Editorial Material
Multidisciplinary Sciences
Alice Bertocchi, Fiona Powrie
Summary: Abnormalities in gut bacteria can lead to hard-to-treat illnesses like inflammatory bowel diseases. Targeting bacteria with viruses shows promise in addressing these conditions.
Article
Gastroenterology & Hepatology
Szymon Ostrowski, Anthony Croft
Summary: This retrospective study aimed to investigate the impact of viral enteric infection on the severity and outcomes of acute severe ulcerative colitis (ASUC). The results showed that infection with viral enteropathogens did not affect disease severity at presentation, the need for rescue therapy, or the success rate of rescue therapy in ASUC patients.
JOURNAL OF CROHNS & COLITIS
(2022)
Article
Multidisciplinary Sciences
Young Hun Chung, Oscar A. Ortega-Rivera, Britney A. Volckaert, Eunkyeong Jung, Zhongchao Zhao, Nicole F. Steinmetz
Summary: Metastatic cancer, accounting for 90% of cancer-related deaths, remains a major challenge in cancer treatment. S100A9, a regulator of inflammation, plays a central role in cancer progression and metastasis, particularly in the lungs. This study developed a plant virus-derived S100A9 vaccine, which effectively prevented tumor seeding and metastatic growth in the lungs by enhancing immunostimulatory cytokines and reducing immunosuppressive factors.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Multidisciplinary Sciences
Ming Yan, Akbar Adjie Pratama, Sripoorna Somasundaram, Zongjun Li, Yu Jiang, Matthew B. Sullivan, Zhongtang Yu
Summary: By mining published rumen metagenomes, we constructed a global rumen virome database (RVD) and analyzed its diversity, virus-host linkages, and potential roles in affecting rumen functions. RVD, containing 397,180 species-level viral operational taxonomic units (vOTUs), significantly improves the detection rate of rumen viruses compared with other databases. The rumen virome is predicted to infect core members of the rumen microbiome, carry diverse auxiliary metabolic genes, and likely impact the rumen ecosystem.
NATURE COMMUNICATIONS
(2023)
Review
Biochemistry & Molecular Biology
Heiko Lokstein, Gernot Renger, Jan P. Goetze
Summary: Chlorophylls, bacteriochlorophylls, and carotenoids are important pigments in photosynthetic organisms, playing a crucial role in light-harvesting and energy transformation. Recent research has made significant progress in understanding the structures and functions of light-harvesting complexes, reaction centers, and photosystems, highlighting the importance of these complexes in adapting to environmental conditions and regulating energy processes. The structural diversity in photosynthetic antenna designs is becoming increasingly apparent, with light-harvesting complexes commonly forming trimeric structures.
Article
Multidisciplinary Sciences
Rebecca Conners, Rayen Ignacia Leon-Quezada, Mathew McLaren, Nicholas J. Bennett, Bertram Daum, Jasna Rakonjac, Vicki A. M. Gold
Summary: Phages, viruses that infect bacteria, are prevalent in every ecosystem on Earth and have various applications in molecular biology and biotechnology. The structure and mechanisms of infection and assembly of filamentous phages, particularly the Ff phages, have been largely unknown. In this study, the researchers used cryo-electron microscopy and a highly efficient system to produce short Ff-derived nanorods, successfully determining the structure of a filamentous virus including the tips. By combining the structure with mutagenesis, they identified important phage domains involved in bacterial attack and release of new viral progeny, leading to the proposal of new models for the phage lifecycle.
NATURE COMMUNICATIONS
(2023)
Article
Engineering, Chemical
Kairu Ye, Yan Yang, Haishuo Chen, Jiatong Wu, Hongyuan Wei, Leping Dang
Summary: The effect of solvents on the pigmentation behavior of Pigment Yellow 180 (PY180) was studied using Hansen solubility parameters (HSPs) and molecular polarity index (MPI) method. It was found that the choice of solvents significantly affects the color of the pigment, and the variation in crystallinity and particle size is the main cause of chromaticity variation.
Article
Immunology
Christopher J. R. Turkington, Ambarish C. Varadan, Shea F. Grenier, Juris A. Grasis
Summary: Recent advances in our understanding of microbial communities have shed light on the importance of microorganisms in and on our bodies, particularly in the context of disease. Viral research has greatly benefited from new community profiling techniques, revealing their significant role in our physiology. Viruses have been implicated in colorectal cancer, both as potential causes and as potential therapeutic options.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Moira B. Dion, Pier-Luc Plante, Edwige Zufferey, Shiraz A. Shah, Jacques Corbeil, Sylvain Moineau
Summary: A large number of new phages have been discovered through viral metagenomics, with their host prediction based on CRISPR spacers which represent past phage-bacteria interactions. A set of tools has been developed for predicting hosts of uncharacterized phages, utilizing a database of over 11 million spacers and a program for large viral datasets. Performance evaluations show promise for gut-virome characterization using this host prediction method.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Immunology
Valery Daubie, Houssein Chalhoub, Bob Blasdel, Hafid Dahma, Maya Merabishvili, Tea Glonti, Nathalie De Vos, Johan Quintens, Jean-Paul Pirnay, Marie Hallin, Olivier Vandenberg
Summary: As the global burden of disease caused by multidrug resistant bacteria is a major concern, exploring credible clinical alternatives to antibiotic therapy, such as personalized phage therapy, is crucial. However, the development of an easy to implement diagnostic tool for determining phage susceptibility remains an open issue. This review summarizes existing methods for determining phage activity on bacteria and discusses potential techniques for implementing a phage susceptibility testing tool in routine clinical microbiology.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Engineering, Environmental
Fangzhou Liu, Bruce Rittmann, Saachi Kuthari, Wen Zhang
Summary: This study incorporated microwave-enabled catalysis into membrane filtration and evaluated viral removal using a model bacteriophage (MS2) as a surrogate. The findings showed that microwave irradiation effectively penetrated the PTFE membrane module and enabled surface oxidation reactions on the membrane-coated catalysts, resulting in strong germicidal effects. A log removal of 2.6 was achieved for MS2 within a contact time as low as 20 s using 125-W microwave irradiation. This research provides new insights to the antiviral mechanisms of this microwave-enabled catalytic membrane filtration.
JOURNAL OF HAZARDOUS MATERIALS
(2023)
Article
Multidisciplinary Sciences
Shitao Huang, Ke Li, Yaoru Pan, Yan Yu, Thomas Wernberg, Thibaut de Bettignies, Jiaping Wu, Chaosheng Zhou, Zhixing Huang, Xi Xiao
Summary: This study found that white LED light is the optimal choice for cultivating Ulva pertusa and Sargassum fusiforme, while red LED light is unfavorable for the growth of S. fusiforme. LEDs have the potential to be a promising supplementary light source for seaweed cultivation.
Article
Biochemistry & Molecular Biology
Elsinraju Devadasu, Jayendra Pandey, Kunal Dhokne, Rajagopal Subramanyam
Summary: The eukaryotic alga Chlamydomonas (C.) reinhardtii is a model organism for studying photosynthetic efficiency. Under severe iron deficiency conditions, changes in thylakoid membrane organization and protein profiles affect photosynthetic efficiency, but supplementation with iron can partially restore the function of iron-deficient cells.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS
(2021)
Article
Food Science & Technology
Pedro Blanco-Picazo, Clara Gomez-Gomez, Sara Morales-Cortes, Maite Muniesa, Lorena Rodriguez-Rubio
Summary: This study analyzed phages and phage particles containing antibiotic resistance genes (ARGs) in five dairy products purchased from local retailers in Barcelona. The experiment identified phages that can infect Escherichia coli and revealed the morphologies of the phage particles. The results indicate that dairy products may serve as a potential source of antibiotic resistance genes that can be transmitted to susceptible hosts.
INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
P. A. Kaminski
Summary: Bacteriophage genomes contain 2,6 diaminopurine, a modified nucleobase that violates Watson and Crick's base pairing rules, found in various types of bacteriophages. The biosynthetic pathway for aminoadenine containing DNA and the exclusion of adenine have been elucidated, providing evidence for the exploration of non-canonical nucleic acids in synthetic biology. This natural deviation from the genetic code exemplifies the possibilities nature presents and serves as proof of concept for the synthetic biology field.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Marco Aras, Volker Hartmann, Jana Hartmann, Marc M. Nowaczyk, Nicole Frankenberg-Dinkel
Article
Multidisciplinary Sciences
Oliver Lampret, Jifu Duan, Eckhard Hofmann, Martin Winkler, Fraser A. Armstrong, Thomas Happe
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Biotechnology & Applied Microbiology
Kerstin Fiege, Nicole Frankenberg-Dinkel
MICROBIAL CELL FACTORIES
(2020)
Article
Multidisciplinary Sciences
Dennis Della Corte, Hugo L. van Beek, Falk Syberg, Marcus Schallmey, Felix Tobola, Kai U. Cormann, Christine Schlicker, Philipp T. Baumann, Karin Krumbach, Sascha Sokolowsky, Connor J. Morris, Alexander Gruenberger, Eckhard Hofmann, Gunnar F. Schroeder, Jan Marienhagen
NATURE COMMUNICATIONS
(2020)
Article
Multidisciplinary Sciences
Vanessa Krauspe, Matthias Fahrner, Philipp Spat, Claudia Steglich, Nicole Frankenberg-Dinkel, Boris Macek, Oliver Schilling, Wolfgang R. Hess
Summary: The protein NblD plays a crucial role in the degradation of phycobilisomes in cyanobacteria under nitrogen-limited conditions. Studies have shown that NblD is essential for maintaining normal growth of cyanobacterial cells during nitrogen limitation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Martin Winkler, Jifu Duan, Andreas Rutz, Christina Felbek, Lisa Scholtysek, Oliver Lampret, Jan Jaenecke, Ulf-Peter Apfel, Gianfranco Gilardi, Francesca Valetti, Vincent Fourmond, Eckhard Hofmann, Christophe Leger, Thomas Happe
Summary: The protein morphing mechanism of [FeFe]-hydrogenase CbA5H controls the reversible transition between catalytic and inactive states, with a conserved cysteine residue protecting the active site from oxygen by acting as a safety cap. This protection mechanism is regulated by three non-conserved amino acids located approximately 13 angstrom away from the active site, demonstrating remote control of the first coordination sphere chemistry of the H-cluster.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Natascha Tomazic, Kristina E. Overkamp, Helen Wegner, Bin Gu, Florian Mahler, Marco Aras, Sandro Keller, Antonio J. Pierik, Eckhard Hofmann, Nicole Frankenberg-Dinkel
Summary: Cryptophytes use phycobiliproteins for photosynthesis, with their assembly involving PBP-lyases and substrate specificity possibly affected by a single amino acid residue.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS
(2021)
Article
Plant Sciences
Bernd Ackermann, Beatrix Duenschede, Bjoern Pietzenuk, Bo Hojen Justesen, Ute Kraemer, Eckhard Hofmann, Thomas Guenther Pomorski, Danja Schuenemann
Summary: Members of the Oxa1/YidC/Alb3 protein family are involved in the insertion, folding, and assembly of membrane proteins in mitochondria, bacteria, and chloroplasts. The thylakoid membrane protein Alb3 interacts with ribosomes during posttranslational insertion of specific proteins, while Alb4, a homolog located in the same membrane, does not show ribosome binding. Alb3 contacts ribosomes via its C-terminal region and at least one additional binding site within its hydrophobic core.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Francesco Tumbarello, Giampaolo Marcolin, Elisa Fresch, Eckhard Hofmann, Donatella Carbonera, Elisabetta Collini
Summary: This study investigated the energy transfer from carotenoids to chlorophylls in marine algae using two-dimensional electronic spectroscopy. Relevant details on the mechanism of excitation transfer were unveiled by comparing mutant and normal systems.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biotechnology & Applied Microbiology
Abdulkadir Yayci, Nathalie Bachmann, Tim Dirks, Eckhard Hofmann, Julia E. Bandow
Summary: This study identified and characterized novel DyP-type peroxidases from Streptomyces chartreusis NRRL 3882, and found that they exhibited distinct preferences in operating conditions and stability. The findings suggest that having different DyP variants in one organism may confer evolutionary benefits. DyP-type peroxidases can be applied in biocatalysis and bioremediation.
JOURNAL OF APPLIED MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Marharyta Varatnitskaya, Julia Fasel, Alexandra Mueller, Natalie Lupilov, Yunlong Shi, Kristin Fuchs, Marco Krewing, Christoph Jung, Timo Jacob, Barbara Sitek, Julia E. Bandow, Kate S. Carroll, Eckhard Hofmann, Lars I. Leichert
Summary: This study helps to identify the residues responsible for RidA's chaperone-like function using a combination of LC-MS/MS analysis, chemo-proteomic approach, and mutagenesis study. The enhanced chaperone activity of RidA is associated with the loss of positive charges on the protein surface and increased overall protein hydrophobicity.
Article
Chemistry, Multidisciplinary
Jifu Duan, Anja Hemschemeier, David J. Burr, Sven T. Stripp, Eckhard Hofmann, Thomas Happe
Summary: In this study, the crystal structures of CN--treated [FeFe]-hydrogenase CpI from Clostridium pasteurianum were obtained, revealing that extrinsic CN- binds to the open coordination site of the cofactor. The binding of CN- leads to conformational changes in conserved residues within the proton transfer pathway, potentially facilitating efficient proton transfer. This observation provides important insights into the mechanism of CN- inhibition and proton transfer in hydrogenases.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemistry & Molecular Biology
Daniel Mann, Kristin Labudda, Sophie Zimmermann, Kai Ulrich Vocke, Raphael Gasper, Carsten Koetting, Eckhard Hofmann
Summary: This study presents time-resolved FTIR spectroscopic measurements of ATP binding and hydrolysis reaction in full-length MsbA. The reaction rates were determined and the study paves the way for investigations of allocrite transport in full-length MsbA using FTIR spectroscopy.
BIOLOGICAL CHEMISTRY
(2023)
Article
Plant Sciences
Federica Frascogna, Benjamin Ledermann, Jana Hartmann, Eugenio Perez Patallo, Fjoralba Zeqiri, Eckhard Hofmann, Nicole Frankenberg-Dinkel
Summary: This study investigated the evolution of the HY2 lineage of FDBRs by studying the enzyme in Klebsormidium nitens. The research revealed that the catalytic activities of phytochromobilin synthase evolved differently in relation to the light environment of the organism.
Article
Chemistry, Multidisciplinary
Claudia Brocks, Chandan K. Das, Jifu Duan, Shanika Yadav, Ulf-Peter Apfel, Subhasri Ghosh, Eckhard Hofmann, Martin Winkler, Vera Engelbrecht, Lars V. Schaefer, Thomas Happe
Summary: This study proposes a new strategy to improve the O-2 stability of [FeFe]-hydrogenases by blocking the O-2 diffusion pathway and protecting the catalytic cofactor.