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Activation of Bacterial F-ATPase by LDAO: Deciphering the Molecular Mechanism

Biochemistry (Moscow) 2025年第3期90卷 374-388页

作者： Bruman, Sofya M. Zubareva, Valeria M. Shugaeva, Tatiana E. Lapashina, Anna S. Feniouk, Boris A. Faculty of Bioengineering and Bioinformatics Lomonosov Moscow State University Moscow 119991 Russian Federation Belozersky Institute of Physico-Chemical Biology Lomonosov Moscow State University Moscow 119991 Russian Federation

Abstract: Proton FOF1 ATP synthase catalyzes the formation of ATP from ADP and inorganic phosphate coupled with transmembrane proton transfer using the energy of the protonmotive force (pmf). As pmf decreases, the dir... 详细信息

Abstract: Proton F_OF₁ ATP synthase catalyzes the formation of ATP from ADP and inorganic phosphate coupled with transmembrane proton transfer using the energy of the protonmotive force (pmf). As pmf decreases, the direction of the reaction is reversed and the enzyme generates pmf, transferring protons across the membrane using the energy of ATP hydrolysis. ATPase activity of the enzyme can be suppressed by ADP in a non-competitive manner (ADP-inhibition), and in a number of bacteria, it can be inhibited by conformational changes in the regulatory C-terminal domain of the ε subunit. Lauryldimethylamine oxide (LDAO), a zwitterionic detergent, is known to attenuate both of these inhibitory mechanisms, significantly increasing the ATPase activity of the enzyme. For this reason, LDAO is sometimes used for semi-quantitative estimation of the enzyme’s susceptibility to these regulatory mechanisms. However, the binding site of LDAO in ATP synthase remains unknown. The mechanism by which the detergent counteracts ADP-inhibition and the inhibition involving the ε subunit is also unclear. We performed molecular docking and predicted that LDAO binding might occur at the catalytic site of ATP synthase, whether empty or containing nucleotides. Molecular dynamics simulations showed that LDAO could affect the mobility of the loop in the β subunit (residues β404-415 in Escherichia coli ATP synthase) near the catalytic site. Mutagenesis of residue β409 in the E. coli enzyme and the corresponding β419 residue in the Bacillus subtilis ATP synthase revealed that the type of side chain of this residue indeed affects LDAO-dependent stimulation of ATPase activity. We also found that LDAO activates the enzyme more strongly in the presence of 100 mM sulfate compared to sulfate-free medium. This phenomenon is likely due to the enhancement of ADP-inhibition of the enzyme by sulfate. © Pleiades Publishing, Ltd. 2025.

关键词： ADP-inhibition ATP-synthase Bacillus subtilis Escherichia coli F-ATPase FOF1 LDAO regulation sulfate

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Developing a Head-Attached Interface Device for Closed-Loop Transcranial Ultrasound Stimulation in the Mouse Brain

Developing a Head-Attached Interface Device for Closed-Loop ...

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18th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2025

作者： Furukawa, Ryo Murakami, Shuichi Tateno, Takashi Bioengineering and Bioinformatics Graduate School of Information Science and Technology Hokkaido University Kita 14 Nishi 9 Kita-ku Hokkaido Sapporo060-0814 Japan Osaka Research Institute of Industrial Science and Technology 2-7-1 Ayumino Izumi Osaka594-1157 Japan Bioengineering and Bioinformatics Faculty of Information Science and Technology Hokkaido University Kita 14 Nishi 9 Kita-ku Hokkaido Sapporo060-0814 Japan

Transcranial ultrasound stimulation (TUS), which can be used to noninvasively stimulate local and deep brain areas, holds significant promise for clinical applications. However, TUS apparatus is typically constructed with several components, including a relatively large single-element ultrasound (US) transducer, a waveguide, and a driving source. These components pose challenges when conducting experiments with freely moving small animals, especially in the context of wearable devices. Additionally, conventional open-loop stimulation systems do not allow for the simultaneous monitoring of neural activity, which can sometimes result in the overactivation of neural responses. In this study, we developed a head-mounted piezoelectric micromachined ultrasound transducer (PMUT) array with integrated monitoring electrodes to serve as a TUS interface for mice. To determine effective array patterns for optimal US beam profiles, we first conducted beamforming simulations. We then microfabricated the PMUT arrays according to the results of these simulations. Subsequently, we performed electroencephalographic (EEG) recordings to evaluate the potential of TUS in mice while simultaneously monitoring neural activities. Finally, we discuss future applications of a closed loop TUS system in the treatment of brain diseases. © 2025 by SCITEPRESS– Science and Technology Publications, Lda.

关键词： Closed loop systems

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MitoEdit: A pipeline for optimizing mtDNA base editing and predicting bystander effects

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Computational and Structural Biotechnology Journal 2025年 27卷 1673-1676页

作者： Shah, Devansh McCastlain, Kelly Chang, Ti-Cheng Zhu, Xun Wu, Gang Kundu, Mondira Department of Cell and Molecular Biology St. Jude Children's Research Hospital MemphisTN38105 United States Department of Bioscience and Bioengineering Indian Institute of Technology Jodhpur Jodhpur342030 India Center for Applied Bioinformatics St. Jude Children's Research Hospital MemphisTN38105 United States

Human mitochondrial DNA (mtDNA) mutations are causally implicated in maternally inherited mitochondrial respiratory disorders;however, the role of somatic mtDNA mutations in both late-onset chronic diseases and cancer remains less clear. Recent advances in mtDNA base editing technologies offer exciting opportunities to model and study these mutations. However, current approaches are hindered by the challenge of unintended bystander edits, which are often identified only through labor-intensive empirical testing, leading to inefficiencies in construct development. To address this limitation, we developed MitoEdit, an innovative computational tool designed to optimize mtDNA base editing by leveraging empirical base editor patterns. MitoEdit enables users to input DNA sequences in a simple text-based format, specify the target base position and define the desired modification. The tool outputs a list of candidate target windows, predicts the number and functional impact of bystander edits and provides flanking nucleotide sequences tailored for TALE (transcription activator-like effectors) array protein binding. In silico evaluations demonstrate that MitoEdit accurately predicts the majority of bystander edits, reducing the number of constructs that need to be tested empirically. By streamlining the design process, MitoEdit accelerates the development of mitochondrial base editing constructs, thereby facilitating functional studies and enabling faster discovery. Ultimately, MitoEdit has the potential to advance disease modeling and support the development of therapeutic strategies for mitochondrial-related disorders. © 2025 The Authors

关键词： Transcription

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Assessment of antibiotic-resistant bacteria and genes in bioaerosol samples collected from Praygaraj, India

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Vegetos 2025年 1-8页

作者： Shukla, Prashant Srivastava, Suyash Pal, Arun Kumar Tripathi, Pooja Lal, Jonathan A. Tripathi, Vijay Department of Molecular and Cellular Engineering Jacob Institute of Biotechnology and Bioengineering Sam Higginbottom University of Agriculture Technology and Sciences U.P Prayagraj 211007 India Department of Computational Biology and Bioinformatics Jacob Institute of Biotechnology and Bioengineering Sam Higginbottom University of Agriculture Technology and Sciences U.P Prayagraj 211007 India Department of Microbiology Graphic Era Deemed to be University Clement Town Dehradun Uttarakhand India

Antimicrobial resistance (AMR) poses a significant global health threat, and resistant bacteria in bioaerosols may reflect ambient air pollution levels. This study aimed to assess the prevalence and characterization of antibiotic-resistant bacteria in bioaerosols across various locations in the Prayagraj region of India. Bioaerosol samples were collected from diverse sites, including city intersections, sewage treatment plants, landfill sites, religious places, fairs, and parks. The resistance profiles of the isolated bacteria were determined using the Kirby-Bauer disk diffusion method. The results revealed significant antibiotic resistance, with the highest resistance observed against trimethoprim (23.26%), followed by amoxicillin (9.30%) and ampicillin (10.08%). Sequence analysis of 16S rRNA genes confirmed that the bioaerosol environment harbours a diverse range of bacterial species, many of which exhibit antibiotic resistance. These findings provide valuable insights for public health professionals and policymakers, helping to develop strategies to mitigate the health risks posed by bioaerosols in the region. © The Author(s) under exclusive licence to Society for Plant Research 2025.

关键词： Antibiotic resistance genes Antibiotic susceptibility Antibiotic-resistant bacteria Bioaerosol Public health

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De Novo Gene Birth

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Molecular Biology 2025年第1期59卷 17-25页

作者： Aristova, E.O. Volkhin, I.A. Denisova, A.A. Nikitin, P.A. Petrukhin, E.R. Faculty of Bioengineering and Bioinformatics Moscow State University Moscow 119234 Russian Federation Life Sciences Research Center Moscow Institute of Physics and Technology (National Research University) Moscow oblast Dolgoprudny 141700 Russian Federation Severtsov Institute of Ecology and Evolution Russian Academy of Sciences Moscow 119071 Russian Federation

Abstract: According to classic ideas, new genes emerge from old genes by duplication or horizontal transfer. Analyses of a large number of genomes in recent decades have shown that some genes have no visible homologs and have presumably emerged de novo from previously noncoding sequences. The review considers possible mechanisms of de novo gene formation, the properties of protein sequences encoded by such genes, and features of their expression and selection. The problem of identification of de novo arising gene is discussed separately. © Pleiades Publishing, Ltd. 2025.

关键词： de novo gene orphan gene pervasive transcription pervasive translation

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REMED-T2D: A robust ensemble learning model for early detection of type 2 diabetes using healthcare dataset

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Computers in Biology and Medicine 2025年 187卷 109771-109771页

作者： Phan, Le Thi Rakkiyappan, Rajan Manavalan, Balachandran Computational Biology and Bioinformatics Laboratory Department of Integrative Biotechnology College of Biotechnology and Bioengineering Sungkyunkwan University Gyeonggi-do Suwon16149 Korea Republic of Department of Mathematics Bharathiar University Tamil Nadu Coimbatore641046 India

Early diagnosis and timely treatment of diabetes are critical for effective disease management and the prevention of complications. Undiagnosed diabetes can lead to an increased risk of several health issues. Although numerous machine learning (ML) models have been designed to detect diabetes, many exhibit unsatisfactory performance, are not publicly available, and lack validation on external datasets. To address these limitations, we have developed REMED-T2D, an advanced ensemble ML approach that enhances predictive accuracy and robustness through the integration of diverse ML algorithms. Our approach involves a rigorous data preprocessing process and systematic evaluation of 20 different algorithms, encompassing both conventional ML and deep learning for diabetes prediction. Firstly, we applied an under-sampling approach to an imbalanced Pima Indian Diabetes dataset and generated five balanced datasets. Using these datasets, we investigated various computational strategies to select the optimal model for accurate diabetes classification. Our results demonstrate that REMED-T2D outperformed state-of-the-art methods on the training dataset, with notable improvements in ACC (1.40–4.60%) and MCC (3.50–9.80%). Extensive external validations revealed that the model trained on a five-feature subset achieved ACC of 92.61 % and 92.26 % on the RTML1 and Pabna datasets, respectively. Moreover, a model based on a seven-feature subset improved ACC by 2.80 % and MCC by 13.27 % on the RTML2 dataset. These results suggest the potential of REMED-T2D to predict diabetes in Asian females. Notably, this is the first study to conduct such a comprehensive analysis using the Pima dataset, incorporating a diverse set of ML algorithms. Furthermore, we have developed a publicly accessible web server (https://***/REMED-T2D/) to facilitate self-monitoring and timely medical interventions. We believe REMED-T2D will assist healthcare professionals in detecting diabetes earlier and

关键词： Adversarial machine learning

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Biosynthesis, therapeutic characteristics, origin and strategies to improve the yield of vasicine in plants

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Vegetos 2025年 1-15页

作者： Padmanabhan, Deepthi Manimekalai, Ramaswamy Senthil-Nathan, Sengottayan Suganthi, Muthusamy Palanisamy, Senthilkumar Department of Genetic Engineering School of Bioengineering SRM Institute of Science and Technology Kattankulathur 603203 India Molecular Biology and Bioinformatics Sugarcane Breeding Institute Tamil Nadu Coimbatore 641 007 India Division of Biopesticides and Environmental Toxicology Sri Paramakalyani Centre for Excellence in Environmental Sciences Manonmaniam Sundaranar University Tamil Nadu Alwarkurichi India Department of Biotechnology Vels Institute of Science Technology and Advanced Studies (VISTAS) Pallavaram Chennai 600 117 India

From the year 2016 to 2019, a total of 196 botanical drugs were registered for clinical trials, out of which 81 drugs were in phase II or III laid an environment for further trials and marketing of the drugs. Vasicine, a pyrroquinazoline alkaloidal compound found in some medicinal plants such as Justicia adhatoda and Sida cordifolia to name a few. Due to its broad range of health-promoting properties, the compound has piqued the attention of nutritionists and medicinal chemists. The compound’s recent pharmacological applications include antiviral activity against SARS-Co-V2, antimicrobial activity against E. aerogenes, S. epidermidis and P. aeruginosa, cytotoxic effect against lung adenocarcinoma and free radical scavenging activity, implying a potential role as an antioxidant. Vasicine was also discovered to have a possible anti-inflammatory property in carrageenan-induced inflammation, as well as neuroprotective efficacy in in vitro experiments on neuroblastoma cells by blocking cholinesterases in Alzheimer’s disease and improving memory and cognition. The integration of a multi-omics approach to elucidate the biosynthetic pathway and key regulatory enzymes laid the basis for metabolically engineering the entire pathway in microbial systems, as well as polyculture of microbes for robust biosynthesis strategies to overcome the limitations of traditional monoculture techniques for bioactive production. Genome editing with CRISPR Cas technologies plays a major role in the transformation of vasicine metabolite engineering to alter the process of biosynthesis and increase large-scale production in plants. © The Author(s) under exclusive licence to Society for Plant Research 2025.

关键词： Medicinal plants Natural products Novel drugs Secondary metabolites

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Exogenous calcium provision facilitates the total lipids overproduction without hindering cellular growth in Chlorella vulgaris

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Journal of the Taiwan Institute of Chemical Engineers 2025年

作者： Hasan, M. Mohamed Vijay, Kannusamy Kumari, Swati Benny, Juliet Ann Sana, Abdul Rasheed Kiruthika, A. Balamurugan, Srinivasan Department of Biotechnology School of Bioengineering SRM Institute of Science and Technology Kattankulathur603203 India Department of Biotechnology Bharathidasan University Tiruchirappalli620024 India School of Biotechnology and Bioinformatics D.Y. Patil Deemed to be University Navi Mumbai400614 India

Background: Oleaginous microalgae exemplify tremendous potential for the biosynthesis of valuable metabolites, particularly lipids, which have garnered significant commercial and ecological interest due to their applications in nutraceuticals and biofuels. Overproduction of algal metabolites via chemical modulators has recently received huge interests;however, their industrial application is still in infancy due to the unavailability of chemicals to orchestrate intricate metabolic circuits at a competitive price. Methods: Hence, in this report, we assessed the impact of calcium, a readily available and inexpensive chemical in regulating microalgal physiological and metabolic properties in Chlorella vulgaris. The present study examined the potential of calcium to regulate the physiological, photosynthetic, and metabolic characteristics of microalgae. Significant findings: The results demonstrated that optimized calcium (T2) fortification notably increased biomass by 1.7-fold and also the photosynthetic pigment accumulation in the treated cells. Interestingly, optimized calcium enhanced total lipid and fatty acid content in the treated cells and the lipid examinations showed that total lipids were increased approximately by 2-fold than that of control groups. Overall, the results could exemplify a chemical modulator-mediated sustainable tool kit for generating industry-suitable microalgal strains. © 2025

关键词： Acetobacter

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Integrating computational and experimental insights into osmolyte-driven activation of Geobacillus kaustophilus L-asparaginase for acrylamide mitigation

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Journal of Molecular Liquids 2025年 423卷

作者： Özdemir, F.İnci Servili, Burak Demirtaş, Özge Şükür, Gözde Tülek, Ahmet Yildirim, Deniz Gebze Technical University Department of Molecular Biology and Genetics Kocaeli Gebze41400 Turkey Kadir Has University of Science and Engineering Bioinformatics and Genetics Program İstanbul Fatih35430 Turkey Iğdır University Postgraduate Education Institute Department of Bioengineering and Sciences Iğdır Merkez76000 Turkey Cukurova University Faculty of Ceyhan Engineering Department of Chemical Engineering Adana Ceyhan01950 Turkey

Osmolytes play a critical role in enhancing the stability and activity of enzymes for industrial applications. This study systematically investigated the effects of various osmolytes on the activity, optimal pH, temperature, stability, metal ion effects, storage, and acrylamide mitigation performance of L-asparaginase from the thermophilic Geobacillus kaustophilus (GkASNase). The experimental findings were further supported by computationally integrated tools such as homology modeling, docking, and molecular dynamics (MD) simulations. Among the selected osmolytes (maltose, sorbitol, trehalose, glycine, and sucrose), GkASNase showed the highest stability during 30 days of storage in the presence of maltose and arginine. Maltose increased GkASNase activity approximately 2-fold at 37 °C and 55 °C. In the presence of osmolytes, the Km values of GkASNase decreased and the Vmax values increased compared to controls at 37 °C and 55 °C. In the presence of osmolytes, the acrylamide mitigation performance of GkASNase increased by 1.7-fold in a 15 min reaction. The computational analysis indicates that L-asparagine as substrate enhances protein compactness and stability, while arginine as osmolyte increases flexibility and optimizes water distribution around the enzyme. These findings provide novel insights into enzyme stabilization that have implications for therapeutic and biotechnological applications. © 2025 Elsevier B.V.

关键词： Maltose

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An empirical codon model for protein sequence evolution (vol 24, pg 1464, 2007)

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MOLECULAR BIOLOGY AND EVOLUTION 2007年第9期24卷 2151-2151页

作者： Kosiol, Carolin Holmes, Ian Goldman, Nick European Molecular Biology Laboratory European Bioinformatics Institute Department of Bioengineering University of California

In the past, 2 kinds of Markov models have been considered to describeprotein sequence evolution. Codon-level models have been mechanistic with a small number ofparameters designed to take into account features, such as transition-transversion bias, codonfrequency bias, and synonymous-nonsynonymous amino acid substitution bias. Amino acid models havebeen empirical, attempting to summarize the replacement patterns observed in large quantities ofdata and not explicitly considering the distinct factors that shape protein evolution. We haveestimated the first empirical codon model (ECM). Previous codon models assume that protein evolutionproceeds only by successive single nucleotide substitutions, but our results indicate that modelaccuracy is significantly improved by incorporating instantaneous doublet and triplet changes. Wealso find that the affiliations between codons, the amino acid each encodes and the physicochemicalproperties of the amino acids are main factors driving the process of codon evolution. Neithermultiple nucleotide changes nor the strong influence of the genetic code nor amino acids'physicochemical properties form a part of standard mechanistic models and their views of how codonevolution proceeds. We have implemented the ECM for likelihood-based phylogenetic analysis, and anassessment of its ability to describe protein evolution shows that it consistently outperformscomparable mechanistic codon models. We point out the biological interpretation of our ECM andpossible consequences for studies of selection.

关键词： Genetic Code Amino Acids Codons Triplets LARGE QUANTITIES Markov models

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