Article
Biochemistry & Molecular Biology
Aisling Brady, Nuria Quiles-Puchalt, Francisca Gallego del Sol, Sara Zamora-Caballero, Alonso Felipe-Ruiz, Jorge Val-Calvo, Wilfried J. J. Meijer, Alberto Marina, Jose R. Penades
Summary: Some Bacillus-infecting bacteriophages utilize a peptide-based communication system, called arbitrium, to coordinate the lysis-lysogeny decision. AimR, a key player in this system, is involved in a complex network of regulation. The SP beta phage, possessing a functional arbitrium system, can optimize production of infective particles while preserving the number of surviving cells, which increases phage persistence in nature.
Article
Virology
Veronique A. Delesalle, Brianne E. Tomko, Albert C. Vill, Katherine B. Lichty, Greg P. Krukonis
Summary: This study describes three virulent phages very similar to SPP1, with greater than 80% nucleotide sequence identity and sharing more than 85% of its protein coding genes. These findings provide insights into the importance of phage adaptation to the environment and gene conservation.
Article
Microbiology
Elhanan Tzipilevich, Philip N. Benfey
Summary: Bacteriophage predation plays a crucial role in bacterial community dynamics and evolution, but its effects in natural habitats, especially in the plant root microbiome, remain understudied. Research has identified a new phage resistance mechanism involving potassium ion modulation and biofilm formation, which has significant implications for plant health. Further studies are needed to explore the full extent of phage-bacterium interactions in diverse microbial communities.
Article
Microbiology
Chen Qin, Wanchun Han, Ying Xu, Ye Zhao, Hong Xu, Bing Tian, Liangyan Wang, Yuejin Hua
Summary: In this study, the biochemical properties and crystal structure of RuvC enzyme from Deinococcus radiodurans were described. DrRuvC exhibited specific binding and cleavage abilities towards HJ DNA, with a preference for Mn2+ as the co-factor. The crystal structure of DrRuvC revealed important amino acid sites for its activities, indicating its typical resolvase characteristics with a specific choice for metal co-factor.
Article
Biotechnology & Applied Microbiology
Yanhua Jiang, Dongqin Xu, Lianzhu Wang, Meng Qu, Fengling Li, Zhijun Tan, Lin Yao
Summary: The recombinant endolysin LysSP1 encoded by Salmonella Typhimurium lytic bacteriophage SLMP1 was obtained in this study, and EDTA was found to enhance its bactericidal activity. LysSP1 showed strong bactericidal activity against Salmonella Typhimurium, exhibited good stability, and demonstrated broad-spectrum bactericidal ability.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Article
Agriculture, Dairy & Animal Science
Yu-Wei Chen, Yu-Hsiang Yu
Summary: This study examined the effects of Bacillus subtilis-fermented products (SFPs) and Bacillus licheniformis-fermented products (LFPs) on broiler growth performance, intestinal morphology, gene expression, cecal microbiota community, and microbial carbohydrate-active enzyme composition. The results showed that LFP treatment resulted in improved body weight and average daily gain compared to the control and SFP treatments. LFPs also increased villus heights in the jejunum and enhanced barrier function and antioxidant gene expression in the jejunum and cecum. The cecal microbiota and carbohydrate-active enzyme composition were also significantly influenced by the treatments. Lactobacillus crispatus abundance was higher in the SFP group, while microbial glycosyltransferase 2 gene expression was higher in the LFP group. Overall, LFPs had a greater positive impact on broiler growth promotion compared to SFPs.
Article
Food Science & Technology
Jurarat Gewtaisong, Ekachai Chukeatirote, Juhee Ahn
Summary: In this study, a virulent bacteriophage BasuTN3 was isolated from Thai fermented soybeans and its stability under different conditions was evaluated. BasuTN3 was found to be specific to Bacillus subtilis strain TN3 and could tolerate a wide range of temperatures and pH conditions, while being susceptible to chloroform, UV, and disinfectants. These findings provide valuable information for understanding the diversity of bacteriophages in fermented soybean products and their interactions with bacterial starter cultures.
FOOD SCIENCE AND BIOTECHNOLOGY
(2023)
Article
Chemistry, Analytical
Mei-yan Wu, Wen-wei Li, Graham Christie, Peter Setlow, Yong-qing Li
Summary: Using Raman tweezers and live-cell phase-contrast microscopy, this study characterized the lysis process of individual Bacillus subtilis cells carrying PBSX prophage during spores' germination, outgrowth, and vegetative growth. The findings showed that nucleic acid intensities in induced cultures decreased rapidly after prophage induction, with a delay before cell burst, and the latent time and burst time varied in cell populations under different culture conditions.
ANALYTICAL CHEMISTRY
(2021)
Article
Microbiology
Huihui Wan, Xiaoying Ouyang, Ting Yang, Tianyun Ye, Minfei Jin, Jing Huang
Summary: In this study, the 4GT gene was cloned and expressed, and its catalytic function and expression conditions were investigated. High yield of recombinant 4GT enzyme was obtained through optimization of fermentation process. This study provides valuable references for the characterization and expression of food-grade enzymes.
CURRENT MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Elhanan Tzipilevich, Osher Pollak-Fiyaksel, Bushra Shraiteh, Sigal Ben-Yehuda
Summary: When bacteria sense infection of their neighbors, a temporary phage tolerance response is triggered, which is primarily executed by the stress-response RNA polymerase sigma factor sigma(X) (SigX). This response activates the dlt operon, encoding enzymes that hinder phage binding and infection, allowing uninfected bacteria to form a protective shield against phage spread.
Article
Food Science & Technology
Angela Maria Catania, Tiziana Civera, Pierluigi Aldo Di Ciccio, Maria Ausilia Grassi, Patrizia Morra, Alessandra Dalmasso
Summary: Processed cheeses from an Italian dairy plant were found to contain Bacillus strains in the initial production hours. Genetic analysis revealed different sequence types for Bacillus cereus strains and identification of a new sequence type for Bacillus subtilis strains. All isolates showed biofilm-forming ability, suggesting the presence of a recurring Bacillus population.
Article
Microbiology
Ke Wu, Zhitao Mao, Yufeng Mao, Jinhui Niu, Jingyi Cai, Qianqian Yuan, Lili Yun, Xiaoping Liao, Zhiwen Wang, Hongwu Ma
Summary: This study constructed the first genome-scale enzyme-constrained model of Bacillus subtilis, which can improve the prediction of microbial phenotype and simulate overflow metabolism. The model was able to accurately predict overflow metabolism and identify target genes for enhancing the yield of commodity chemicals.
Article
Multidisciplinary Sciences
Priyanka Sheladiya, Chintan Kapadia, Vimal Prajapati, Hesham Ali El Enshasy, Roslinda Abd Malek, Najat Marraiki, Nouf S. S. Zaghloul, R. Z. Sayyed
Summary: This study isolated alkaline-tolerant and moderate-temperature pectate lyase-producing bacteria and investigated the characteristics and influencing factors of the enzyme under different conditions. The results showed that the pectate lyase from this strain has potential for industrial applications, particularly in the clarification of fruit juices.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Ramamoorthy Sathishkumar, Ramachandran Kannan, Sekar Jinendiran, Natesan Sivakumar, Gopal Selvakumar, Rajaram Shyamkumar
Summary: In this study, the production of exopolysaccharide (EPS) by a potential endosymbiotic bacterium associated with sponge was optimized using response surface methodology. The purified EPS exhibited strong antioxidant activity and moderate anticoagulant efficacy, with the potential applications in food and pharmaceutical industries highlighted for the future.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Biotechnology & Applied Microbiology
Jorge Frias, Duarte Toubarro, Alexandra Fraga, Claudia Botelho, Jose Teixeira, Jorge Pedrosa, Nelson Simoes
Summary: A new fibrinolytic enzyme with direct thrombolytic action was reported in this paper, showing potential industrial applications.
JOURNAL OF MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Yuki Suzuki, Ibuki Kawamata, Kohei Mizuno, Satoshi Murata
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2020)
Article
Biochemical Research Methods
Deepak Karna, Morgan Stilgenbauer, Sagun Jonchhe, Kazuya Ankai, Ibuki Kawamata, Yunxi Cui, Yao-Rong Zheng, Yuki Suzuki, Hanbin Mao
Summary: By utilizing DNA origami nanosprings, the clustering of integrin molecules can be controlled under different pH conditions to modulate cell motions. The nanospring coils and inhibits cell movement under acidic conditions, while it uncoils and allows cells to move under neutral conditions.
BIOCONJUGATE CHEMISTRY
(2021)
Article
Microbiology
Ester Serrano, Cristina Ramos, Juan C. Alonso, Silvia Ayora
Summary: Natural chromosomal transformation in prokaryotes plays a crucial role in evolution, with the integration of DNA from related species influenced by sequence divergence. In Bacillus subtilis cells, integration of homeologous sequences is initiated in a specific segment and decreases in frequency with higher sequence divergence. RecA and other recombination proteins are essential for gene acquisition from bacteria of related species, highlighting their importance in generating genetic diversity.
ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Yuki Mori, Hiroki Oi, Yuki Suzuki, Kumi Hidaka, Hiroshi Sugiyama, Masayuki Endo, Shigeyoshi Matsumura, Yoshiya Ikawa
Summary: Ribozymes with modular architecture have been designed, forming closed trimers and closed tetramers based on assembly of unit RNAs (L-RNAs). By tuning their structural elements, closed pentamers and closed hexamers were further extended, with their assembly properties analyzed using electrophoretic mobility shift assay (EMSA) and atomic force microscopy (AFM).
Article
Multidisciplinary Sciences
Audrey Labarde, Lina Jakutyte, Cyrille Billaudeau, Beatrix Fauler, Maria Lopez-Sanz, Prishila Ponien, Eric Jacquet, Thorsten Mielke, Silvia Ayora, Rut Carballido-Lopez, Paulo Tavares
Summary: Infection of Bacillus subtilis by bacteriophage SPP1 leads to the hijacking of host replication proteins to assemble hybrid viral-bacterial replisomes, doubling the cell total DNA content within 15 minutes. The replisomes operate at several independent locations within a single viral DNA focus positioned asymmetrically in the cell. These findings demonstrate that bacteriophages restructure the host cytoplasm to confine the essential processes for their multiplication at different cellular locations.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Cell Biology
Ruben Torres, Carolina Gandara, Begona Carrasco, Ignacio Baquedano, Silvia Ayora, Juan C. Alonso
Summary: DisA synthesizes c-di-AMP second messenger, but its synthesis is suppressed upon replication perturbation, while RecG blocks c-di-AMP synthesis in the presence of HJ DNA. DisA limits RecG-mediated ATP hydrolysis and DNA unwinding, suggesting a coordinated role in genome integrity maintenance in Bacillus subtilis spores.
Article
Biology
Matthieu Corvaisier, Jingkai Zhou, Darina Malycheva, Nicola Cornella, Dimitrios Chioureas, Nina M. S. Gustafsson, Catalina Ana Rossello, Silvia Ayora, Tongbin Li, Kristina Ekstrom-Holka, Karin Jirstrom, Lisa Lindstrom, Maria Alvarado-Kristensson
Summary: The study revealed the importance of gamma-tubulin location changes in cell survival and genome integrity. Gamma-tubulin’s nuclear accumulation facilitates the transport and recruitment of PCNA to chromatin, contributing to cell proliferation and maintenance of genome stability. The complex formation between PCNA and gamma-tubulin plays a crucial role in tumor growth and DNA repair through replication fork progression.
COMMUNICATIONS BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Carolina Gandara, Ruben Torres, Begona Carrasco, Silvia Ayora, Juan C. Alonso
Summary: Our study reveals that DisA interacts with RuvAB and RecU to limit fork remodeling and Holliday junction cleavage, providing time for damage repair and replication restart to maintain genome integrity.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Polymer Science
Kazuki Fukushima, Kodai Matsuzaki, Masashi Oji, Yuji Higuchi, Go Watanabe, Yuki Suzuki, Moriya Kikuchi, Nozomi Fujimura, Naofumi Shimokawa, Hiroaki Ito, Takashi Kato, Seigou Kawaguchi, Masaru Tanaka
Summary: A novel polymer conjugate has been developed to form anisotropic nanoassemblies independent of the crystalline nature of the hydrophobic block. Molecular dynamics simulations show that rigid hydrogen-bonding motifs contribute to the anisotropic alignment of block copolymers, and amorphous hydrophobic blocks containing these motifs can form nonspherical assemblies. Enhanced cell proliferation is observed in cell cultures containing anisotropic polymer assemblies with specific aspect ratios or lengths.
Article
Biochemistry & Molecular Biology
Cristina Ramos, Rogelio Hernandez-Tamayo, Maria Lopez-Sanz, Begona Carrasco, Ester Serrano, Juan C. Alonso, Peter L. Graumann, Silvia Ayora
Summary: This study explores the role of RecD2 in DNA replication and its interaction with RecA. The results demonstrate that RecD2 counteracts the inhibition of leading and lagging strand synthesis by physically interacting with RecA. Additionally, RecD2 overcomes replicative stress by modulating RecA-mediated DNA strand exchange and branch migration.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Chemistry, Multidisciplinary
Antti Elonen, Ashwin Karthick Natarajan, Ibuki Kawamata, Lukas Oesinghaus, Abdulmelik Mohammed, Jani Seitsonen, Yuki Suzuki, Friedrich C. Simmel, Anton Kuzyk, Pekka Orponen
Summary: This study presents an algorithmic design process and software pipeline for rendering 3D wireframe polyhedral nanostructures in single-stranded RNA. Users can create models of desired nanostructures using standard 3D graphic design software, and the pipeline generates corresponding RNA nucleotide sequences for experimental folding in the laboratory.
Article
Chemistry, Multidisciplinary
Kotaro Watanabe, Ibuki Kawamata, Satoshi Murata, Yuki Suzuki
Summary: The progress of scaffolded DNA origami technology has allowed for the construction of dynamic nanodevices that mimic shapes and motions of mechanical elements. A multi-reconfigurable 3 x 3 lattice structure consisting of movable joints has been proposed, which can transform into various shapes based on selected signal DNAs. Sequential reconfiguration of the nanolattice and its assemblies has also been demonstrated through a strand displacement reaction.
Review
Biophysics
Yusuke Sato, Yuki Suzuki
Summary: Self-assembled supramolecular structures in living cells play a crucial role in various cellular events, and DNA nanotechnology has enabled the construction of various-shaped nanostructures through programmed self-assembly. Moreover, DNA is utilized to build artificial molecular circuits, capable of activating/inactivating or producing/decomposing target DNA molecules. These dynamically regulated self-assembled systems exhibit features such as component association/dissociation and DNA circuit-regulated structural formation.
BIOPHYSICS AND PHYSICOBIOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Deepak Karna, Wei Pan, Shankar Pandey, Yuki Suzuki, Hanbin Mao
Summary: By incorporating pH responsive i-motif elements, DNA origami nanosprings that respond to pH changes in the environment have been constructed. The innovative force jump approach in optical tweezers allowed direct measurement of spring constants and dynamic recoiling responses under different forces, revealing two distinct force regions with different spring constants. The nanosprings showed slower recoiling rates, and were found to be up to 50 times stiffer compared to reported DNA origami nanosprings with a different design.
Article
Biochemistry & Molecular Biology
Ivana Duic, Hisashi Tadakuma, Yoshie Harada, Ryo Yamaue, Katashi Deguchi, Yuki Suzuki, Shige H. Yoshimura, Hiroki Kato, Kunio Takeyasu, Takashi Fujita
NUCLEIC ACIDS RESEARCH
(2020)