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
Biotechnology & Applied Microbiology
Stephen Nayfach, Antonio Pedro Camargo, Frederik Schulz, Emiley Eloe-Fadrosh, Simon Roux, Nikos C. Kyrpides
Summary: CheckV is an automated pipeline for identifying closed viral genomes, estimating completeness of genome fragments, and removing host-related regions. By comparing sequences with a large database of complete viral genomes, CheckV assesses the quality of viral genomes assembled from metagenome data. Removing host contamination improves the accurate identification of auxiliary metabolic genes and interpretation of viral-encoded functions.
NATURE BIOTECHNOLOGY
(2021)
Article
Microbiology
Fadi G. Alnaji, William K. Reiser, Joel Rivera-Cardona, Aartjan J. W. te Velthuis, Christopher B. Brooke
Summary: Deletion-containing viral genomes (DelVGs) are commonly produced during influenza A virus infection, influenced by specific molecular mechanisms such as direct sequence repeats and base enrichment. DelVGs face a significant bottleneck during genome packaging, with larger DelVGs showing signs of enrichment in packaged virions, suggesting size as an important determinant of packaging efficiency.
Article
Cell Biology
Enrico Caragliano, Stefano Bonazza, Giada Frascaroli, Jiajia Tang, Timothy K. Soh, Kay Grunewald, Jens B. Bosse, Wolfram Brune
Summary: Human cytomegalovirus forms replication compartments in the host cell nucleus using liquid-liquid phase separation with specific proteins, ensuring efficient viral genome replication.
Article
Virology
Elizabeth T. Ogunbunmi, Aaron P. Roznowski, Bentley A. Fane
Summary: Most icosahedral viruses condense their genomes into volume-constrained capsids, but ssDNA viruses have specific genome biosynthesis and packaging mechanisms. The packaging of ssDNA genomes combines elements from both dsDNA and ssRNA systems, potentially affecting both packaging and postpackaging phenomena.
JOURNAL OF VIROLOGY
(2021)
Article
Biology
Jorge Miguel Silva, Diogo Pratas, Tania Caetano, Sergio Matos
Summary: This study provides a comprehensive understanding of the structure and complexity of viral genomes through the use of data compression and feature classification methods. By identifying redundant and complex groups within viral genomes and quantifying the abundance of inverted repeats, it is possible to accurately differentiate viral genomes at different taxonomic levels. Additionally, the use of complexity profiles allows for a direct analysis of the complexity of human herpesviruses.
Article
Virology
Tristan R. Grams, Terri G. Edwards, David C. Bloom
Summary: Herpes simplex virus 1 (HSV-1) utilizes a long noncoding RNA called the latency-associated transcript (LAT) to silence the virus in neurons. This study demonstrates that LAT binds both the cellular transmembrane protein 43 (TMEM43) and HSV-1 genomes in human neurons, resulting in the localization of the viral genomes to the nuclear periphery and repression of viral transcription. Additionally, TMEM43 appears to play a similar role in regulating cellular genes.
JOURNAL OF VIROLOGY
(2023)
Article
Microbiology
Joseph M. Dybas, Krystal K. Lum, Katarzyna Kulej, Emigdio D. Reyes, Richard Lauman, Matthew Charman, Caitlin E. Purman, Robert T. Steinbock, Nicholas Grams, Alexander M. Price, Lydia Mendoza, Benjamin A. Garcia, Matthew D. Weitzman
Summary: Viral infections cause extensive remodeling of the cellular proteome. This study developed a global proteomics approach to analyze changes in the host proteome during adenovirus serotype 5 (Ad5) virus infection. The results reveal cellular processes manipulated by viral products and host factors counteracted by early viral proteins during infection.
Article
Multidisciplinary Sciences
Joshua Pajak, Rockney Atz, Brendan J. Hilbert, Marc C. Morais, Brian A. Kelch, Paul J. Jardine, Gaurav Arya
Summary: Research has identified the crucial role of a glutamate-switch residue in coupling ATP binding to DNA gripping in viral packaging ATPases. Through molecular dynamics simulations and experimental validation, a signaling pathway mediated by the glutamate switch that regulates conformational transitions upon ATP hydrolysis has been revealed in the study.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Virology
Jaime Leonardo Moreno-Gallego, Alejandro Reyes
Summary: Viruses play a significant role in microbial ecosystems, and research on viral taxonomy has made progress through the identification of potential markers for studying viral genetic information. By studying and clustering common features of viral genes, a set of signature ViPhOGs has been established.
Article
Biochemistry & Molecular Biology
Vladimir R. Chechetkin, Vasily V. Lobzin
Summary: The study indicates that RNAPS in coronaviruses exhibit a quasi-periodic distribution in the genome, influenced by weakly specific interactions during evolution. Specific motifs are strongly correlated with packaging signals and highly conserved throughout lineages, making them promising therapeutic targets.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biology
Axel A. Guzman-Solis, Viridiana Villa-Islas, Miriam J. Bravo-Lopez, Marcela Sandoval-Velasco, Julie K. Wesp, Jorge A. Gomez-Valdes, Maria de la Luz Moreno-Cabrera, Alejandro Meraz, Gabriela Solis-Pichardo, Peter Schaaf, Benjamin R. TenOever, Daniel Blanco-Melo, Maria C. Avila Arcos
Summary: The introduction of new pathogens after European colonization led to a dramatic population decline of Indigenous inhabitants in the Americas. Research on ancient viruses from individuals buried during epidemics in Mexico City enriches the discussion on the etiology of infectious diseases during the Colonial period, providing direct molecular evidence of ancient viruses being transported to the Americas through the transatlantic slave trade.
Article
Veterinary Sciences
Aijun Sun, Shuaikang Yang, Jun Luo, Man Teng, Yijie Xu, Rui Wang, Xiaojing Zhu, Luping Zheng, Yanan Wu, Yongxiu Yao, Venugopal Nair, Gaiping Zhang, Guoqing Zhuang
Summary: The processing and packaging of herpesvirus genomic DNA are regulated by a packaging-associated terminase complex involving viral proteins pUL15, pUL28, and pUL33. Through the study on Marek's disease virus homologs UL28 and UL33, it was found that they are essential for MDV replication by regulating DNA cleavage and packaging. The restoration of replication ability in viruses recovered from the revertant construct or UL28 co-transfection suggests the crucial role of UL28 and UL33 in MDV replication.
VETERINARY RESEARCH
(2021)
Review
Cell Biology
Xuwen Li, Zijian Zhang, Xinlong Luo, Jacob Schrier, Andrew D. Yang, Tao P. Wu
Summary: N-6-methyladenine (N-6-mA, m(6)dA, or 6mA) is a prevalent DNA modification in prokaryotes and has been recently identified in higher eukaryotes, such as mammals. It can serve as an epigenetic mark and play critical roles in various biological processes, but the function and regulatory mechanism of 6mA in eukaryotes, especially mammals, are still poorly understood and require further research.
Article
Biochemistry & Molecular Biology
Kristopher Kieft, Alyssa Adams, Rauf Salamzade, Lindsay Kalan, Karthik Anantharaman
Summary: The researchers developed a software called vRhyme for constructing viral metagenome-assembled genomes (vMAGs). The software showed superior performance in constructing complete and uncontaminated vMAGs compared to existing tools. The application of vRhyme in human skin samples led to the identification of new viral genomes.
NUCLEIC ACIDS RESEARCH
(2022)
Meeting Abstract
Biophysics
Geoffrey C. Rollins, Justin L. MacCallum, Ken A. Dill
BIOPHYSICAL JOURNAL
(2010)
Meeting Abstract
Biophysics
Justin L. MacCallum, Geoffrey C. Rollins, Ken A. Dill
BIOPHYSICAL JOURNAL
(2010)
Meeting Abstract
Biophysics
Geoffrey Rollins, Ken Dill
BIOPHYSICAL JOURNAL
(2012)
Article
Biochemistry & Molecular Biology
Emma McCullagh, Justin Farlow, Christopher Fuller, Juliet Girard, Joanna Lipinski-Kruszka, Dan Lu, Thomas Noriega, Geoffrey Rollins, Russell Spitzer, Michael Todhunter, Hana El-Samad
NATURE CHEMICAL BIOLOGY
(2009)