Article
Multidisciplinary Sciences
Filip Mihalic, Leandro Simonetti, Girolamo Giudice, Marie Rubin Sander, Richard Lindqvist, Marie Berit Akpiroro Peters, Caroline Benz, Eszter Kassa, Dilip Badgujar, Raviteja Inturi, Muhammad Ali, Izabella Krystkowiak, Ahmed Sayadi, Eva Andersson, Hanna Aronsson, Ola Soderberg, Doreen Dobritzsch, Evangelia Petsalaki, Anna K. Overby, Per Jemth, Norman E. Davey, Ylva Ivarsson
Summary: Viruses hijack and deregulate cellular functions by mimicking host short linear motifs (SLiMs). In this study, a pan-viral approach is used to discover 1712 SLiM-based virus-host interactions, revealing novel host proteins hijacked by viruses and cellular pathways frequently deregulated. Furthermore, structural and biophysical analyses demonstrate that viral mimicry-based interactions have similar properties to endogenous interactions. The discovery of polyadenylate-binding protein 1 as a potential antiviral target highlights the therapeutic potential of this research in combating epidemics and pandemics.
NATURE COMMUNICATIONS
(2023)
Article
Microbiology
Ann-Katrin Llarena, Marina Aspholm, Kristin O'Sullivan, Grzegorz Wegrzyn, Toril Lindback
Summary: This study investigates a novel type of Eru-phages lacking the traditional replication genes O and P found in Stx phages. It reveals that Eru1-phages carried by highly pathogenic EHEC strains exhibit a less stable lysogenic state compared to classical Stx phages, indicating a potential association with a high-virulence phenotype in host EHEC strains.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Chuqing Sun, Jingchao Chen, Menglu Jin, Xueyang Zhao, Yun Li, Yanqi Dong, Na Gao, Zhi Liu, Peer Bork, Xing-Ming Zhao, Wei-Hua Chen
Summary: In this study, DNA methylation patterns in 8848 high-quality phages from 104 fecal samples were analyzed using single-molecule real-time sequencing. The results show that 97.60% of gut phages exhibit methylation, and certain factors correlate with methylation densities. Phages with higher methylation densities have potential viability advantages. More than one-third of the phages possess their own DNA methyltransferases (MTases), and increased MTase copies are associated with higher genome methylation densities and specific methylation motifs. These findings indicate the widespread utilization of DNA methylation by gut DNA phages as an evasion mechanism against host defense systems.
Article
Genetics & Heredity
Hannah Strobel, Elijah Horwitz, Justin Meyer
Summary: The relationship between stability and evolvability of viruses is more complex than previously thought. Destabilized variants are more likely to evolve the necessary mutations to use a new receptor, while excessively unstable variants lose all function. These findings provide evidence for a new molecular model of host-range expansion evolution and suggest instability as a potential predictor of viral host-range evolution.
Article
Microbiology
Samuel J. Magaziner, George P. C. Salmond
Summary: Widespread multidrug antimicrobial resistance has led to a renewed interest in phage therapy. However, the narrow host range and unintended effects of phages on host physiology and pathogen evolution limit their deployment. This study identifies a novel RBP family related to known RBPs of T4 and lambda, with potential for use in synthetic strategies to expand therapeutic phage host ranges.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Luca Barberi, Francoise Livolant, Amelie Leforestier, Martin Lenz
Summary: DNA is tightly packed and curved due to polyvalent cations inducing an effective attraction. Using cryo electron microscopy, the interaction between highly curved helices was studied, revealing the dependence of helix spacing in DNA toroidal condensates on their location within the torus. This sheds light on the characteristics of the interaction potential and the softness of the interaction compared to previous bulk samples.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Soil Science
Nakul Dar, Charleton P. P. Thompson, Kurt Williamson
Summary: Despite limited knowledge about viruses in soil, this study utilized marker genes to investigate the genetic diversity of viruses in 42 soil samples. The results suggest that geographic distance may be more important than environmental source in explaining sequence-based differences across samples.
BIOLOGY AND FERTILITY OF SOILS
(2023)
Article
Multidisciplinary Sciences
Maria Cebria-Mendoza, Cristina Arbona, Luis Larrea, Wladimiro Diaz, Vicente Arnau, Carlos Pena, Juan Vicente Bou, Rafael Sanjuan, Jose M. Cuevas
Summary: Human blood metagenomics has revealed the presence of different types of viruses, with anelloviruses being the most frequently found family. A study in Spain confirmed the extensive presence of anelloviruses in blood samples, with nearly 97% of the viral sequence reads belonging to this family. Genomic analysis identified diverse anellovirus strains and suggested potential novel species, challenging the previously suggested pathological role of anelloviruses.
SCIENTIFIC REPORTS
(2021)
Article
Microbiology
George Muscatt, Ryan Cook, Andrew Millard, Gary D. Bending, Eleanor Jameson
Summary: Soil microbes and viruses interact in playing crucial roles in the global carbon cycling. In this study, a publicly available metagenomic data set was used to investigate the interactions between viruses and their hosts in soil depth intervals. Contrary to previous assumptions, viruses were found to infect dominant soil hosts rather than being predominantly lysogenic. Additionally, evidence was provided for the potential of soil viruses to enhance the remineralization of soil carbon. This research emphasizes the need for further exploration of subsurface viral communities to improve our understanding of soil viral functions.
Article
Biotechnology & Applied Microbiology
Konrad Sachse, Martin Hoelzer, Fabien Vorimore, Lisa-Marie Barf, Carsten Sachse, Karine Laroucau, Manja Marz, Kevin Lamkiewicz
Summary: This study analyzed the whole-genome sequences of 61 C.psittaci strains and found genetic markers associated with host tropism. Four major clades were identified within the species, with the first clade mainly composed of psittacine and human isolates, and strains from different non-psittacine hosts clustering in other clades. The study also revealed that sequence variation in the major outer membrane porin MOMP can lead to structural changes in immunogenic domains, and host change is associated with loss of genes in the plasticity zone. Overall, the genomic divergence of C.psittaci strains is correlated with host preference and includes gene deletions, structural variations, and different repertoires of virulence factors in the plasticity zone.
Article
Multidisciplinary Sciences
Thomas Kruse, Caroline Benz, Dimitriya H. Garvanska, Richard Lindqvist, Filip Mihalic, Fabian Coscia, Raviteja Inturi, Ahmed Sayadi, Leandro Simonetti, Emma Nilsson, Muhammad Ali, Johanna Kliche, Ainhoa Moliner Morro, Andreas Mund, Eva Andersson, Gerald McInerney, Matthias Mann, Per Jemth, Norman E. Davey, Anna K. Overby, Jakob Nilsson, Ylva Ivarsson
Summary: The study identified 269 peptide-based interactions for 18 coronaviruses, highlighting the importance of short peptide interaction motifs in viral hijacking of host proteins. The specific interaction between SARS-CoV-2 N protein and human G3BP1/2 proteins was found to disrupt stress granules, with implications for the development of novel antiviral reagents. The results demonstrate the potential of peptide inhibitors to specifically target viral-host interactions for combating SARS-CoV-2 infection.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Suzette N. Palmer, Sruthi Chappidi, Chelsea Pinkham, Dustin C. Hancks
Summary: Research suggests that RIPK3 and MLKL show strong positive selection in primates and bats, possibly as a response to various pathogen-encoded inhibitors. The evolution of poxviral MLKL genes is characterized by gene replacements mediated by duplication and deletion events. MLKL protein expression is stimulated by interferons in human and mouse cells.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Microbiology
Stefanie Widder, Irene Goerzer, Benjamin Friedel, Nina Rahimi, Stefan Schwarz, Peter Jaksch, Sylvia Knapp, Elisabeth Puchhammer-Stoeckl
Summary: This study provides a detailed analysis of virome dynamics after lung transplantation, revealing host, body compartment, and time-specific dependency patterns among viruses. The results also suggest genetic adaptation to the host microenvironment at the level of the virome and support the hypothesis of functional complementarity between Anellovirus groups and other persistent viruses.
Article
Biochemistry & Molecular Biology
Jianli Cao, Gang Lu, Lei Wen, Peng Luo, Yaoqiang Huang, Ronghui Liang, Kaiming Tang, Zhenzhi Qin, Chris Chun-Yiu Chan, Kenn Ka-Heng Chik, Jiang Du, Feifei Yin, Zi-Wei Ye, Hin Chu, Dong-Yan Jin, Kwok-Yung Yuen, Jasper Fuk-Woo Chan, Shuofeng Yuan
Summary: The study characterized the interaction between SFTSV and host proteins, identified drug compounds that could potentially inhibit SFTSV infection, with artenimol and omacetaxine mepesuccinate showing in vitro antiviral activity.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Microbiology
Maikke B. Ohlson, Jennifer L. Eitson, Alexandra I. Wells, Ashwani Kumar, Seoyeon Jang, Chunyang Ni, Chao Xing, Michael Buszczak, John W. Schoggins
Summary: Viruses rely on host ribosomes for protein synthesis, but the specific factors involved in translation of viral RNAs are not fully understood. Through a CRISPR screen, researchers identified multiple host factors, including 60S ribosome biogenesis proteins, that are required for viral protein synthesis. In addition, the study revealed the importance of SBDS and SPATA5 in viral replication for a wide range of viruses.
Article
Cell Biology
Miriam V. Gutschow, John C. Mason, Keara M. Lane, Inbal Maayan, Jacob J. Hughey, Bryce T. Bajar, Debha N. Amatya, Sean D. Valle, Markus W. Covert
MOLECULAR BIOLOGY OF THE CELL
(2019)
Meeting Abstract
Biophysics
Markus Covert
BIOPHYSICAL JOURNAL
(2019)
Article
Biochemistry & Molecular Biology
Keara Lane, Marta Andres-Terre, Takamasa Kudo, Denise M. Monack, Markus W. Covert
Article
Biology
Hee Won Yang, Steven D. Cappell, Ariel Jaimovich, Chad Liu, Mingyu Chung, Leighton H. Daigh, Lindsey R. Pack, Yilin Fan, Sergi Regot, Markus Covert, Tobias Meyer
Article
Biochemistry & Molecular Biology
Katie Bodner, Arin L. Melkonian, Angela I. M. Barth, Takamasa Kudo, Yu Tanouchi, Markus W. Covert
Review
Biochemistry & Molecular Biology
Katie Bodner, Arin L. Melkonian, Markus W. Covert
Summary: Bacteriophages play a crucial role in human health by altering the severity of bacterial infections, and recent studies have uncovered their ability to modulate the physiology of mammalian cells. Understanding the interactions between phages and mammalian cells has important implications for phage therapy.
TRENDS IN MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Markus W. Covert, Taryn E. Gillies, Takamasa Kudo, Eran Agmon
Summary: Quantitative systems biology is at a turning point, with the potential to have a global impact in biological research and applications. Drawing lessons from meteorology, there is an opportunity to forecast the next steps and achieve similar global influence in the field through mathematical modeling.
Article
Biochemical Research Methods
Eran Agmon, Ryan K. Spangler, Christopher J. Skalnik, William Poole, Shayn M. Peirce, Jerry H. Morrison, Markus W. Covert
Summary: Vivarium is a software tool for building integrative multiscale models, providing an interface that allows computational biologists to easily define mechanistic models and combine them as an integrated multiscale model. It streamlines the integrative modeling effort by making individual models into modules that can be wired together and run with Vivarium's discrete-event simulation engine. This tool has been demonstrated to successfully build composite models that combine various modeling frameworks, and it has the potential to support future efforts in integrating more types of models at different biological scales.
Article
Biochemistry & Molecular Biology
Martina Maritan, Ludovic Autin, Jonathan Karr, Markus W. Covert, Arthur J. Olson, David S. Goodsell
Summary: Building structural models of entire cells presents a challenge that requires integration of multiple sources of biological data and enhanced computational modeling methods. The study presents 3D structural models of an entire Mycoplasma genitalium cell, combining experimental and homology-modeled structures to provide a structural representation for all proteins, DNA, and RNA molecules. The models establish a framework for further research and exploration of mesoscale properties, highlighting the importance of data gathering methodologies.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Takamasa Kudo, Keara Lane, Markus W. Covert
Summary: By integrating live-cell imaging with pooled library-based screening, we developed a method that enables intracellular multiplexing and allows for long-term observation and analysis of phenotypes of interest, directly connecting behavior to the cellular genotype.
Article
Mathematical & Computational Biology
Travis A. Ahn-Horst, Luis Santiago Mille, Gwanggyu Sun, Jerry H. Morrison, Markus W. Covert
Summary: Growth and environmental responses are crucial for organisms' survival and adaptation. A study on a whole-cell model of E. coli found that small molecule feedback inhibition pathways and dysregulated amino acid synthesis pathways play important roles in growth regulation and concentration fluctuations at the single-cell level, respectively.
NPJ SYSTEMS BIOLOGY AND APPLICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Heejo Choi, Markus W. Covert
Summary: In this study, a whole-cell model was used to investigate the inconsistencies between in vitro tRNA aminoacylation measurements and in vivo protein synthesis demands in E. coli. The results showed that kinetic measurements of aminoacyl-tRNA synthetase were insufficient for cellular proteome maintenance, leading to significant impacts on cellular phenotypes. This study deepens our understanding of translation in an in vivo context.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemical Research Methods
Christopher K. Skalnik, Sean Cheah, Mica H. Yang, Mattheus M. Wolff, Ryan Spangler, Lee W. Talman, Jerry Morrison, Shayn Peirce, Eran Agmon, Markus Covert
Summary: This study used a detailed mathematical model of individual Escherichia coli cells to investigate their response to different antibiotics, taking into account cell-to-cell variations in gene and protein expression. The research is important for understanding the development of antibiotic resistance and developing new mechanistic models.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Biochemical Research Methods
Katie Bodner, Arin L. Melkonian, Markus W. Covert
Article
Multidisciplinary Sciences
Derek N. Macklin, Travis A. Ahn-Horst, Heejo Choi, Nicholas A. Ruggero, Javier Carrera, John C. Mason, Gwanggyu Sun, Eran Agmon, Mialy M. DeFelice, Inbal Maayan, Keara Lane, Ryan K. Spangler, Taryn E. Gillies, Morgan L. Paull, Sajia Akhter, Samuel R. Bray, Daniel S. Weaver, Ingrid M. Keseler, Peter D. Karp, Jerry H. Morrison, Markus W. Covert