Article
Microbiology
Anna Munke, Kei Kimura, Yuji Tomaru, Han Wang, Kazuhiro Yoshida, Seiya Mito, Yuki Hongo, Kenta Okamoto
Summary: This paper focuses on one major group of marine algae viruses, the single-stranded DNA (ssDNA) viruses from the Bacilladnaviridae family. The study reveals the structure of the capsid protein of a bacilladnavirus and the organization of the ssDNA genome, providing insights into the importance of genetic recombination for the emergence and evolution of ssDNA viruses.
Review
Microbiology
Hannah E. Hanford, Juanita Von Dwingelo, Yousef Abu Kwaik
Summary: Bacterial pathogens have evolved unique effector proteins, termed nucleomodulins, that interact with host cells and target the host cell nucleus to regulate gene expression through various mechanisms. These nucleomodulins induce short- or long-term epigenetic modifications in host cells, influencing chromatin dynamics, transcriptional regulation, and cellular signaling pathways. Continued research on nucleomodulins will enhance our understanding of how they manipulate host cell gene regulation and alter the host cell epigenome.
Article
Cell Biology
Carlos Molina-Santiago, David Vela-Corcia, Daniel Petras, Luis Diaz-Martinez, Alicia Isabel Perez-Lorente, Sara Sopena-Torres, John Pearson, Andres Mauricio Caraballo-Rodriguez, Pieter C. Dorrestein, Antonio de Vicente, Diego Romero
Summary: The study reveals the coexistence mechanism between Pseudomonas chlororaphis and Bacillus amyloliquefaciens, including tolerance and biological inhibition caused by mutations. Nutrient specialization and mutations in basic biological functions are key factors driving the coexistence of two competitive bacterial species.
Article
Chemistry, Multidisciplinary
Sunidhi C. Shetty, Naresh Yandrapalli, Kerstin Pinkwart, Dorothee Krafft, Tanja Vidakovic-Koch, Ivan Ivanov, Tom Robinson
Summary: In this work, researchers have successfully constructed artificial cells with multiple compartments using a microfluidic platform, enabling directed biochemical reactions along specific spatial pathways. By creating multivesicular vesicles with multiple compartments, they demonstrated directed chemical communication between different enzymes, providing a new experimental platform for studying enzyme cascade compartmentalization effects.
Article
Biochemistry & Molecular Biology
Gareth S. A. Wright
Summary: The internalization of a bacteria by an archaeal cell accelerated eukaryotic evolution by utilizing a specific copper chaperone to activate CuZnSOD for combating oxidative stress. The adoption of a single protein interface with structural characteristics necessary for homodimerization and heterodimerization played a crucial role in evolution.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Microbiology
Ana Paula Chung, Romeu Francisco, Paula V. V. Morais, Rita Branco
Summary: In this study, an integrated approach combining experimental and genomic analysis was used to investigate the potential mechanisms involved in bioleaching ability and strategies to cope with high metal concentrations in five mine isolates. The study found that amino acids play an important role in the gallium leaching mechanism, and resistance mechanisms influence the efficiency of gallium bioleaching from gallium arsenide.
FRONTIERS IN MICROBIOLOGY
(2022)
Review
Medicine, General & Internal
Eva Torres-Sangiao, Alexander Dyason Giddey, Cristina Leal Rodriguez, Zhiheng Tang, Xiaoyun Liu, Nelson C. Soares
Summary: The global COVID-19 pandemic has emphasized the threat posed by bacteria, fungi, viruses, and parasites to human health. Infectious diseases continue to be the leading cause of death worldwide, with antibiotic resistance on the rise. The challenge in medical microbiology is to develop new experimental approaches to identify and understand the molecular mechanisms of microbial survival and immune evasion. Proteomics has played a crucial role in uncovering the molecular mechanisms of drug resistance and pathogenicity, and recent advancements in mass spectrometry have further enhanced its capabilities. This review aims to explore the synergies between modern proteomics and microbiology and their potential for translational applications in clinical practice.
FRONTIERS IN MEDICINE
(2022)
Article
Multidisciplinary Sciences
Fernando Rodriguez, Irina A. Yushenova, Daniel DiCorpo, Irina R. Arkhipova
Summary: This study discovered a DNA methyltransferase, N4CMT, derived from bacteria in bdelloid rotifers that can deposit 4mC on active transposons and certain tandem repeats, thereby silencing these genes. This suggests that horizontal gene transfer has the potential to drive regulatory innovation in eukaryotes.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Ilka Erven, Elena Abraham, Thomas Hermanns, Ulrich Baumann, Kay Hofmann
Summary: Distinct families of eukaryotic deubiquitinases (DUBs) are regulators of ubiquitin signaling. In addition to the known large tegument proteins of herpesviruses, a new class of DUBs has been identified in eukaryotes and bacteria. This class, named VTD (Viral tegument-like DUB), shows distant homology with the herpesvirus tegument proteins and has diverse specificity for different types of ubiquitin chains.
NATURE COMMUNICATIONS
(2022)
Article
Biology
Sravan Kumar Miryala, Anand Anbarasu, Sudha Ramaiah
Summary: The study of host-pathogen interactions and protein-protein interactions in cardiovascular diseases reveals dense interactions between human and E. coli genes, which play crucial roles in the onset and progression of the diseases and can be explored for new drug discovery.
COMPUTERS IN BIOLOGY AND MEDICINE
(2021)
Review
Biochemistry & Molecular Biology
Shaojun Yang, William Shu Ching Ngai, Peng R. Chen
Summary: Bacteria have evolved various effector proteins to enhance their survival within the host, with unique mechanisms and high specificity towards host targets. Recent advancements in protein chemistry allow for precise control of protein activity, enabling manipulation of kinase-mediated signal transductions, protein translation inhibition, and genetic editing within host cells. Harnessing a diverse array of prokaryotic effectors presents exciting opportunities for investigating cellular processes and developing therapeutic interventions in eukaryotic systems.
CURRENT OPINION IN CHEMICAL BIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Arnaud Kengmo Tchoupa, Bart A. Eijkelkamp, Andreas Peschel
Summary: This review discusses how bacteria adapt to host-derived antimicrobial fatty acids and highlights their altered response to antibiotics. Understanding bacterial adaptation strategies to fatty acids is of prime importance for the rational design of antimicrobial combination therapies.
TRENDS IN MICROBIOLOGY
(2022)
Review
Immunology
Ailing Zhao, Jiazheng Sun, Yipin Liu
Summary: Bacterial biofilms are complex microbial communities surrounded by extracellular polymeric substances. They are a significant problem in treating bacterial infections and can exhibit increased resistance to antibiotics, causing device-related and non-device infections and posing a serious threat to global health. Therefore, early detection and search for new treatments are essential. This paper systematically reviews the formation, infections, detection methods, and potential treatment strategies of bacterial biofilms, aiming to provide researchers with the latest progress in their detection and treatment.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Multidisciplinary Sciences
Sara Perez-Garcia, Mario Garcia-Navarrete, Diego Ruiz-Sanchis, Cristina Prieto-Navarro, Merisa Avdovic, Ornella Pucciariello, Krzysztof Wabnik
Summary: This study constructs a minimal synthetic system that converts chemical signals into synchronized gene expression among eukaryotic communities. The research finds that increasing the speed of chemical rhythms and incorporating feedback in the system architecture can tune synchronization and precision of cell collectives. This synchronization mechanism remains robust in consortia composed of two strains, demonstrating the ability to maintain spatial-temporal synchronization under stress.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Physical
Ziyang Dai, Guangxing Zhao, Fangxing Ma, Wenhai Zhang, Yan Gong, Hongkun Li, Xiuming Zhang, Naibo Lin, Lei Liu, Da Zhan
Summary: A series of structure modified polymeric carbon nitride photocatalysts were prepared from the same precursor using a step-by-step method. These photocatalysts showed different catalytic activities in degrading Rhodamine (RhB) and methyl orange (MO). The study focused on the roles of active species and proposed a reasonable degradation mechanism to interpret the photocatalytic phenomena.
APPLIED SURFACE SCIENCE
(2021)
Article
Chemistry, Multidisciplinary
Shay Laps, Fatima Atamleh, Guy Kamnesky, Shaked Uzi, Michael M. Meijler, Ashraf Brik
Summary: This study presents a new approach for synthesizing disulfide-rich bioactive molecules, addressing previous challenges in preparation. Experimental results demonstrate the essential role of the order of disulfide bond formation in proteins with knotted structures. This methodology was utilized to synthesize novel analogues of plectasin with enhanced efficacy against MRSA.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Microbiology
Antonia Delago, Rachel Gregor, Luba Dubinsky, Rambabu Dandela, Adi Hendler, Pnina Krief, Josep Rayo, Amir Aharoni, Michael M. Meijler
Summary: The study revealed that yeast can sense quorum sensing molecules from bacteria, particularly C12 from Pseudomonas aeruginosa. Exposure to C12 induced a significant stress response in yeast cells, showing a unique gene expression pattern.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Eden Ozer, Karin Yaniv, Einat Chetrit, Anastasya Boyarski, Michael M. Meijler, Ronen Berkovich, Ariel Kushmaro, Lital Alfonta
Summary: Pseudomonas aeruginosa, an opportunistic pathogen, is a flagellated bacterium that serves as a top model organism for biofilm studies. A new flagella biotracking tool was developed to elucidate the location and role of bacterial flagella throughout the biofilm life cycle. Results from genetic labeling of flagella and comparison of biofilm structures between wild-type and flagella knockout strains suggest a potential structural role for flagella in biofilm formation, possibly as a scaffold.
Article
Ecology
Rachel Gregor, Maraike Probst, Stav Eyal, Alexander Aksenov, Goor Sasson, Igal Horovitz, Pieter C. Dorrestein, Michael M. Meijler, Itzhak Mizrahi
Summary: Research has shown that different mammalian species have distinct gut microbial compositions, which to some extent reflect their diverse effects on host metabolism rather than just functional redundancy.
Letter
Biochemical Research Methods
Daniel Petras, Vanessa V. Phelan, Deepa Acharya, Andrew E. Allen, Allegra T. Aron, Nuno Bandeira, Benjamin P. Bowen, Deirdre Belle-Oudry, Simon Boecker, Dale A. Cummings, Jessica M. Deutsch, Eoin Fahy, Neha Garg, Rachel Gregor, Jo Handelsman, Mirtha Navarro-Hoyos, Alan K. Jarmusch, Scott A. Jarmusch, Katherine Louie, Katherine N. Maloney, Michael T. Marty, Michael M. Meijler, Itzhak Mizrahi, Rachel L. Neve, Trent R. Northen, Carlos Molina-Santiago, Morgan Panitchpakdi, Benjamin Pullman, Aaron W. Puri, Robin Schmid, Shankar Subramaniam, Monica Thukral, Felipe Vasquez-Castro, Pieter C. Dorrestein, Mingxun Wang
Article
Biochemistry & Molecular Biology
Ioannis Tsirkas, Daniel Dovrat, Manikandan Thangaraj, Ineke Brouwer, Amit Cohen, Zohar Paleiov, Michael M. Meijler, Tineke Lenstra, Amir Aharoni
Summary: The coexistence of DNA replication and transcription during S-phase requires tight coordination to prevent conflicts. This study developed a live-cell imaging approach to monitor the real-time progression of replisomes and transcription dynamics during a transcription-replication encounter. The findings showed a wave of partial transcriptional repression ahead of the moving replication fork, and revealed the negative impact of conflicts on both processes.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Chemistry, Multidisciplinary
Shaked Uzi-Gavrilov, Zohar Tik, Omer Sabti, Michael M. Meijler
Summary: Chemical communication between P. aeruginosa and S. aureus in biofilms of cystic fibrosis patients was found to promote cooperation, leading to increased disease severity and antibiotic resistance. Through metabolomics analysis and synthetic validation, it was discovered that S. aureus can convert pyochelin into a compound with reduced affinity for iron, allowing it to coexist more readily with P. aeruginosa and forming robust dual-species biofilms.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Multidisciplinary
Nadeem Alatawneh, Michael M. Meijler
Summary: Phenazines are secondary metabolites produced by bacteria that exhibit a wide range of activities against different species. In this study, the activity of phenazine-based natural products and their analogs on Gram-positive bacteria, such as Staphylococcus aureus, was investigated. Hydroxyl-containing phenazines with a 5,10-dioxide scaffold were found to strongly inhibit the growth of S. aureus. The chelation of essential metals, leading to nutrient deprivation, was identified as a significant contributor to the antibacterial activity of these phenazines.
ISRAEL JOURNAL OF CHEMISTRY
(2023)
Article
Ecology
Xiaoyu Shan, Akshit Goyal, Rachel Gregor, Otto X. Cordero
Summary: This study develops an unsupervised, annotation-free method that can identify microbial functional groups based on variation in microbiome data and environmental variables. The authors demonstrate its application in various datasets, including the Tara oceans microbiome and animal gut microbiomes. This work advances our understanding of structure-function relationships in complex microbiomes and provides an objective and systematic approach to discover functional groups.
NATURE ECOLOGY & EVOLUTION
(2023)
Article
Chemistry, Multidisciplinary
Alex Yashkin, Josep Rayo, Larson Grimm, Martin Welch, Michael M. Meijler
Summary: In recent years, there has been a troubling increase in antibiotic resistance among bacterial pathogens globally, highlighting the importance of understanding the mechanisms that pathogens use to survive in complex environments. The human pathogen Pseudomonas aeruginosa employs various small molecules to regulate quorum sensing, with N-butyryl-L-homoserine lactone playing a significant role in its virulence regulon. Through activity-based protein profiling, researchers have identified uncharacterized proteins in the P. aeruginosa QS network and uncovered a new role of this natural autoinducer in inhibiting pyocyanin production through its interaction with PhzB1/2.
Article
Biotechnology & Applied Microbiology
Alexander A. Aksenov, Ivan Laponogov, Zheng Zhang, Sophie L. F. Doran, Ilaria Belluomo, Dennis Veselkov, Wout Bittremieux, Louis Felix Nothias, Melissa Nothias-Esposito, Katherine N. Maloney, Biswapriya B. Misra, Alexey V. Melnik, Aleksandr Smirnov, Xiuxia Du, Kenneth L. Jones, Kathleen Dorrestein, Morgan Panitchpakdi, Madeleine Ernst, Justin J. J. van der Hooft, Mabel Gonzalez, Chiara Carazzone, Adolfo Amezquita, Chris Callewaert, James T. Morton, Robert A. Quinn, Amina Bouslimani, Andrea Albarracin Orio, Daniel Petras, Andrea M. Smania, Sneha P. Couvillion, Meagan C. Burnet, Carrie D. Nicora, Erika Zink, Thomas O. Metz, Viatcheslav Artaev, Elizabeth Humston-Fulmer, Rachel Gregor, Michael M. Meijler, Itzhak Mizrahi, Stav Eyal, Brooke Anderson, Rachel Dutton, Raphael Lugan, Pauline Le Boulch, Yann Guitton, Stephanie Prevost, Audrey Poirier, Gaud Dervilly, Bruno Le Bizec, Aaron Fait, Noga Sikron Persi, Chao Song, Kelem Gashu, Roxana Coras, Monica Guma, Julia Manasson, Jose U. Scher, Dinesh Kumar Barupal, Saleh Alseekh, Alisdair R. Fernie, Reza Mirnezami, Vasilis Vasiliou, Robin Schmid, Roman S. Borisov, Larisa N. Kulikova, Rob Knight, Mingxun Wang, George B. Hanna, Pieter C. Dorrestein, Kirill Veselkov
Summary: This study developed a machine learning approach that enables auto-deconvolution of gas chromatography-mass spectrometry data for the analysis and comparison of chemical compounds.
NATURE BIOTECHNOLOGY
(2021)
Review
Chemistry, Multidisciplinary
Yikuan Liu, Xiaona Liu, An Su, Chengtao Gong, Shenwei Chen, Liwei Xia, Chengwei Zhang, Xiaohuan Tao, Yue Li, Yonghe Li, Tulai Sun, Mengru Bu, Wei Shao, Jia Zhao, Xiaonian Li, Yongwu Peng, Peng Guo, Yu Han, Yihan Zhu
Summary: Covalent organic frameworks are crystalline porous materials with designable structures and functions, which can acquire multifunctionalities and have versatile applications in gas separation/storage, catalysis, and optoelectronic devices.
CHEMICAL SOCIETY REVIEWS
(2024)
Review
Chemistry, Multidisciplinary
Heyang Zhang, Jo Vandesompele, Kevin Braeckmans, Stefaan C. De Smedt, Katrien Remaut
Summary: Gene therapy has the potential to revolutionize the treatment of inherited and acquired diseases, but its success rate is currently limited. This review focuses on the obstacles faced by gene therapies in the human body, such as nucleic acid degradation by abundant nucleases, and discusses strategies to reduce degradation and methods to assess nucleic acid integrity.
CHEMICAL SOCIETY REVIEWS
(2024)
Review
Chemistry, Multidisciplinary
Chenxi Duan, Chunming Cui
Summary: Low valent group 14 compounds with diazaborolyl substituents exhibit unique structures and reactivity due to the combination of sigma-electron donation and steric hindrance. The modulation of the HOMO-LUMO gap by the diazaborolyl substituents results in novel reaction patterns in the activation of small molecules and inert chemical bonds.
CHEMICAL SOCIETY REVIEWS
(2024)
Review
Chemistry, Multidisciplinary
David E. Salazar Marcano, Nada D. Savic, Kilian Declerck, Shorok A. M. Abdelhameed, Tatjana N. Parac-Vogt
Summary: Metal-oxo clusters have great potential in various fields and can react with biomolecules, making them promising for applications in disease treatment and energy development. They can also be used in the development of inorganic drugs and bioanalytical tools.
CHEMICAL SOCIETY REVIEWS
(2024)
Review
Chemistry, Multidisciplinary
Lana K. Moree, Logan A. V. Faulkner, James D. Crowley
Summary: In this tutorial review, the general methods for synthesizing heterometallic metallosupramolecular architectures (MSAs), specifically heterometallic cages, are examined. The intrinsic properties and potential applications of these cages as host-guest systems and reaction catalysts are discussed.
CHEMICAL SOCIETY REVIEWS
(2024)
