Article
Multidisciplinary Sciences
Irina V. Mikheyeva, Jiawei Sun, Kerwyn Casey Huang, Thomas J. Silhavy
Summary: This study demonstrates that loss of BamD in Escherichia coli leads to reduction in outer membrane proteins (OMPs), weakening the outer membrane and altering cell shape. This results in outer membrane rupture in spent medium. In response to the loss of OMPs, phospholipids flip into the outer leaflet, creating tension between the membrane leaflets and contributing to membrane rupture. Suppressor mutations that halt phospholipid removal prevent rupture but do not restore membrane stiffness or normal cell shape, suggesting a possible connection between outer membrane stiffness and cell shape.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Ibrahim S. Al'Abri, Daniel J. Haller, Zidan Li, Nathan Crook
Summary: Directed evolution is a powerful method for engineering biology without detailed sequence-function relationships. To address the evolution of multigene pathways, the Inducible Directed Evolution (IDE) approach was developed and successfully applied in accelerating tagatose catabolism and improving utilization of melezitose in E. coli.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Lorena Ilcu, Lukas Denkhaus, Anton Brausemann, Lin Zhang, Oliver Einsle
Summary: Mono- and multiheme cytochromes c in Escherichia coli are matured through covalent attachment of heme using the complex Ccm-system. Cryo-electron microscopic structures of the heme translocation complex CcmABCD from E. coli are reported, showcasing its mechanism of shuttling heme across the membrane to the heme chaperone CcmE. ATP hydrolysis at CcmA and a conserved heme-handling motif (WxWD) at CcmC facilitate the rotation and covalent attachment of heme.
NATURE COMMUNICATIONS
(2023)
Article
Infectious Diseases
Xiaowei Dai, Min Yuan, Yu Lu, Xiaohong Zhu, Chao Liu, Yifan Zheng, Shuyi Si, Lijie Yuan, Jing Zhang, Yan Li
Summary: The need for novel antibiotics is urgent due to the increasing antibiotic resistance in Gram-negative bacteria. Lpt proteins play a crucial role in the biosynthesis of LPS and could be a potential target for new antibiotics. This study successfully identified a potential antibacterial agent, IMB-0042, which disrupts LptA/LptC interaction and inhibits LPS transport.
Article
Biochemistry & Molecular Biology
Wee Boon Tan, Shu-Sin Chng
Summary: The Tol-Pal trans-envelope complex plays important roles in outer membrane stability and cell division in Gram-negative bacteria. Recent studies have also revealed its involvement in outer membrane lipid homeostasis and septal wall separation. However, the exact mechanisms of Tol-Pal's functions are still unclear.
MOLECULAR MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Masaya Fujita, Shodai Yano, Koki Shibata, Mizuki Kondo, Shojiro Hishiyama, Naofumi Kamimura, Eiji Masai
Summary: TonB-dependent transporters play a crucial role in the outer membrane transport of nutrients in microbes, with certain genes being important for the uptake of lignin-derived aromatics. Studies have shown that the tonB1 operon genes in SYK-6 are involved in the outer membrane transport of lignin-derived aromatic compounds, while exbB2/tolQ and exbD3/tolR are suggested to constitute the Tol-Pal system maintaining outer membrane integrity.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Amina Ezzeroug Ezzraimi, Nadji Hannachi, Antoine Mariotti, Clara Rolland, Anthony Levasseur, Sophie Alexandra Baron, Jean-Marc Rolain, Laurence Camoin-Jau
Summary: This study aimed to investigate the interaction between Escherichia coli and platelets, evaluate the antibacterial effect of platelets, and assess bacterial effects on platelet activation. The results showed that platelets inhibited the growth of certain strains while promoting the growth of others. The degree of platelet activation was negatively correlated with bacterial growth.
Article
Agriculture, Dairy & Animal Science
Han Wang, Fang Yang, Zhe-wen Song, Hao-tian Shao, Dong-ying Bai, Yan-bo Ma, Tao Kong, Fan Yang
Summary: This study found that the challenge of Escherichia coli lipopolysaccharide (LPS) affects the pharmacokinetics of danofloxacin in broilers, leading to decreased AUC, Cmax, and t(1/2 lambda z) parameters, and increased Tmax and lambda z parameters.
Article
Microbiology
Roberto Jhonatan Olea-Ozuna, Sebastian Poggio, EdBergstrom, Elva Quiroz-Rocha, Daniela A. Garcia-Soriano, Diana X. Sahonero-Canavesi, Jonathan Padilla-Gomez, Lourdes Martinez-Aguilar, Isabel M. Lopez-Lara, Jane Thomas-Oates, Otto Geiger
Summary: The biosynthesis of sphingolipids in Caulobacter crescentus is crucial for the survival of the bacterium and the integrity of its outer membrane. Mutants deficient in serine palmitoyltransferase showed decreased survival during stationary growth phase, especially at elevated temperatures. At least five structural genes are required for dihydroceramide biosynthesis in C. crescentus.
ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Nicolas Waisbord, Amin Dehkharghani, Jeffrey S. Guasto
Summary: Through microfluidic experiments, it was found that individual magnetotactic bacteria display three distinct regimes when directed upstream through pores, resembling the electrical conductivity of a diode. This diode-like behavior persists at the pore scale, impacting flow conductivity in higher dimensional geometries. The study has implications for magnetotactic bacteria survival strategies in sediments and potential drug delivery applications in vascular networks.
NATURE COMMUNICATIONS
(2021)
Review
Biochemistry & Molecular Biology
Anatoly V. Skalny, Michael Aschner, Xin Gen Lei, Viktor A. Gritsenko, Abel Santamaria, Svetlana I. Alekseenko, Nagaraja Tejo Prakash, Jung-Su Chang, Elena A. Sizova, Jane C. J. Chao, Jan Aaseth, Alexey A. Tinkov
Summary: The present study reviewed the association between Zn status and gut microbiota characteristics, as well as the potential role of Zn-induced microbiota in modulating systemic effects. The data showed a close relationship between Zn metabolism and gut microbiota, with Zn being a significant factor for gut bacteria biodiversity. Physiological and nutritional Zn doses improved gut wall integrity, while Zn overexposure induced substantial alterations in gut microbiota.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biology
Ankith Sharma, Rajdeep Chowdhury, Siegfried M. Musser
Summary: A single molecule photobleaching analysis reveals that the Tat receptor complex is a tetramer with equal stoichiometry of TatB and TatC in its native membrane environment. This finding provides insights into the structure and function of the receptor complex.
COMMUNICATIONS BIOLOGY
(2022)
Article
Biology
Naima G. Sharaf, Mona Shahgholi, Esther Kim, Jeffrey Y. Lai, David G. VanderVelde, Allen T. Lee, Douglas C. Rees
Summary: NmMetQ is a lipoprotein that binds multiple methionine analogs and plays dual roles in bacterial transport processes, tethering to membranes via a lipid anchor. It has been found to stimulate the ATPase activity of NmMetNI and may also have additional functions on the bacterial surface.
Article
Chemistry, Multidisciplinary
Charles Burridge, Christopher A. Waudby, Tomasz Wlodarski, Anais M. E. Cassaignau, Lisa D. Cabrita, John Christodoulou
Summary: This study used solution-state NMR spectroscopy to measure transverse proton relaxation rates for methyl groups in folded ribosome-nascent chain complexes, revealing interactions between the nascent chain and ribosome surface driven predominantly by electrostatics. By observing changes in these interactions as subsequent domain emerges, the impact on free energy landscapes associated with co-translational folding process can be deduced.
Article
Chemistry, Multidisciplinary
Oleksii Zdorevskyi, Amina Djurabekova, Jonathan Lasham, Vivek Sharma
Summary: Respiratory complex I is an redox-driven proton pump that contributes to mitochondrial ATP generation. The recent cryo-EM structural data revealed the positions of water molecules in the membrane domain of the complex, but the flow of protons in the membrane-bound subunits is still unclear. Computer simulations on high-resolution structural data show that protons can travel through the antiporter-like subunits, including at the subunit-subunit interface parallel to the membrane. Our simulations also demonstrate the role of conserved tyrosine residues and electrostatic effects in facilitating proton transfer. These results challenge prevailing proton pumping models of respiratory complex I.
Article
Microbiology
Stefano Gualdi, Kirsty Agnoli, Alessandra Vitale, Steven Higgins, Leo Eberl
Summary: Members of the genus Burkholderia exhibit remarkable abilities to adapt to various environmental conditions and are often found in soils contaminated with heavy metals. This study identified genes associated with silver and gold tolerance in the opportunistic pathogen Burkholderia cenocepacia H111, highlighting the importance of arginine metabolism, citrate biosynthesis, ABC transporters, and cysteine biosynthesis. Additionally, it was discovered that membrane proteins and specific genes, such as P-type ATPase CadA, play crucial roles in the tolerance to silver and gold ions. These findings have potential implications for enhancing the antibacterial effectiveness of silver and gold ions against drug-resistant pathogens.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Sarah Paszti, Alessandra Vitale, Yilei Liu, Rubina Braunwalder, Ratchara Kalawong, Olivier Biner, Gabriella Pessi, Leo Eberl
Summary: In this study, the researchers investigated the survival mechanism of Burkholderia cenocepacia under anaerobic conditions. They identified 71 fitness determinants associated with anaerobic survival and found that the two-component system RoxS/RoxR and FliA play important roles in virulence and swarming/swimming, respectively.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemical Research Methods
Sandra Goetze, Peter Schueffler, Alcibiade Athanasiou, Anika Koetemann, Cedric Poyet, Christian Daniel Fankhauser, Peter J. Wild, Ralph Schiess, Bernd Wollscheid
Summary: Using Mass Spectrometry-GUidED Immunoassay DEvelopment (MS-GUIDE), we screened 48 literature-derived biomarker candidates to evaluate their potential utility in risk stratification scoring of prostate cancer patients. Machine learning analysis prequalified fibronectin and vitronectin as candidate biomarkers. Clinical-grade ELISAs were developed for these candidates and tested in a larger patient cohort.
CLINICAL PROTEOMICS
(2022)
Article
Microbiology
Susanna Bidgood, Jerzy Samolej, Karel Novy, Abigail Collopy, David Albrecht, Melanie Krause, Jemima Burden, Bernd Wollscheid, Jason Mercer
Summary: This study investigates the composition of poxviruses and the role of poxvirus redox proteins in host cells. Using mass spectrometry, a large number of candidate cellular and viral proteins, including redox proteins, were identified. The results show that poxvirus infection has an antioxidative effect on host cells and deletion of redox proteins is insufficient to modulate host cell redox reactions, suggesting the existence of functional redundancy.
Editorial Material
Microbiology
Leo Eberl
ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Kathrin Frey, Sandra Goetze, Lucia Rohrer, Arnold von Eckardstein, Bernd Wollscheid
Summary: This study used chemoproteomic technologies to analyze the interaction between high-density lipoprotein (HDL) and cell surface receptors, identifying numerous potential HDL receptors, including the known scavenger receptor B1 (SCRB1) and other co-regulated receptors. Additionally, the study found that vascular endothelial growth factor A (VEGF-A) can remodel the cell surface composition, affecting the binding and uptake of HDL. Furthermore, the study identified another HDL receptor, receptor tyrosine-protein kinase Mer (MERTK), and demonstrated its contribution to HDL binding and its spatial proximity to SCRB1 on endothelial cells.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Microbiology
Gabriela Purtschert-Montenegro, Gerardo Carcamo-Oyarce, Marta Pinto-Carbo, Kirsty Agnoli, Aurelien Bailly, Leo Eberl
Summary: Research has found that the plant root colonizer Pseudomonas putida strain IsoF is able to use a type IVB secretion system (T4BSS) to kill a wide range of soil and plant-associated Gram-negative bacteria, invade existing biofilms, and protect tomato plants against the phytopathogen Ralstonia solanacearum.
NATURE MICROBIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Elisabeth Steiner, Rebecca E. Shilling, Anja M. Richter, Nadine Schmid, Mustafa Fazli, Volkhard Kaever, Urs Jenal, Tim Tolker-Nielsen, Leo Eberl
Summary: The BDSF quorum sensing receptor RpfR is a negative regulator of the bep gene cluster in B. cenocepacia. There is a correlation between intracellular c-di-GMP levels and bep expression, except when the intracellular c-di-GMP level is changed by site directed mutagenesis of the EAL or GGDEF domain of RpfR. RpfR and BerB physically interact and give specificity to the regulation of the bep genes.
NPJ BIOFILMS AND MICROBIOMES
(2022)
Article
Microbiology
Anya Schnyder, Leo Eberl, Kirsty Agnoli
Summary: This study investigated the potential of the resident microbiota of apple blossoms in combating plant disease-causing organisms, and identified two candidate biocontrol strains. These strains may already be part of the human diet, making them promising candidates for biocontrol applications.
Review
Microbiology
Masanori Toyofuku, Stefan Schild, Maria Kaparakis-Liaskos, Leo Eberl
Summary: Extracellular vesicles are fundamental to living matter and are produced by species across all domains of life. In bacteria, membrane vesicles (MVs) can be generated from the outer membrane or through explosive cell lysis induced by genotoxic stress. Recent research has shown that similar mechanisms of vesicle formation exist in Gram-positive and Gram-negative bacteria. This review discusses the different types of MV and their cargo packaging mechanisms.
NATURE REVIEWS MICROBIOLOGY
(2023)
Article
Microbiology
Sebastian Hug, Benjamin Heiniger, Kim Bolli, Sarah Paszti, Leo Eberl, Christian H. Ahrens, Gabriella Pessi
Summary: Paraburkholderia sabiae LMG24235 is a nitrogen-fixing betaproteobacterium that effectively kills important plant pathogens in a contact-dependent manner. The strain contains two predicted gene clusters encoding type VI secretion systems, one of which is essential for competition against several plant pathogens in vitro and for protecting potato tubers from bacterial soft rot disease in vivo.
MICROBIOLOGY SPECTRUM
(2023)
Article
Plant Sciences
Paula Belles-Sancho, Yilei Liu, Benjamin Heiniger, Elia von Salis, Leo Eberl, Christian H. Ahrens, Nicola Zamboni, Aurelien Bailly, Gabriella Pessi
Summary: Rhizobia control the expression of auxin synthesis genes through NifA, leading to increased auxin levels in non-fixing mutant strains, which enhances root infection rates and plays a role in early symbiotic interactions.
FRONTIERS IN PLANT SCIENCE
(2022)
Correction
Hematology
Beat Bornhauser, Gunnar Cario, Anna Rinaldi, Thomas Risch, Virginia Rodriguez Martinez, Moritz Schuette, Hans-Joerg Warnatz, Nastassja Scheidegger, Paulina Mirkowska, Martina Temperli, Claudia Moller, Angela Schumich, Michael Dworzak, Andishe Attarbaschi, Monika Brueggemann, Mathias Ritgen, Ester Mejstrikova, Andreas Hofmann, Barbara Buldini, Pamela Scarparo, Giuseppe Basso, Oscar Maglia, Giuseppe Gaipa, Tessa Lara Skroblyn, Quy A. Ngo, Geertruij te Kronnie, Elena Vendramini, Renate Panzer-Gruemayer, Malwine Jeanette Barz, Blerim Marovca, Mathias Hauri-Hohl, Felix Niggli, Cornelia Eckert, Martin Schrappe, Martin Stanulla, Martin Zimmermann, Bernd Wollscheid, Marie-Laure Yaspo, Jean-Pierre Bourquin
Meeting Abstract
Endocrinology & Metabolism
Patrick Forny, Ximena Bonilla, David Lamparter, Wenguang Shao, Tanja Plessl, Caroline Frei, Anna Bingisser, Sandra Goetze, Audrey Van Drogen, Keith Harshman, Patrick Pedrioli, Florian Traversi, Ioannis Xenarios, Ruedi Aebersold, Nicola Zamboni, Gunnar Ratsch, Emmanouil Dermitzakis, Bernd Wollscheid, D. Sean Froese, Matthias R. Baumgartner
MOLECULAR GENETICS AND METABOLISM
(2022)