Article
Biochemistry & Molecular Biology
Kohki Ishida, Akira Nakamura, Shuichi Kojima
Summary: This study reports the crystal structures of AlbE and AlbF homologs, revealing their formation of heterodimeric complexes. Although similar to M16B family metalloproteases, the AlbEF complex has a shallower and more open substrate-binding chamber with a surface that is electrically complementary to the precursor of subtilosin.
Article
Biochemistry & Molecular Biology
David S. Wishart, Ray Kruger, Aadhavya Sivakumaran, Karxena Harford, Selena Sanford, Rahil Doshi, Nitya Kehrtarpal, Omolola Fatokun, Daphnee Doucet, Ashley Zubkowski, Hayley Jackson, Gina Sykes, Miguel Ramirez-Gaona, Ana Marcu, Carin Li, Kristen Yee, Christiana Garros, Dorsa Yahya Rayat, Jeanne Coleongco, Tharuni Nandyala, Vasuk Gautam, Eponine Oler
Summary: PathBank is a database that provides comprehensive metabolite pathway information. With the latest update of PathBank 2.0, there have been significant improvements in the number, quality, and functionality of pathways, making it more useful for interpreting metabolomics data.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Microbiology
Emilia Ghelardi, Ana Teresa Abreu y Abreu, Christian Boggio Marzet, Guillermo Alvarez Calatayud, Marcos Perez, Ana Paula Moschione Castro
Summary: Bacillus clausii is a probiotic with good tolerance and beneficial properties for human health. Although widely used, its advantages are not fully disseminated. Some properties of Bacillus clausii may bring more health benefits in other therapeutic areas.
Review
Biochemistry & Molecular Biology
Morgan E. Milton, John Cavanagh
Summary: Bacterial biofilms provide protection to bacteria against environmental challenges, especially antibiotics. Bacillus subtilis has been extensively studied as a model organism to understand biofilm formation, and this review summarizes the structural and biochemical studies on the protein signaling network responsible for the transition from planktonic to biofilm state. Deciphering the molecular mechanisms of these regulatory proteins can help us exploit critical features of the biofilm pathway for possible therapeutic interventions.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Seunghyun Sim, Yue Hui, David A. Tirrell
Summary: The incorporation of living cells into materials presents both challenges and possibilities. In this study, a new class of 3D-printable materials based on poly(N-hydroxymethylacrylamide) is developed, which allows the cross-linking of spore-forming bacteria into a polymeric scaffold. These embedded cells and spores can become metabolically active and produce proteins after re-swelling in nutrient-rich media. The leak-free scaffold enables protein production while preventing cell escape. This research demonstrates the potential utility of living composite materials in various applications.
Article
Biochemistry & Molecular Biology
Peiwen Lv, Yan Shang, Ye Zhang, Wenkai Wang, Yuanxiang Liu, Dandan Su, Wei Wang, Chunfang Li, Cuiqing Ma, Chunyu Yang
Summary: The ACR3 family is a common pathway that confers high-level resistance to toxic metalloids. Through studying the structure and conservation of Acr3 antiporter, critical residues in TM9 Motif C and TM5 Motif B were identified for substrate binding and ionization process.
Article
Multidisciplinary Sciences
Sarah Gingichashvili, Doron Steinberg, Ronit Vogt Sionov, Osnat Feuerstein, Noa E. Cohen
Summary: In this study, computational analytics were used to quantify the morphological response of Bacillus subtilis to the proximity of an antimicrobial source. The results revealed that the inner core, characterized by wrinkled formations, is more preserved compared to the periphery. Additionally, a crescent-shaped colony morphology and changes in the growth substrate of macrocolonies exposed to the antimicrobial were observed.
SCIENTIFIC REPORTS
(2022)
Article
Food Science & Technology
Wenqiang Shen, Yaojun Liu, Xinyue Zhang, Xiong Zhang, Xiaoping Rong, Lihong Zhao, Cheng Ji, Yuanpei Lei, Fengjuan Li, Jing Chen, Qiugang Ma
Summary: In this study, the potential ameliorative effects of probiotic Bacillus subtilis and biodegradable Bacillus subtilis on ZEN toxicosis in gilts were compared. The results showed that the biodegradable Bacillus subtilis had significant protective effects on growth performance, immune function, hormone secretion, and ZEN elimination in gilts compared to the probiotic Bacillus subtilis.
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
Plant Sciences
Li-Hsuan Ho, Yung- Lee, Shu-Ying Hsieh, I-Shiuan Lin, Yun-Chien Wu, Han-Yu Ko, Patrick A. Klemens, H. Ekkehard Neuhaus, Yi-Min Chen, Tzu-Pi Huang, Chih-Hsin Yeh, Woei-Jiun Guo
Summary: Gastrodia elata, a mycoheterotrophic orchid, relies on symbiotic fungus Armillaria for carbon distribution, with sucrose identified as a major sugar transported. The high-affinity sucrose transporter gene GeSUT4 plays a key role in active sucrose transport and carbon allocation, highlighting the evolutionary importance of sucrose transporters in plant-microbe interactions. Transgenic Arabidopsis overexpressing GeSUT4 showed larger leaves but were sensitive to excess sucrose, demonstrating the regulation role of GeSUT4 in sugar allocation.
PLANT CELL AND ENVIRONMENT
(2021)
Article
Food Science & Technology
Wen Zhang, Qiuxia Tong, Jiahong You, Xucong Lv, Zhibin Liu, Li Ni
Summary: Research has shown that dietary supplementation with Bacillus subtilis in tilapia can reduce the colonization and growth of spoilage bacteria Pseudomonas spp., decrease total volatile basic nitrogen (TVB-N) production, and improve the flavor of fish. The study also found that treatment with B. subtilis could inhibit the growth of various bacteria and reduce the production of aromatic spoilage compounds associated with these bacteria. This suggests that B. subtilis has great potential as a microecological preservative for fish.
Editorial Material
Biochemistry & Molecular Biology
Bing Wang, Irina Artsimovitch
Summary: Bacillus subtilis utilizes uncoupled transcription and translation strategies to meet its unique regulatory needs, showing that bacteria employ diverse gene expression strategies.
TRENDS IN MICROBIOLOGY
(2021)
Article
Mathematics, Applied
Jianyu Hu, Xiaoli Chen, Jinqiao Duan
Summary: We investigate the quantitative network of gene expression dynamics in the competence development of Bacillus subtilis, quantifying the most probable transition pathways for both excitable and bistable dynamics and analyzing how noise intensity affects the transition phenomena.
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
Food Science & Technology
Felix Kofi Agbeko Kuebutornye, Yishan Lu, Zhiwen Wang, Jan Mraz
Summary: This study proves the probiotic traits of Bacillus velezensis TPS3N, Bacillus subtilis TPS4, and Bacillus amyloliquefaciens TPS17, which were isolated from the gut of Nile tilapia, through genomic analysis. Gene clusters responsible for acid and bile tolerance, adhesion, and colonization of the host's gut were identified. Gene markers for bacteriocins and secondary metabolites were also found, suggesting their potential use as alternatives to traditional antibiotics. In addition, the isolates were shown to enhance the host's immunity, aid in digesting complex feed ingredients, and possess genes for synthesizing vitamins and amino acids. This study provides valuable insights into these isolates and opens avenues for genetic manipulations to enhance their characteristics.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Tiago Pedreira, Christoph Elfmann, Neil Singh, Joerg Stuelke
Summary: The new field of synthetic biology focuses on creating artificially designed organisms, with a major breakthrough being the development of the minimal genome bacterium JCVI-syn3A. To better understand the functions of the genes and proteins of artificial bacteria, the SynWiki database was established, providing interactive protein-protein interaction information.
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.
Article
Microbiology
Larissa Krueger, Christina Herzberg, Dennis Wicke, Patricia Scholz, Kerstin Schmitt, Asan Turdiev, Vincent T. Lee, Till Ischebeck, Joerg Stuelke
Summary: In Bacillus subtilis, the c-di-AMP receptor protein DarB binds to pyruvate carboxylase, activating the enzyme's activity. This interaction occurs under conditions of potassium starvation and glutamate demand.
Article
Biochemistry & Molecular Biology
Jana L. Heidemann, Piotr Neumann, Larissa Krueger, Dennis Wicke, Liza Vinhoven, Andreas Linden, Achim Dickmanns, Joerg Stuelke, Henning Urlaub, Ralf Ficner
Summary: The bacterial second messenger c-di-AMP controls essential cellular processes, and its binding to the protein DarB regulates the stringent response. We determined the crystal structures of DarB in different states and found that DarB forms a homodimer, binding two cyclic dinucleotide molecules or two AMP molecules. Our findings provide insights into the mechanism of stringent response regulation by c-di-AMP and have implications for drug development.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Microbiology
Christoph Elfmann, Bingyao Zhu, Tiago Pedreira, Ben Hossbach, Maria Lluch-Senar, Luis Serrano, Joerg Stuelke
Summary: The article introduces the significance of Mycoplasma pneumoniae and its database MycoWiki. As a minimal organism, M. pneumoniae can provide insights into the basic requirements for cellular life. MycoWiki integrates various data sources to facilitate the analysis of protein functions.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Janek Meissner, Thorben Schramm, Ben Hossbach, Katharina Stark, Hannes Link, Joerg Stuelke
Summary: Bacillus subtilis can deal with toxic histidine by overexpressing the amino acid exporter AzlCD. The expression of the azl operon requires the mutational inactivation of the repressor AzlB.
JOURNAL OF BACTERIOLOGY
(2022)
Review
Microbiology
Joerg Stuelke, Anika Grueppen, Marc Bramkamp, Stefan Pelzer
Summary: Next to Escherichia coli, Bacillus subtilis is the most studied and best understood organism that also serves as a model for many important pathogens. Due to its ability to form heat-resistant spores that can germinate even after very long periods of time, B. subtilis has attracted much scientific interest. Another feature is its genetic competence, making it amenable to genetic manipulation and investigation.
JOURNAL OF BACTERIOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Dennis Wicke, Janek Meissner, Robert Warneke, Christoph Elfmann, Joerg Stuelke
Summary: Model organisms like Bacillus subtilis have been extensively studied, but a significant number of proteins in these organisms still have unknown functions. The Understudied Proteins Initiative aims to address this issue. Highly expressed proteins that are poorly studied are likely to play important roles in cellular processes and should be a priority for further research.
MOLECULAR MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Francis J. O'Reilly, Andrea Graziadei, Christian Forbrig, Rica Bremenkamp, Kristine Charles, Swantje Lenz, Christoph Elfmann, Lutz Fischer, Joerg Stuelke, Juri Rappsilber
Summary: Accurately modeling protein structures and their complexes using AI is revolutionizing molecular biology. In this study, we used a combination of crosslinking mass spectrometry and CoFrac-MS to identify protein-protein interactions in a Gram-positive bacterium. By predicting the structures of these interactions and validating them with crosslinking MS data, we proposed novel structural models of protein assemblies and identified new interactors of important cellular machineries. This approach provides insights into protein-protein interactions inside intact cells and is applicable to genetically intractable organisms.
MOLECULAR SYSTEMS BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Christoph Elfmann, Joerg Stuelke
Summary: The development of AlphaFold and its variant AlphaFold-Multimer has revolutionized protein structure prediction in the field of structural biology. However, interpreting these predictions can be challenging for non-experts. To address this issue, the PAE Viewer webserver has been introduced, which provides an integrated visualization of predicted protein complexes and allows the evaluation of prediction quality using the Predicted Aligned Error (PAE) metric. Moreover, it enables the integration of experimental cross-linking data to enhance the interpretation of structure predictions.
NUCLEIC ACIDS RESEARCH
(2023)
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.
