems reduce csg operon expression through activation of the Rcs and Cpx two-component systems. These findings reveal a dual-layered strategy employed by E. coli to prevent intracellular accumulation of extracellular amyloids at both protein degradation and transcriptional regulation levels. This study provides insights into the mechanisms ensuring cellular homeostasis during curli biogenesis.

microbiology↗

bioRxiv2023

Evidence of the simultaneous replications of active viruses in specimens positive for multiple respiratory viruses

Genetic diagnostic assays for the detection of respiratory viruses sometimes show simultaneous multiple infections with low copy numbers. In such cases, the disease is considered caused by a single etiologic agent and others are nonspecific reactions and/or contaminations. Interferon-dependent interference is seen in dual infections of influenza and respiratory syncytial virus, which are the main causes of respiratory infections. Virus isolation is one of the solutions in detecting other active viruses present in specimens, and the air-liquid interface culture of human bronchial/tracheal epithelial cells (HBTEC-ALI) is optimal for the isolation of respiratory viruses owing to its wide range of susceptibility. In this study, we successfully confirmed the replications of various viruses from specimens with low copy numbers and passed 2-3 viruses simultaneously using HBTEC-ALI cultures, mainly including human bocavirus 1 and/or human rhinovirus.

microbiology↗

bioRxiv2021

Nasal delivery of single-domain antibodies improve symptoms of SARS-CoV-2 infection in an animal model

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes the disease COVID-19 can lead to serious symptoms, such as severe pneumonia, in the elderly and those with underlying medical conditions. While vaccines are now available, they do not work for everyone and therapeutic drugs are still needed particularly for treating life-threatening conditions. Here, we showed nasal delivery of a new, unmodified camelid single-domain antibody (VHH), termed K-874A, effectively inhibited SARS-CoV-2 titers in infected lungs of Syrian hamsters without causing weight loss and cytokine induction. In vitro studies demonstrated that K-874A neutralized SARS-CoV-2 in both VeroE6/TMPRSS2 and human lung-derived alveolar organoid cells. Unlike other drug candidates, K-874A blocks viral membrane fusion rather than viral attachment. Cryo-electron microscopy revealed K-874A bound between the receptor binding domain and N-terminal domain of the virus S protein. Further, infected cells treated with K-874A produced fewer virus progeny that were less infective. We propose that direct administration of K-874A to the lung via a nebulizer could be a new treatment for preventing the reinfection of amplified virus in COVID-19 patients. Author summaryVaccines for COVID-19 are now available but therapeutic drugs are still needed to treat life-threatening cases and those who cannot be vaccinated. We discovered a new heavy-chain single-domain antibody that can effectively neutralize the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes COVID-19. Unlike other drug candidates, which prevent the virus from attaching to the receptor on the host cell, this new antibody acts by blocking the virus membrane from fusing with the host cell membrane. We studied the behavior of the new antibody in vitro using VeroE6/TMPRSS2 cells and human lung organoids. When delivered through the nose to infected Syrian hamsters, we found that this antibody could prevent the typical symptoms caused by SARS-CoV-2. Our results are significant because delivering simple drugs directly to infected lungs using a nebulizer could increase the potency of the drugs while reducing the risk of immune reaction that could occur if the drugs escape or are delivered through the blood stream.

microbiology↗

bioRxiv2020

A highly attenuated vaccinia virus strain LC16m8-based vaccine for severe fever with thrombocytopenia syndrome

Severe fever with thrombocytopenia syndrome (SFTS) caused by Dabie bandavirus (formerly SFTS virus [SFTSV]) is an emerging hemorrhagic infectious disease with a high case-fatality rate. One of the best strategies for preventing SFTS is to develop a vaccine, which is expected to induce both humoral and cellular immunity. We applied a highly attenuated but still immunogenic vaccinia virus strain LC16m8 (m8) as a recombinant vaccine for SFTS. Recombinant m8s expressing SFTSV nucleoprotein (m8-N), envelope glycoprotein precursor (m8-GPC), and both N and GPC (m8-N+GPC) in the infected cells were generated. Both m8-GPC- and m8-N+GPC-infected cells were confirmed to produce SFTSV-like-particles (VLP) in vitro, and the N was incorporated in the VLP produced by the infection of cells with m8-N+GPC. Specific antibodies to SFTSV were induced in mice inoculated with each of the recombinant m8s, and the mice were fully protected from lethal challenge with SFTSV at both 103 TCID50 and 105 TCID50. In mice that had been immunized with vaccinia virus strain Lister in advance of m8-based SFTSV vaccine inoculation, protective immunity against the SFTSV challenge was also conferred. The pathological analysis revealed that mice immunized with m8-GPC or m8-N+GPC did not show any histopathological changes without any viral antigen-positive cells, whereas the control mice showed focal necrosis with inflammatory infiltration with SFTSV antigen-positive cells in tissues after SFTSV challenge. The passive serum transfer experiments revealed that sera collected from mice inoculated with m8-GPC or m8-N+GPC but not with m8-N conferred protective immunity against lethal SFTSV challenge in naive mice. On the other hand, the depletion of CD8-positive cells in vivo did not abrogate the protective immunity conferred by m8-based SFTSV vaccines. Based on these results, the recombinant m8-GPC and m8-N+GPC were considered promising vaccine candidates for SFTS. Author SummarySevere fever with thrombocytopenia syndrome (SFTS) is an emerging viral hemorrhagic fever with a high case-fatality rate (approximately 5% to >40%). Indigenous SFTS has been reported in China, Japan, South Korea, and Vietnam. Thus, the development of an effective vaccine for SFTS is urgently needed. Vaccinia virus (VAC) was previously used as a vaccine for smallpox. Unfortunately, after these strains, the so-called second generation of VAC used during the eradication campaign was associated with severe adverse events, and the third generation of VAC strains such as LC16m8 (m8) and modified vaccinia Ankara (MVA) was established. m8 is confirmed to be highly attenuated while still maintaining immunogenicity. m8 is licensed for use in healthy people in Japan. At the present time, approximately 100,000 people have undergone vaccination with m8 without experiencing any severe postvaccine complications. At present, third-generation VAC strains are attractive for a recombinant vaccine vector, especially for viral hemorrhagic infectious diseases, such as Ebola virus disease, Lassa fever, Crimean-Congo hemorrhagic fever, and SFTS. We investigated the practicality of an m8-based recombinant vaccine for SFTS as well as other promising recombinant VAC-based vaccines for viral hemorrhagic infectious diseases.

microbiology↗

bioRxiv2020

Hierarchical Model for the Role of J-Domain Proteins in Distinct Cellular Functions

In Escherichia coli, the major bacterial Hsp70 system consists of DnaK, three J-domain proteins (JDPs: DnaJ, CbpA, and DjlA), and one nucleotide exchange factor (NEF: GrpE). JDPs determine substrate specificity for the Hsp70 system; however, knowledge on their specific role in bacterial cellular functions is limited. In this study, we demonstrated the role of JDPs in bacterial survival during heat stress and the DnaK-regulated formation of curli--extracellular amyloid fibers involved in E. coli biofilm formation. Genetic analysis with a complete set of JDP-null mutant strains demonstrated that only DnaJ is essential for survival at high temperature, while DnaJ and CbpA are indispensable in DnaK regulation of curli production. Additionally, we found that DnaJ and CbpA are involved in the expression of the master regulator CsgD through the folding of MlrA; this keeps CsgA in a translocation-competent state by preventing its aggregation in the cytoplasm. Our findings support a hierarchical model wherein the role of JDPs in the Hsp70 system differs according to individual cellular functions.

molecular biology↗