Article
Biotechnology & Applied Microbiology
Jiajia Li, Jie Yang, Weishan Xin, Sirui Wu, Xujuan Wang, Chuanfa Wang, Zhong Zhang
Summary: Combining High-pressure Thermal Treatment (HPTT) and Potassium Sorbate (PS) has a stronger spore inactivation effect. The combination treatment resulted in a higher inactivation rate of Bacillus subtilis spores compared to HPTT treatment alone. It also caused changes in spore permeability, size, inner membrane damage, and reduced enzyme activity. Consequently, the combination of HPTT and PS is proposed as a promising strategy for Bacillus subtilis spore inactivation.
Article
Biochemistry & Molecular Biology
Jaewan Park, Junghun Kim, Zion Choi, Minsun Hong
Summary: Bacillus subtilis expresses flavonoid-detoxifying enzymes to counteract the antibacterial effects of flavonoids, and their expression is negatively regulated by transcription factors including YetL. The crystal structure of YetL is reported in this study, along with a proposed flavonoid-induced regulatory mechanism.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Food Science & Technology
Leonidas Georgalis, Kah Yen Claire Yeak, Christina Tsimpou, Pablo S. Fernandez, Marjon Wells-Bennik, Alberto Garre
Summary: This study demonstrates that the commonly accepted vitalistic arguments may fail to describe microbial inactivation, and proposes dynamic stress acclimation as an alternative explanation for survivor curves with an upwards curvature. The research also introduces an innovative experimental approach to evaluate the suitability of different hypotheses for bacterial response. The findings provide insights into the possible magnitude of stress acclimation during dynamic treatments and evaluate the contribution of the SigB general stress response system to heat resistance.
FOOD RESEARCH INTERNATIONAL
(2023)
Article
Engineering, Environmental
Yuejun Yu, Andraz Suligoj, Zach Shidlovsky, Dina Shachar, Sima Yaron, Yaron Paz
Summary: Wastewater contains toxins that can harm bacteria in bioreactors, requiring pretreatment with AOP. Designing an integrated system to reduce the load on AOP is challenging due to the constantly changing nature of toxic compounds. There is a need for inexpensive and fast technologies to evaluate toxicity under unknown compound conditions.
CHEMICAL ENGINEERING JOURNAL
(2022)
Article
Multidisciplinary Sciences
Kathryn H. Gunn, Saskia B. Neher
Summary: Lipoprotein lipase (LPL) hydrolyzes triglycerides from circulating lipoproteins, and the structure of an active LPL dimer reveals a hydrophobic pore adjacent to the active site. The dimerization interface and pore may play a role in substrate specificity and acyl chain release from LPL.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Yudhajeet Basak, Jae-Hun Jeoung, Lilith Domnik, Holger Dobbek
Summary: In this study, the time-dependent structural changes induced by the presence of air on the metal centers of CODH-II were analyzed, revealing that inactivation is a multistep process. Oxygen attacks the Ni ion and blocking the open coordination site with a cyanide ligand stabilizes the cluster structure, protecting CODHs from oxidation. In the irreversible phase, nickel is lost, iron ions rearrange, and sulfido ligands disappear. The findings have important implications for protecting CODHs from over-oxidation.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
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
Biochemistry & Molecular Biology
Amy E. Medlock, Wided Najahi-Missaoui, Mesafint T. Shiferaw, Angela N. Albetel, William N. Lanzilotta, Harry A. Dailey
Summary: Ferrochelatase is an important enzyme involved in catalyzing heme synthesis in humans, serving a regulatory and catalytic role in the pathway. Studies on its crystal structures, kinetic properties, and catalytic cycle have provided insights into its functions. However, questions regarding metal ion delivery, active site residue roles, and the catalytic mechanism remain open for further investigation.
BIOCHEMICAL JOURNAL
(2021)
Article
Chemistry, Physical
Thomas J. Summers, Reza Hemmati, Justin E. Miller, Donatus A. Agbaglo, Qianyi Cheng, Nathan J. DeYonker
Summary: This work compares the interactions between ligands and residues in an x-ray crystal structure and structures from a molecular dynamics simulation, and finds that the measured ligand-residue interactions in the crystal structure are not predictive of active site contacts in the molecular dynamics structures. The variability in interatomic contacts among structures is not correlated with variability in interaction energies. However, using interaction energies can be a useful tool to characterize and rank residue importance in computational enzymology workflows.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Biology
Taylor B. Updegrove, Jailynn Harke, Vivek Anantharaman, Jin Yang, Nikhil Gopalan, Di Wu, Grzegorz Piszczek, David M. Stevenson, Daniel Amador-Noguez, Jue D. Wang, L. Aravind, Kumaran S. Ramamurthi
Summary: Hydrolysis of nucleoside triphosphates releases similar amounts of energy, with ATP typically used for energy-intensive reactions and GTP serving as a switch. The bacterial cytoskeletal protein SpoIVA, evolved from a TRAFAC class of P-loop GTPases, failed to polymerize after reengineering its nucleotide-binding pocket to mimic ancestral GTPase activity, highlighting the critical role of the nucleotide base in specific biological functions. The evolutionary pressure that drove the change in nucleotide preference in SpoIVA was suggested to be increased levels of ATP relative to GTP at the end of sporulation.
Article
Biotechnology & Applied Microbiology
Jing Wu, Wei Li, Shi-guang Zhao, Sen-he Qian, Zhou Wang, Meng-jie Zhou, Wen-song Hu, Jian Wang, Liu-xiu Hu, Yan Liu, Zheng-lian Xue
Summary: In this study, SinR(quad) was found to significantly enhance MK-7 synthesis by forming more wrinkly and smooth biofilms, upregulating the expression levels of most NADH dehydrogenases, and providing a higher membrane potential to stimulate the accumulation of components in the electron transport system.
MICROBIAL CELL FACTORIES
(2021)
Article
Biochemistry & Molecular Biology
Qin Liao, Zhongqing Ren, Emma E. Wiesler, Clay Fuqua, Xindan Wang
Summary: Unlike eukaryotes and archaea, bacterial chromosomes usually have a single replication origin. However, a dicentric bacterial chromosome with two replication origins was discovered in Agrobacterium tumefaciens, and both replication origins and their partitioning systems are essential for cell survival.
Article
Chemistry, Multidisciplinary
Ivan Bondarchuk, Valery Perevozkin, Sergey Bondarchuk, Alexander Vorozhtsov
Summary: A mathematical model is proposed for estimating the characteristics of thermal inactivation of vegetative bacterial cells and their spores. The model is used to solve the inverse problem of identifying the model parameters from experimental data, and the results show its adequacy and accuracy. The developed model can be used for selective deactivation of pathogens in food products.
APPLIED SCIENCES-BASEL
(2022)
Article
Chemistry, Multidisciplinary
Nikolay Solakov, Milena Kostova, Kamelia Loginovska, Zlati Markov, Ana Caroline de Oliveira, Yordan Muhovski
Summary: This study investigated adenosine precursors and biologically active peptides, focusing on Ganoderma lucidum and Cordyceps sinensis. The results demonstrated that optimized composition of the culture medium led to an increase in adenosine content, which is of practical significance.
APPLIED SCIENCES-BASEL
(2022)
Article
Biochemistry & Molecular Biology
Charlotte Da Silva, Camille Lamarche, Carole Pichereaux, Emmanuelle Mouton-Barbosa, Gauthier Demol, Sebastien Boisne, Etienne Dague, Odile Burlet-Schiltz, Flavien Pillet, Marie-Pierre Rols
Summary: Low-energy electron beams (LEEB) are a safe and practical sterilization solution for industrial applications. To address the limitations of LEEB, we developed a low-energy pulsed electron beam generator (LEPEB) that can effectively and efficiently eradicate bacteria in a wide range of industrial applications.
BIOELECTROCHEMISTRY
(2024)
Article
Microbiology
Srinand Paruthiyil, Azul Pinochet-Barros, Xiaojuan Huang, John D. Helmann
JOURNAL OF BACTERIOLOGY
(2020)
Article
Microbiology
Hualiang Pi, Brian M. Wendel, John D. Helmann
JOURNAL OF BACTERIOLOGY
(2020)
Article
Microbiology
Azul Pinochet-Barros, John D. Helmann
JOURNAL OF BACTERIOLOGY
(2020)
Article
Biology
Yesha Patel, Heng Zhao, John D. Heimann
Article
Biochemistry & Molecular Biology
Ahmed Gaballa, Tina Tianjiao Su, John D. Helmann
Summary: The bacterial cytosol is maintained in a reducing environment with the help of the thiol bacillithiol (BSH); a variety of proteins and enzymes work together to counteract protein S-bacillithiolation resulting from disulfide stress, forming a complex redox network.
Review
Microbiology
Ankita J. Sachla, John D. Helmann
Summary: Synthesis of the bacterial cell envelope relies on regulated partitioning of resources from central metabolism and key metabolic junctions for precursor allocation. Enzymes like GlmS and MurA play critical roles in directing intermediates towards peptidoglycan synthesis, while shared resources such as lipid carriers and amino acids are essential for envelope assembly. Limited resources must be shared between cellular pathways, with potential benefits from metabolite scavenging or symbiotic relationships with hosts.
CURRENT OPINION IN MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Ankita J. Sachla, Yuanchan Luo, John D. Helmann
Summary: Cell physiology heavily relies on metalloenzymes, which can be disrupted by imbalances in metal ion pools. Bacillus subtilis requires manganese for growth and has mechanisms for import and efflux to maintain homeostasis. Dysfunctional cytochrome aa(3)-type quinol oxidase plays a central role in metal-induced intoxication.
MOLECULAR MICROBIOLOGY
(2021)
Article
Microbiology
Ankita J. Sachla, Alexander J. Alfonso, John D. Helmann
Summary: This study presents a streamlined method for bacterial strain construction using the CRISPR-Cas9 system, targeting nearly 4,000 Bacillus subtilis strains with an integrated erm resistance cassette. By utilizing a single plasmid with a gRNA targeted to erm, genome editing can be directed to nonessential genes as well as sites near essential genes. This method allows for the facile transfer of mutations and genetic constructions without intermediate cloning steps, making it a rapid and versatile approach for a wide range of genome manipulations.
MICROBIOLOGY SPECTRUM
(2021)
Article
Microbiology
Brian M. Wendel, Hualiang Pi, Larissa Krueger, Christina Herzberg, Joerg Stuelke, John D. Helmann
Summary: Osmotic stress is a significant challenge for cells, and maintaining cellular osmolyte potassium (K+) and importing or synthesizing compatible solutes are important for cell survival. It is known that high salt stress leads to transient accumulation of K+ in bacteria, resulting in bacteriostasis until compatible solutes accumulate and K+ levels are restored. In this study, using Bacillus subtilis as a model, it is shown that K+ fluxes perturb Mg2+ homeostasis and that Mg2+ reimport is critical for adaptation and growth resumption. Furthermore, cyclic di-AMP is found to coordinate with Mg2+ and K+ levels, suggesting its role in the cellular response to osmotic stress.
Review
Microbiology
Caroline H. Steingard, John D. Helmann
Summary: The Fur protein is a member of the FUR superfamily that regulates metal homeostasis in bacteria in response to iron, zinc, manganese, and nickel binding. It interacts with other regulators and small molecules to integrate signals related to metal ion balance.
JOURNAL OF BACTERIOLOGY
(2023)
Article
Microbiology
Jessica R. Willdigg, Yesha Patel, John D. Helmann
Summary: Understanding the coordination of cell wall and membrane synthesis is crucial for understanding bacterial growth, division, and resistance to cell envelope stresses. Balanced synthesis of the peptidoglycan cell wall and the cell membrane is critical for maintaining cell shape and pressure. In Bacillus subtilis, a loss of class A penicillin-binding proteins leads to impaired peptidoglycan synthesis, and compensatory mutations that decrease fatty acid synthesis can restore growth. Inhibiting fatty acid synthesis with cerulenin can also restore growth of the PG-limited cells and counteract the effects of beta-lactam antibiotics.
Review
Biotechnology & Applied Microbiology
Erhard Bremer, Alexandra Calteau, Antoine Danchin, Colin Harwood, John D. Helmann, Claudine Medigue, Bernhard O. Palsson, Agnieszka Sekowska, David Vallenet, Abril Zuniga, Cristal Zuniga
Summary: The majority of genomic sequences are automatically annotated, but depend on manual annotation efforts using verified experimental data. This article summarizes the updated functional annotation of Bacillus subtilis strain 168, highlighting new metabolic insights, the role of metals in metabolism and biosynthesis, functions related to biofilm formation, features controlling cell growth, and protein agents allowing class discrimination. The updated sequence, including new genomic objects and literature review, is available at the International Nucleotide Sequence Database Collaboration (INSDC: AccNum AL009126.4).
MICROBIAL BIOTECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
Bixi He, Ankita J. Sachla, John D. Helmann
Summary: In this study, the authors provide evidence that TerC family proteins are involved in the metalation of enzymes during export through the general secretion pathway. They found that Bacillus subtilis strains lacking MeeF and MeeY have reduced protein export capacity and decreased levels of manganese in the secreted proteome. MeeF and MeeY co-purify with proteins of the general secretory pathway and are essential for the function of the Mn2+-dependent lipoteichoic acid synthase.
NATURE COMMUNICATIONS
(2023)
Article
Biology
Vichanan Yamkamon, Khin Phyu Pyar Htoo, Sakda Yainoy, Thummaruk Suksrichavalit, Tienrat Tangchaikeeree, Warawan Eiamphungporn
Article
Microbiology
Brian M. Wendel, Hualiang Pi, Larissa Krueger, Christina Herzberg, Jorg Stuelke, John D. Helmann
Summary: Cells regulate potassium and magnesium ions concentration under high osmotic stress to maintain viability. The reimport of magnesium ions is crucial for cell growth resumption.