Article
Biophysics
Nikola Ojkic, Shiladitya Banerjee
Summary: Research shows that the bacterium Bacillus subtilis exhibits highly robust cell geometry, with a well-conserved scaling relationship between surface area and volume regulated by nutrient-dependent production of metabolic enzymes. Theoretical predictions suggest different modes of cell shape transformations in various bacterial species, with mechanisms proposed for cell shape adaptation to different nutrient perturbations. Organisms with high surface-to-volume scaling exponent gamma, like B. subtilis, show less sensitivity in cell width to growth-rate changes compared to organisms with low gamma, such as Acinetobacter baumannii.
BIOPHYSICAL JOURNAL
(2021)
Article
Multidisciplinary Sciences
Eszter Csibra, Guy-Bart Stan
Summary: A validated method and accompanying R package, FPCountR, is presented for the precise quantification of fluorescent protein reporters per bacterial cell without protein purification. The authors describe an assay protocol for the calibration of fluorescence readings, as well as methods for determining protein concentration and activity. They also investigate how cells can interfere with protein counting via fluorescence quenching and provide a correction for this effect.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Qihui Liang, Yiying Zhang, Hong Zhang, Si Wu, Weibin Gong, Sarah Perrett
Summary: Glutathionylation of hHsp70 acts as a molecular switch under oxidative stress, regulating chaperone activity and transmitting redox signals. This process involves unfolding of the C-terminal alpha-helical lid and blocking of the substrate-binding site. In-cell NMR data demonstrates the conformational transition of hHsp70 in response to diamide stimulation, with the ability to spontaneously recover. The study also highlights the power of in-cell NMR for studying protein structures in real-time in living cells.
ACS CHEMICAL BIOLOGY
(2023)
Article
Gastroenterology & Hepatology
Nadege Bossuet, Cecile Guyonnet, Camille Chagneau, Min Tang-Fichaux, Marie Penary, Dorian Loubet, Priscilla Branchu, Eric Oswald, Jean-Philippe Nougayrede
Summary: Up to 25% of healthy human feces-derived E. coli strains carry the pks genomic island, which is responsible for synthesizing colibactin, a genotoxic compound implicated in colorectal cancer. However, the expression conditions of colibactin in the gut remain poorly understood. In this study, it is demonstrated that colibactin production is highest under anoxic conditions and decreases with increased oxygen concentration. The positive regulation of colibactin production and genotoxicity by the aerobic respiration control (ArcA) in response to oxygen availability suggests that the pks biosynthetic pathway is adapted for the anoxic intestinal lumen and hypoxic infected or tumor tissue.
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, Analytical
Francesca Sannelli, Ke-Chuan Wang, Pernille Rose Jensen, Sebastian Meier
Summary: This study presents an improved approach for in-cell NMR assays and provides a comprehensive collection of spectral data for metabolite identification and intracellular pH measurements. The use of glucose and pyruvate as probe molecules enables the detection of metabolic changes in cancer cells and reveals the impact of pyruvate on tumor metabolism.
ANALYTICAL METHODS
(2023)
Article
Biology
Matthew Jessop, Karine Huard, Ambroise Desfosses, Guillaume Tetreau, Diego Carriel, Maria Bacia-Verloop, Caroline Mas, Philippe Mas, Angelique Fraudeau, Jacques-Philippe Colletier, Irina Gutsche
Summary: Bacterial homologous lysine and arginine decarboxylases play important roles in acid stress response, physiology, antibiotic resistance, and virulence. In this study, the polymerisation behavior of the arginine decarboxylase from Providencia stuartii is investigated and compared with the lysine decarboxylase from Escherichia coli. The findings reveal significant differences in their assembly mechanisms and provide a basis for future exploration of supramolecular assembly in the superfamily of arginine and lysine decarboxylases.
COMMUNICATIONS BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Theodore A. Chavkin, Loc-Duyen Pham, Aleksandar Kostic
Summary: The study found that oral probiotics EcN can reduce postprandial glycemic response in mice, but not through direct glucose uptake. Further exploration is needed to understand the potential indirect mechanisms of EcN on host glucose metabolism.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Enrico Orsi, Nico J. Claassens, Pablo Nikel, Steffen N. Lindner
Summary: Synthetic biology has revolutionized the ability to redesign microbial metabolic networks by combining metabolic pathway-modularization with growth-coupled selection schemes. This powerful tool enables deep rewiring of cell factories' biochemistry for rational bioproduction.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Serena Petracchini, Daniel Hamaoui, Anne Doye, Atef Asnacios, Florian Fage, Elisa Vitiello, Martial Balland, Sebastien Janel, Frank Lafont, Mukund Gupta, Benoit Ladoux, Jerome Gilleron, Teresa M. Maia, Francis Impens, Laurent Gagnoux-Palacios, Mads Daugaard, Poul H. Sorensen, Emmanuel Lemichez, Amel Mettouchi
Summary: This study reveals a new function of Optineurin (OPTN) in mechanobiology, regulating HACE1-dependent Rac1 activity and controlling integrin-mediated mechanotransduction and bacterial invasion.
NATURE COMMUNICATIONS
(2022)
Article
Hematology
Mouli Pal, Weili Bao, Rikang Wang, Yunfeng Liu, Xiuli An, William B. Mitchell, Cheryl A. Lobo, Caterina Minniti, Patricia A. Shi, Deepa Manwani, Karina Yazdanbakhsh, Hui Zhong
Summary: The study reveals that free heme suppresses human B-cell differentiation, affecting the immune response in sickle cell disease patients. Nonalloimmunized patients' B cells are inhibited by heme, while alloimmunized patients are insensitive. Quinine is identified as a potent inhibitor of B-cell activity in alloimmunized patients, reversing their resistance to heme suppression.
Article
Chemistry, Multidisciplinary
Robert W. Harkness, Zev A. Ripstein, Justin M. Di Trani, Lewis E. Kay
Summary: DegP is a periplasmic protein involved in the transport of pathogenicity-related virulence factors. It functions as a bi-functional protease and chaperone to maintain protein homeostasis in Gram-negative bacteria under stress conditions. It forms cage-like structures by reorganizing high-order preformed apo oligomers, which can encapsulate clients of various sizes.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Agronomy
Long Ma, Nirodha Weeraratne, Saliya Gurusinghe, Jesmin Aktar, K. M. Shamsul Haque, Philip Eberbach, Geoff G. Gurr, Leslie A. Weston
Summary: The introduction of exotic dung beetles in southern Australia has reduced the amount of livestock dung on the soil surface, but its impact on pasture quality and soil nutrient mobility has not been studied in the Riverina region of New South Wales. This study evaluated the effects of a common introduced dung beetle (Bubas bison) on water quality and soil microbiome using lysimetry and DNA assessment. The results showed that dung beetles and soil type influenced pasture performance and microbial communities, although water quality seemed unaffected.
Article
Biochemistry & Molecular Biology
Chaille T. Webb, Wei Yang, Blake T. Riley, Brooke K. Hayes, Komagal Kannan Sivaraman, Tess R. Malcolm, Stephen Harrop, Sarah C. Atkinson, Itamar Kass, Ashley M. Buckle, Nyssa Drinkwater, Sheena McGowan
Summary: This study investigates the structure and dynamics of the M17 aminopeptidase from Plasmodium falciparum and identifies a metal-dependent dynamic regulatory mechanism that controls the transition between the active and inactive states of the protein. The rearrangement of the binuclear metal center and substrate-binding pocket is coupled with a loop movement, rendering the protein inactive. This research provides insights into the functional role of oligomerization and reveals a novel role for metal cofactors in enzyme regulation.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Physics, Fluids & Plasmas
Alidivinas Prusokas, Michelle Hawkins, Conrad A. Nieduszynski, Renata Retkute
Summary: Cell plating, a common laboratory procedure in microbiology, involves spreading liquid suspension of cells on a surface for colony growth. The impact of parameters on colony growth has not been extensively studied, but investigating these parameters can help to better understand and control the outputs of microbiology techniques.
Article
Microbiology
Corey Westfall, Ana Lidia Flores-Mireles, John Isaac Robinson, Aaron J. L. Lynch, Scott Hultgren, Jeffrey P. Henderson, Petra Anne Levin
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2019)
Article
Biochemistry & Molecular Biology
Fangwei Si, Guillaume Le Treut, John T. Sauls, Stephen Vadia, Petra Anne Levin, Suckjoon Jun
Review
Biochemistry & Molecular Biology
Petra Anne Levin, Sattar Taheri-Araghi
JOURNAL OF MOLECULAR BIOLOGY
(2019)
Article
Biology
Elizabeth A. Mueller, Alexander J. F. Egan, Eefjan Breukink, Waldemar Vollmer, Petra Anne Levin
Article
Multidisciplinary Sciences
Nguyen-Hung Le, Katharina Peters, Akbar Espaillat, Jessica R. Sheldon, Joe Gray, Gisela Di Venanzio, Juvenal Lopez, Bardya Djahanschiri, Elizabeth A. Mueller, Seth W. Hennon, Petra Anne Levin, Ingo Ebersberger, Eric P. Skaar, Felipe Cava, Waldemar Vollmer, Mario F. Feldman
Review
Microbiology
Elizabeth A. Mueller, Petra Anne Levin
Article
Biochemistry & Molecular Biology
Elizabeth A. Mueller, Abbygail G. Iken, Mehmet Ali Oeztuerk, Matthias Winkle, Mirko Schmitz, Waldemar Vollmer, Barbara Di Ventura, Petra Anne Levin
Summary: The study reveals changes in the activity of two amidases, AmiB and AmiC, in E. coli under growth medium-related conditions, with the stimulation mediated through periplasmic amidase activators.
MOLECULAR MICROBIOLOGY
(2021)
Article
Biology
Justin J. Miller, Ishaan T. Shah, Jayda Hatten, Yasaman Barekatain, Elizabeth A. Mueller, Ahmed M. Moustafa, Rachel L. Edwards, Cynthia S. Dowd, Paul J. Planet, Florian L. Muller, Joseph M. Jez, Audrey R. Odom John
Summary: Carboxy ester prodrugs play a crucial role in increasing the oral absorption and potency of antibiotics, but their therapeutic potential is limited by rapid hydrolysis by serum esterases. Bacterial esterases GloB and FrmB have been identified as activators of carboxy ester prodrugs in Staphylococcus aureus, with specific substrate preferences. Studies on the substrate specificities of human and mouse sera have identified potential prodrugs resistant to serum esterases but susceptible to microbial degradation, expanding the range of molecules for targeting staphylococcal pathogens.
Editorial Material
Biotechnology & Applied Microbiology
Amanda Dicks, Himanshi Bhatia, Adam W. Clemens, Marissa C. Locke, Elizabeth A. Mueller, Daniel Murphy, Nathan Pomper, Anne E. Robinson, Kathleen M. Schoch
NATURE BIOTECHNOLOGY
(2021)
Correction
Biology
Justin J. Miller, Ishaan T. Shah, Jayda Hatten, Yasaman Barekatain, Elizabeth A. Mueller, Ahmed M. Moustafa, Rachel L. Edwards, Cynthia S. Dowd, Geoffrey C. Hoops, R. Jeremy Johnson, Paul Planet, Florian L. Muller, Joseph Jez, Audrey R. Odom John
Review
Cell Biology
Douglas R. Kellogg, Petra Anne Levin
Summary: Pioneering work discovered that bacterial cell size is proportional to growth rate set by nutrient availability, known as the growth law. Recent studies have shown that the relationship between growth rate, nutrients, and cell size is more complex than originally thought.
TRENDS IN CELL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Min Kyung Shinn, Megan C. Cohan, Jessie L. Bullock, Kiersten M. Ruff, Petra A. Levin, Rohit V. Pappu
Summary: Intrinsically disordered regions (IDRs) play a role in autoregulating folded enzymes. The C-terminal tail (CTT) of bacterial cell division protein FtsZ, which includes a disordered C-terminal linker (CTL) and a well-conserved C-terminal peptide (CT17), has been found to make contacts with the T7 loop. Nonrandom sequence patterns within the CTL mediate CTT-core interactions and modulate FtsZ functionalities.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)