Article
Biotechnology & Applied Microbiology
Audrey Vingadassalon, Florence Lorieux, Maud Juguet, Alba Noel, Luisa D. F. Santos, Laura Marin Fernandez, Jean-Luc Pernodet, Stephanie Bury-Mone, Sylvie Lautru
Summary: The production of specialized metabolites by Streptomyces bacteria is typically regulated temporally and involves global and pathway-specific mechanisms. The biosynthesis of congocidine, a pyrrolamide metabolite, in Streptomyces ambofaciens ATCC23877 is controlled by the transcriptional regulator Cgc1. This study reveals a new feed-forward induction mechanism in which congocidine induces its own biosynthesis by activating the transcription of cgc1.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Microbiology
Mengjun Hu, Yuyan Zhang, Xiaozhen Huang, Mu He, Jinyu Zhu, Zengfeng Zhang, Yan Cui, Shoukui He, Xianming Shi
Summary: The PhoPQ two-component system plays a crucial role in the resistance formation of quinolone and cephalosporin-resistant S. Enteritidis. PhoP regulates genes associated with envelope homeostasis, the osmotic stress response, and the redox balance to confer antibiotic resistance. Additionally, PhoQ senses quinolones and cephalosporins by directly binding to them. These findings provide insights into bacterial antibiotic resistance and suggest PhoPQ as a potential drug target for overcoming S. Enteritidis resistance.
Article
Biotechnology & Applied Microbiology
Xinbo Huang, Mingxia Wang, Xia Wu, Yanfen Zou, Jinming Xu, Congcong Cao, Qian Ma, Bo Yu, Yuchen Liu, Yaoting Gui
Summary: In this study, a group of single-stranded DNA aptamers with high affinity and high specificity for the Cas9 protein were obtained. The aptamers were found to effectively regulate dCas9-modulated gene transcription and improve the efficiency of gene homologous recombination repair mediated by CRISPR-Cas9. These findings suggest a potential method to better control precise gene editing and enrich the diversity of modulating tools for the CRISPR-Cas9 system.
Article
Biochemistry & Molecular Biology
Tanaya Basu Roy, Siddhartha P. Sarma
Summary: This study decodes the details of transcriptional autoregulation by the MazE9 antitoxin in the Mycobacterium tuberculosis MazEF9 toxin-antitoxin system. The researchers found that MazE9 specifically interacts with the mazEF9 operon and identified the thermodynamic and kinetic parameters of this interaction. The study also showed that MazE9 is unlikely to cross-regulate with the functionally related mazEF6 operon. Additionally, an interesting feature of MazE9 is the cis-trans conformational isomerization of proline residues in its intrinsically disordered C-terminal domain.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2023)
Editorial Material
Biochemistry & Molecular Biology
Andrew P. Hinck
Summary: This commentary highlights the landmark manuscript published in 1957 by Arieh Berger and K. Linderstrom-Lang that describes the measurement and analysis of hydrogen exchange rates. The manuscript, which has been widely referenced, is recognized for its significant impact on characterizing the structure and dynamics of natively folded proteins and folding intermediates.
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
(2022)
Article
Biochemistry & Molecular Biology
Luyi Cheng, Elise N. White, Naomi L. Brandt, Angela M. Yu, Alan A. Chen, Julius B. Lucks
Summary: The study investigates the structure and function of the Bacillus subtilis yxjA purine riboswitch and suggests a potential mechanism whereby ligand binding induces conformational changes in RNA structures. The results provide insight into how RNA functions in gene regulation.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Malgorzata M. Duszczyk, Harry Wischnewski, Tamara Kazeeva, Rajika Arora, Fionna E. Loughlin, Christine von Schroetter, Ugo Pradere, Jonathan Hall, Constance Ciaudo, Frederic H. -T. Allain
Summary: DND1 is an RNA-binding protein essential for germline development, mediating its function through a non-canonical AU-rich RNA recognition mode by the tandem RRMs, while the dsRBD plays a role in recruiting effector complexes for target regulation. The authors report an unusual mode of AU-rich RNA recognition by the RRMs of DND1 in a 27.5 kDa NMR structure and provide additional insight on DND1 function from cell-based experiments.
NATURE COMMUNICATIONS
(2022)
Review
Microbiology
Michal Wojcicki, Olga Swider, Kamila J. Daniluk, Paulina Srednicka, Monika Akimowicz, Marek L. Roszko, Barbara Sokolowska, Edyta Juszczuk-Kubiak
Summary: The widespread use of antibiotics has led to the development of multidrug resistance in many bacterial strains, including Salmonella. Salmonella, a common pathogen causing intoxication from contaminated food and water, is pharmacologically treated with antibiotics like fluoroquinolones, ceftriaxone, and azithromycin. Understanding the molecular mechanisms behind antibiotic resistance in Salmonella is essential for choosing effective treatment and addressing the significant global concern of increasing antibiotic resistance.
Review
Plant Sciences
Liyang Su, Siqi Wan, Junmei Zhou, Qing Song Shao, Bingcong Xing
Summary: This review discusses the roles of transcription factors (TFs) in regulating plant seed development, noting that different TFs or TF families may have similar functions in this process, and some members of the same TF family may have opposite roles.
PHYSIOLOGIA PLANTARUM
(2021)
Review
Biochemistry & Molecular Biology
Koh Takeuchi, Yutaka Kofuku, Shunsuke Imai, Takumi Ueda, Yuji Tokunaga, Yuki Toyama, Yutaro Shiraishi, Ichio Shimada
Summary: Multi-spanning membrane proteins transfer information and materials through a membrane by changing their conformations, and their dynamics are closely related to their function. NMR reveals dynamics information that can discriminate function-related dynamics from random fluctuations. Studies using solution NMR have contributed to revealing the structural basis of the function of multi-spanning membrane proteins.
Article
Chemistry, Multidisciplinary
William J. Gibson, Ananthan Sadagopan, Veronika M. Shoba, Amit Choudhary, Matthew Meyerson, Stuart L. Schreiber
Summary: The abnormal localization of proteins in cells is closely related to the development of various diseases. Researchers have designed bifunctional compounds to regulate protein localization and transport. The results show potential applications of this method in cancer treatment and the ability to rewiring cell circuitry.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Endocrinology & Metabolism
Joseph D. D. Racca, Deepak Chatterjee, Yen-Shan Chen, Ratan K. K. Rai, Yanwu Yang, Millie M. M. Georgiadis, Elisha Haas, Michael A. A. Weiss
Summary: The Y-encoded transcription factor SRY plays a crucial role in male differentiation in therian mammals. A high-mobility-group (HMG) box is present in this factor, which allows it to bind to specific DNA sequences and bend the DNA. A study found sex-reversal mutations in the HMG box at position 72, which is invariant among mammalian orthologs. Interestingly, aromatic rings confer higher transcriptional activity compared to other side chains observed at DNA interfaces. Biochemical studies showed that a specific mutation in the aromatic ring accelerates the dissociation of the protein-DNA complex. Molecular dynamics simulations suggest that the mutation disrupts the water-mediated clamp at the tail-DNA interface, resulting in attenuated transcriptional activity. The conservation of this water-mediated clamp suggests its general importance in SRY and metazoan SOX domains.
FRONTIERS IN ENDOCRINOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Zhen He, Zunhui Ke, Wei Wang, Yahui Liu, Haoran Zhang, Yan Li
Summary: Saro_0803 is a transcriptional factor that regulates the transcription of the stilbene-degrading enzyme gene nov1 in Novosphingobium aromaticivorans DSM 12444. It acts as a biosensor component for resveratrol biosynthesis by dissociating from the nov1 promoter in the presence of resveratrol. The molecular mechanisms of Saro_0803's interactions with nov1 promoter and resveratrol are not well understood.
Article
Microbiology
Ronald Rodriguez, Nick Campbell-Kruger, Jesus Gonzalez Camba, John Berude, Rachel Fetterman, Sarah Stanley
Summary: Mycobacterium abscessus (Mabs) is an emerging pathogen responsible for difficult-to-treat respiratory and cutaneous infections. It has high levels of antibiotic resistance and Ethionamide (ETH) shows potential as a treatment option.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2023)
Article
Biochemistry & Molecular Biology
Rupesh Kumar, Maged Mostafa Mahmoud, Hanaa M. Tashkandi, Shafiul Haque, Steve Harakeh, Kalaiarasan Ponnusamy, Shazia Haider
Summary: This study aimed to identify key molecules in colorectal cancer using a computational systems biology approach. A protein-protein interaction network was constructed, and TP53, CTNBB1, AKT1, EGFR, HRAS, JUN, RHOA, and EGF were identified as key molecules. Regulatory networks of these key molecules were also constructed, revealing important regulatory factors. Biochemical investigation of these key regulators could provide further understanding of their role in the pathophysiology of colorectal cancer.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemical Research Methods
Anne Birk Frahm, Pernille Rose Jensen, Jan Henrik Ardenkjaer-Larsen, Demet Yigit, Mathilde Hauge Lerche
JOURNAL OF MAGNETIC RESONANCE
(2020)
Article
Multidisciplinary Sciences
Chee-Seng Hee, Judith Habazettl, Christoph Schmutz, Tilman Schirmer, Urs Jenal, Stephan Grzesiek
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Chemistry, Multidisciplinary
Pernille R. Jensen, Rikke K. Knudsen, Sebastian Meier
ACS SUSTAINABLE CHEMISTRY & ENGINEERING
(2020)
Article
Multidisciplinary Sciences
Ronja M. Malinowski, Seyed M. Ghiasi, Thomas Mandrup-Poulsen, Sebastian Meier, Mathilde H. Lerche, Jan H. Ardenkjaer-Larsen, Pernille R. Jensen
SCIENTIFIC REPORTS
(2020)
Article
Biochemistry & Molecular Biology
Layara Akemi Abiko, Marco Rogowski, Antoine Gautier, Gebhard Schertler, Stephan Grzesiek
Summary: The study presents strategies for E. coli expression of GPCRs and developed an optimized protocol with quantification of losses in receptor material during solubilization and purification steps, resulting in final yields of 0.2-0.3 mg per liter; High-quality NMR studies were successfully conducted using E. coli-expressed mutants, with similar results to mutants expressed in insect cells.
JOURNAL OF BIOMOLECULAR NMR
(2021)
Article
Chemistry, Analytical
Anne B. Frahm, Deborah Hill, Sotirios Katsikis, Trygve Andreassen, Jan Henrik Ardenkjaer-Larsen, Tone Frost Bathen, Siver Andreas Moestue, Pernille Rose Jensen, Mathilde Hauge Lerche
Summary: Hyperpolarized C-13 isotope resolved spectroscopy enhances NMR signal intensity for metabolic flux analysis in mouse prostate tissue. By employing binary classification and feature analysis, a successful discrimination between normal and cancerous prostate tissue samples was achieved with a 95% success rate. This approach provides detailed metabolic information and can lead to high predictive classification of tissue types based on isotopomers from uniquely identified metabolites.
Article
Chemistry, Physical
Allan R. E. Hansen, Kasper Enemark-Rasmussen, Frans A. A. Mulder, Pernille R. Jensen, Sebastian Meier
Summary: Electrochemical reduction allows for the capture and utilization of CO2 by converting it into small chemicals and fuels. However, there is a lack of well-established analytical standard operating procedures for accurately quantifying short-chain acids, aldehydes, and alcohols. The smallest organic compounds produced through electrochemical reduction of CO2 require slow NMR quantifications, which can be improved by using paramagnetic contrast agents or cooling water/DMSO for T-1-optimized measurements. H-1 NMR experiments commonly used in the study of biological mixtures are not suitable for quantitative analysis of T-1-optimized samples.
JOURNAL OF PHYSICAL CHEMISTRY C
(2022)
Article
Chemistry, Physical
Francesca Sannelli, Sanni Gao, Pernille Rose Jensen, Sebastian Meier
Summary: By mixing glucose and furfural in suitable ratios, novel strategies for C-C bond formation on furfural can be achieved with the help of low-cost biological catalysts. The presence of furfural is shown to modulate glucose metabolism and favor the accumulation of acetaldehyde, redirecting glucose carbons towards C-C bond formation. This strategy allows for a relative influx of at least 80% of glucose carbons into the C-C bond formation on furfural in non-engineered yeasts, showing potential for the upgrading of lignocellulosic biomass.
Article
Chemistry, Multidisciplinary
Feng-Jie Wu, Pascal S. Rieder, Layara Akemi Abiko, Philip Roessler, Alvar D. Gossert, Daniel Haeussinger, Stephan Grzesiek
Summary: The method presented in this study utilizes antibodies tagged with lanthanoid DOTA chelators to efficiently assign nuclei of biomacromolecules, providing insights into their chemical shift changes during functional dynamics.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Physical
Allan R. E. Hansen, Pernille R. Jensen, Sebastian Meier
Summary: The conversion of lignocellulosic biomass and its components to precursor chemicals offers great potential in expanding the range of industrial chemicals and reducing reliance on fossil resources. However, challenges in this green transition include the multifunctionality of biosourced reactants and the search for highly selective conversion processes. Recent research has shown that chemocatalytic conversion of carbohydrates to lactate and its ester variants using concentrated aqueous solutions of barium hydroxide is highly selective. This study used sensitive enhanced NMR to track the reaction cascade and identified key intermediates in the pathway, providing valuable insights into the process.
CATALYSIS SCIENCE & TECHNOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Sebastian Meier, Allan R. Hansen, Pernille Rose Jensen
Summary: Carbohydrates are expected to play a central role in future organic chemical production, but the understanding of accessible pathways for carbohydrate upgrading is still inadequate. The complex structure of carbohydrates, with various functional groups and stereochemistries, can result in a diverse range of isomers during the conversion process. In this study, the conversion of C5 carbohydrates using Lewis acidic SnCl4 in dimethyl sulfoxide (DMSO)/water system was investigated. The effects of removing individual functional groups on the pathways of carbohydrate conversion were evaluated. The removal of the hydroxy group at C5 was found to enhance the selectivity of carbohydrate conversion through an acyclic pathway, rather than the formation of furanic compounds or humins. Blocking the primary alcohol in xylose may be beneficial for biomass conversion strategies. Additionally, the conversion of pentose followed second-order kinetics, even without intermolecular reactions leading to humin formation.
ACS SUSTAINABLE CHEMISTRY & ENGINEERING
(2023)
Article
Chemistry, Analytical
Francesca Sannelli, Pernille Rose Jensen, Sebastian Meier
Summary: The central carbon metabolism of microbes has potential applications in sustainable bioproduction. A deeper understanding of central metabolism could enhance the control of activity and selectivity in whole-cell catalysis. NMR spectroscopy can be used to track cellular pathways and optimize pathway usage, allowing for the design of conditions for glucose influx into specific industrial precursors. By inducing overflow at the pyruvate level, glucose conversion to 2,3-butanediol can be significantly increased. This study suggests a reassessment of canonical metabolism using in-cell spectroscopy may be warranted.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Francesca Sannelli, Ke-Chuan Wang, Pernille Rose Jensen, Sebastian Meier
Summary: Changes in metabolism are a common feature of many diseases, and in-cell NMR assays can provide real-time insights into disease metabolism. This study aimed to improve in-cell NMR assays by developing a comprehensive collection of spectral data for central carbon metabolites and intracellular pH. Using enriched glucose as a probe molecule, early glycolytic intermediates and intracellular pH were detected in prostate cancer cell lines. The addition of non-enriched pyruvate as an adjuvant allowed for the detection of reactions in the pentose phosphate pathway. The findings suggest a rerouting of cancer cell metabolism in response to pyruvate in the tumor environment.
ANALYTICAL METHODS
(2023)
Article
Chemistry, Multidisciplinary
Pernille Rose Jensen, Francesca Sannelli, Ludvig Tving Stauning, Sebastian Meier
Summary: The improved sensitivity of a suitable C-13 NMR approach allows for the observation of more extensive reaction networks, assay time windows, and relative flux measurements in living cells.
CHEMICAL COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Pernille Rose Jensen, Sebastian Meier
CHEMICAL COMMUNICATIONS
(2020)