Article
Biology
Gita Naseri, Hannah Raasch, Emmanuelle Charpentier, Marc Erhardt
Summary: In this study, a set of arabinose-inducible artificial transcription factors (ATFs) were developed using CRISPR/dCas9 and Arabidopsis-derived DNA-binding proteins to control gene expression in E. coli and Salmonella over a wide range of inducer concentrations. The transcriptional output of the ATFs varied greatly, particularly in Salmonella strains rewired for arabinose catabolism. The developed ATFs were used to engineer a Salmonella biosensor strain and regulate beta-carotene biosynthesis in E. coli, resulting in significantly higher production compared to traditional methods.
COMMUNICATIONS BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Gi Bae Kim, Ji Yeon Kim, Jong An Lee, Charles J. Norsigian, Bernhard O. Palsson, Sang Yup Lee
Summary: The functional annotation of open reading frames in microbial genomes is still incomplete. In this study, a deep learning model called DeepECtransformer was developed to predict specific catalytic functions for un-annotated genes. Experimental validation confirmed the accuracy of the predicted enzymatic activities for three proteins and revealed that the neural network relies on functional motifs of enzymes to predict EC numbers.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Hendrik Melior, Siqi Li, Maximilian Stoetzel, Sandra Maass, Rubina Schuetz, Saina Azarderakhsh, Aleksei Shevkoplias, Susanne Barth-Weber, Kathrin Baumgardt, John Ziebuhr, Konrad U. Foerstner, Zoe Chervontseva, Doerte Becher, Elena Evguenieva-Hackenberg
Summary: Trans-acting regulatory RNAs, such as rnTrpL in Sinorhizobium meliloti, have the ability to pair with multiple mRNAs and may adjust their target specificity based on metabolic or environmental conditions. Tetracycline exposure can alter the target specificity of rnTrpL towards ribosomal protein-encoding mRNA, indicating the potential for sRNA target prioritization to shift in response to changing environmental cues.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Iman Yassine, Sophie Lefevre, Elisabeth E. Hansen, Corinne Ruckly, Isabelle Carle, Monique Lejay-Collin, Laetitia Fabre, Rayane Rafei, Dominique Clermont, Maria Pardos de la Gandara, Fouad Dabboussi, Nicholas R. Thomson, Francois-Xavier Weill
Summary: The study applies a core genome multilocus sequence typing scheme to Shigella sequence data and describes its population structure.
NATURE COMMUNICATIONS
(2022)
Article
Biotechnology & Applied Microbiology
Syed Shujaat Ali Zaidi, Masood Ur Rehman Kayani, Xuegong Zhang, Younan Ouyang, Imran Haider Shamsi
Summary: This study identified operons in whole-genomes and metagenomes using MetaRon, achieving high prediction accuracy. It also uncovered a strong association between type 2 diabetes and specific proteins, showcasing the potential of operons in disease association studies. The application of MetaRon to diverse scales of metagenomic data shows promise in understanding gene regulation and therapeutic metagenomics.
Article
Biotechnology & Applied Microbiology
Xian Xu, Xiaoting Chu, Bangmian Du, Chunyan Huang, Chengjia Xie, Zhidong Zhang, Ling Jiang
Summary: Violacein is a broad-spectrum antibacterial pigment mainly produced by Gram-negative bacteria. The discovery of a new violacein operon and the construction of engineered E. coli strains have significantly increased violacein production.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
V. V. Fomin, S. V. Bazhenov, O. V. Kononchuk, V. O. Matveeva, A. P. Zarubina, S. E. Spiridonov, I. V. Manukhov
Summary: The transcription of Photorhabdus luminescens lux-operon increases significantly under high temperature, and this increase is associated with an increase in the transcription of luxCDABE genes.
Article
Oncology
Shingo Tsuji, Katherine Reil, Kinsey Nelson, Veronica H. Proclivo, Kathleen L. McGuire, Matthew J. Giacalone
Summary: The combination of VAX014 and systemic PD-1/PD-L1 blockade has shown significant improvement in bladder tumor clearance rates and the development of protective antitumor immunologic memory. This study provides a rationale for further clinical investigation of VAX014 and systemic PD-1/PD-L1 blockade in advanced-stage bladder cancer.
CANCER IMMUNOLOGY RESEARCH
(2022)
Article
Multidisciplinary Sciences
Timothy C. Yu, Winnie L. Liu, Marcia Brinck, Jessica E. Davis, Jeremy Shek, Grace Bower, Tal Einav, Kimberly D. Insigne, Rob Phillips, Sriram Kosuri, Guillaume Urtecho
Summary: The study analyzed the expression dynamics of thousands of genes with inducible promoters, revealing the impact of RNA polymerase and LacI repressor binding site strengths on gene expression. By fitting a statistical mechanics model, properties of theoretically optimal inducible promoters were accurately modeled. Through the examination of three alternative promoter architectures, the study showed how repositioning binding sites within promoters influences the combinatorial effects observed between promoter elements.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Ryan T. Santilli, John E. Williamson, Yoshitaka Shibata, Rosalie P. Sowers, Andrew N. Fleischman, Song Tan
Summary: The Penn State Protein Ladder system produces protein molecular weight markers through plasmid expression in E. coli, allowing for easy migration, purification, and detection on SDS-PAGE gels. Additionally, polycistronic expression vectors have been designed for more efficient production and as positive controls for recombinant protein expression and purification in research laboratories.
SCIENTIFIC REPORTS
(2021)
Article
Biotechnology & Applied Microbiology
Maxsueli Aparecida Moura Machado, Vinicius Silva Castro, Adelino da Cunha Neto, Ricardo Cesar Tavares Carvalho, Kim Stanford, Carlos Adam Conte-Junior, Eduardo Eustaquio de Souza Figueiredo
Summary: This study aimed to characterize Escherichia coli (E. coli) and shiga toxin-producing E. coli (STEC) isolates from Brazilian beef to determine their heat resistance and the presence of the transmissible locus of stress tolerance (tLST). Results showed that 3 out of 22 STEC isolates were heat resistant, 12 were moderately resistant, and 7 were sensitive to heat treatments. Whole genome sequencing (WGS) analysis revealed that the heat-resistant isolates carried tLST genes with high similarity to the homeostasis module genes in E. coli. However, no stx genes associated with tLST-positive isolates were found, although virulence and resistance genes were detected in extraintestinal pathogenic E. coli (ExPEC).
JOURNAL OF APPLIED MICROBIOLOGY
(2023)
Article
Infectious Diseases
Pei Yee Woh, May Pui Shan Yeung, William Bernard Goggins
Summary: This study aimed to determine the multiple antibiotic resistance index (MARI) of Salmonella isolated from children hospitalized for gastroenteritis in Hong Kong. The results showed that Salmonella had the highest resistance to ampicillin, ciprofloxacin, and tetracycline, while MDR strains had high resistance towards ampicillin, tetracycline, cotrimoxazole, chloramphenicol, and ciprofloxacin. MARI revealed that 80.2% of Salmonella, including all MDR strains, had indexes greater than 0.2.
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
(2023)
Article
Multidisciplinary Sciences
Md Atikur Rahman, Uzma Habiba Heme, Md Anowar Khasru Parvez
Summary: Members of the Bacillus genus, such as Bacillus paralicheniformis strain Bac84, are capable of secreting biomolecules with industrial applications. However, many proteins in the genome of Bac84 are functionally uncharacterized. This study aimed to annotate the functions of these hypothetical proteins using in-silico approaches. As a result, 37 proteins were successfully assigned a function, and 12 proteins were identified with adaptational roles in unfavorable environments and 8 proteins were predicted to have biotechnological potentials. The performance evaluation of the tools used showed high accuracy, indicating the rationality of the annotation strategy employed. This research provides valuable insights into the functional characterization of unknown proteins and the identification of new biotechnological targets.
Article
Biotechnology & Applied Microbiology
Ahmed E. Zoheir, Morgan S. Sobol, Laura Meisch, Diana Ordonez-Rueda, Anne-Kristin Kaster, Christof M. Niemeyer, Kersten S. Rabe
Summary: The RGB-S reporter, a plasmid containing red, green, and blue fluorescent proteins, allows for simultaneous, independent, and real-time analysis of the transcriptional response of Escherichia coli to physiological stress, genotoxicity, and cytotoxicity. This bioreporter is compatible with standard analysis and Fluorescent Activated Cell Sorting (FACS) combined with transcriptome analysis. The RGB-S reporter reveals the impact of various stressors on non-stress-related metabolic pathways and enables spatiotemporal analysis of live biofilms.
NPJ BIOFILMS AND MICROBIOMES
(2023)
Review
Microbiology
Aditya Kamat, Anjana Badrinarayanan
Summary: Cells have specialized pathways to sense and respond to DNA damage, with bacteria having the well-studied SOS response and other SOS-independent DNA damage responses. The diversity in response and repair mechanisms raises important questions about their influence on genomes and vice versa. This review discusses recent insights on three SOS-independent bacterial DNA damage responses, exploring the mysteries of their diversity generation and regulation in cells for genome integrity maintenance.
CURRENT OPINION IN MICROBIOLOGY
(2023)
Article
Immunology
Erin R. Murphy, Johanna Rossmanith, Jacob Sieg, Megan E. Fris, Hebaallaha Hussein, Andrew B. Kouse, Kevin Gross, Chunxi Zeng, Jennifer Hines, Franz Narberhaus, Peter W. Coschigano
INFECTION AND IMMUNITY
(2020)
Article
Microbiology
Beate Sauerbrei, Jan Arends, Danja Schunemann, Franz Narberhaus
JOURNAL OF BACTERIOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Christian Twittenhoff, Vivian B. Brandenburg, Francesco Righetti, Aaron M. Nuss, Axel Mosig, Petra Dersch, Franz Narberhaus
NUCLEIC ACIDS RESEARCH
(2020)
Article
Microbiology
Alexander Kraus, Mareen Weskamp, Jennifer Zierles, Miriam Balzer, Ramona Busch, Jessica Eisfeld, Jan Lambertz, Marc M. Nowaczyk, Franz Narberhaus
JOURNAL OF BACTERIOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Jessica Eisfeld, Alexander Kraus, Christian Ronge, Michelle Jagst, Vivian B. Brandenburg, Franz Narberhaus
Summary: The study revealed that the LysR-type regulator VtlR (also known as LsrB) controls the expression of sRNAs including AbcR1 and PmaR, impacting the expression of numerous genes, including ABC transporter genes and other sRNA genes. VtlR/LsrB was identified as the master regulator of many sRNAs, orchestrating the response of cells to environmental conditions by harnessing the regulatory power of sRNAs.
MOLECULAR MICROBIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Julia Kleetz, Leon Welter, Ann-Sophie Mizza, Meriyem Aktas, Franz Narberhaus
Summary: This study expands our understanding of bacterial phosphatidylcholine (PC) formation through the identification, purification, and characterization of Pmts from phylogenetically diverse thermophilic bacteria. Insights into the functional characteristics of Pmt enzymes in thermophilic actinomycetes and proteobacteria are provided.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Microbiology
Simon Czolkoss, Pia Borgert, Tessa Poppenga, Georg Hoelzl, Meriyem Aktas, Franz Narberhaus
Summary: Some soil-dwelling bacteria have the ability to metabolize exogenous lyso-phospholipids and convert them into non-canonical lipid bis(monoacylglycero)phosphate (BMP), indicating a remarkable adaptive response of bacterial membranes to environmental changes.
ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Microbiology
Dominik Wuellner, Maren Gesper, Annika Haupt, Xiaofei Liang, Pei Zhou, Pascal Dietze, Franz Narberhaus, Julia E. Bandow
Summary: This study investigated the physiological response of Pseudomonas aeruginosa to various antibiotics, revealing cellular defense strategies and similarities in response profiles. The findings provide insights into the effects of commonly used antibiotics on P. aeruginosa and contribute to the evaluation of novel compounds.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2022)
Article
Biotechnology & Applied Microbiology
Julia Kleetz, Georgios Vasilopoulos, Simon Czolkoss, Meriyem Aktas, Franz Narberhaus
Summary: Escherichia coli is a common model bacterium with a membrane composition that can be readily tailored to include non-native lipids such as phosphatidylcholine (PC) for biotechnology applications.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Article
Microbiology
Stephan Pienkoss, Soheila Javadi, Paweena Chaoprasid, Thomas Nolte, Christian Twittenhoff, Petra Dersch, Franz Narberhaus
Summary: This study explores the temperature-dependent synthesis of the secretion regulator YopN in the foodborne pathogen Yersinia pseudotuberculosis, demonstrating its role in controlling effector protein translocation through the type III secretion system. The research reveals a critical RNA thermometer-mediated regulation of YopN expression at infection-relevant temperatures, highlighting the importance of adjusting cellular concentration of surveillance factors for controlled translocation of virulence factors in bacterial pathogens.
Article
Biochemical Research Methods
Vivian B. Brandenburg, Franz Narberhaus, Axel Mosig
Summary: This study introduces a novel pre-training approach using inverse folding to generate training data, which significantly enhances the performance of neural networks in identifying RNA structural motifs. Through systematic in silico mutagenesis experiments, this method shows great potential in recognizing RNA structural motifs such as intrinsic transcription terminators.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Anna-Maria Moeller, Simon Brueckner, Lea-Janina Tilg, Blanka Kutscher, Marc M. Nowaczyk, Franz Narberhaus
Summary: This study investigates the function of the outer membrane (OM) in Gram-negative bacteria and the mechanism of LPS biosynthesis. The results show that LapB is a multi-functional protein that regulates the synthesis of LPS and PL by interacting with key enzymes.
MOLECULAR MICROBIOLOGY
(2023)
Review
Engineering, Environmental
Mischa Juette, Mohammad Sajjad Abdighahroudi, Torsten Waldminghaus, Susanne Lackner, Holger V. . Lutze
Summary: Water disinfection is crucial for ensuring safe drinking water, particularly in the face of climate change. Chemical oxidants can form secondary oxidants during disinfection processes, which can cause additional damage to bacteria. This study reviews the complex interactions between reactive species in disinfection processes and their potential impact on disinfection effectiveness. It provides a quantitative overview of disinfection strength based on inactivation kinetics and typical exposures. The study also highlights the resistance of wild strains compared to lab-cultivated strains and discusses the role of secondary oxidants in pathogen inactivation, as well as possible defense responses of bacteria and other additional effects.
Article
Genetics & Heredity
Daniel R. Scheller, Franziska I. Becker, Andrea Wimbert, Dominik D. Meggers, Stephan Pienkoss, Christian D. Twittenhoff, Lisa R. Knoke, Lars I. D. Leichert, Franz Narberhaus
Summary: Pathogenic bacteria like Yersinia pseudotuberculosis encounter reactive oxygen species (ROS) as a defense mechanism in mammalian hosts. In response, the bacteria mount an oxidative stress response. This study analyzes the transcriptional and translational regulation of ROS defense genes by examining RNA structure, gene expression, and enzymatic assays. The results reveal a multilayered regulation and an important role of RNAT-controlled katY expression in the oxidative stress response of Yersinia.
Article
Biochemistry & Molecular Biology
Janka J. Schmidt, Donata C. L. E. Remme, Jessica Eisfeld, Vivian B. Brandenburg, Hannah Bille, Franz Narberhaus
Summary: Agrobacterium tumefaciens is a plant pathogen that exhibits resistance to beta-lactam antibiotics through the regulation of specific genes. In this study, researchers uncovered the important role of the transcriptional regulator LsrB acting upstream of AmpR in inducible resistance.
MOLECULAR MICROBIOLOGY
(2023)