Article
Virology
Chelsea T. Barrett, Hadley E. Neal, Kearstin Edmonds, J. Lizbeth Reyes Zamora, Carole L. Moncman, Andreea Popa, Everett Clinton Smith, Stacy R. Webb, Rebecca Ellis Dutch
Summary: Hendra virus uses two surface glycoproteins to infect host cells, with the TM region of the F protein playing a key role in stability and fusion. Mutations at residues M491 and L492 have been shown to alter F protein function, indicating their involvement in the fusion process.
Article
Virology
Caterynne Melo Kauffmann, Alessandra de Jesus Boari, Joao Marcos Fagundes Silva, Rosana Blawid, Tatsuya Nagata
Summary: A new sobemovirus, named mimosa mosaic virus (MimMV), was discovered and isolated from a mimosa plant using high-throughput sequencing. The genome sequence, confirmed by Sanger sequencing, consists of 4595 nucleotides. Phylogenetic analysis based on predicted amino acid sequences showed that MimMV shares 52.7% and 31.8% sequence identity with the P2b protein and coat protein of blueberry shoestring virus, respectively. The complete genome sequence of MimMV shares less than 47% identity with other sobemoviruses, suggesting that it belongs to a new species named Sobemovirus mimosae.
ARCHIVES OF VIROLOGY
(2023)
Article
Biochemistry & Molecular Biology
Junho Lee, Byeongho Moon, Dong Wook Lee, Inhwan Hwang
Summary: Protein biogenesis is a complex process in eukaryotic cells, and the targeting of proteins to different organelles involves organelle-specific import machinery and organelle-specific targeting signals. While the targeting of signal-anchored (SA) proteins to the endoplasmic reticulum (ER) is understood, the mechanisms for targeting SA proteins to mitochondria and chloroplasts are still unclear. This study investigated the targeting specificity of SA proteins for mitochondria and chloroplasts and found that multiple motifs surrounding and within the transmembrane domains (TMDs) play a role in mitochondrial targeting, whereas the absence of these motifs results in chloroplast targeting through a post-translational mechanism.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Nellt Frenkel, Felix Jonas, Miri Carmi, Gilad Yakaov, Naama Barkai
Summary: Deletion of the gene encoding the enzyme required for pre-replication H3 acetylation wave, Rtt109, leads to an increase in replication fork velocity. The study shows that Rtt109-dependent N-terminal acetylation regulates fork velocity, while K56 acetylation affects replication dynamics only when N-terminal acetylation is compromised. Acetylation of newly synthesized histones may slow replication by promoting replacement of nucleosomes evicted by the incoming fork, thus protecting genome integrity.
Article
Virology
Kevin W. Joseph, Elias K. Halvas, Leah D. Brandt, Sean C. Patro, Jason W. Rausch, Abha Chopra, Simon Mallal, Mary F. Kearney, John M. Coffin, John W. Mellors
Summary: This study presents an efficient method for amplifying and sequencing HIV-1 proviruses and their integration sites. Using this method, near-full-length proviruses and their 5'-host-virus junctions were amplified from individuals on ART, with 41.2% of amplifications yielding proviruses. The study also identified structural asymmetries between the long terminal repeats (LTRs) of proviruses, which has implications for the detection and quantification of proviruses. This method allows for a more accurate and comprehensive characterization of HIV-1 proviruses that persist on ART.
JOURNAL OF VIROLOGY
(2022)
Article
Biochemistry & Molecular Biology
Veronique Jonckheere, Petra Van Damme
Summary: The study identified a novel proteoform of the evolutionary conserved N-alpha acetyltransferase Naa40p, named Naa40p25, and revealed the differences in cellular localization, translation function, and protein interactions between this proteoform and the canonical Naa40(L) form; Additionally, two new Naa40p substrates were discovered, and Lge1 was confirmed as the first redundant substrate for yNatA and yNatD.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Infectious Diseases
Jonathan Daniel Ip, Kin-Hang Kok, Wan-Mui Chan, Allen Wing-Ho Chu, Wai-Lan Wu, Cyril Chik-Yan Yip, Wing-Kin To, Owen Tak-Yin Tsang, Wai-Shing Leung, Thomas Shiu-Hong Chik, Kwok-Hung Chan, Ivan Fan-Ngai Hung, Kwok-Yung Yuen, Kelvin Kai-Wang To
Summary: The study aimed to determine viral genome diversity in serial samples of COVID-19 patients by performing targeted deep sequencing of the spike gene using nanopore and Illumina sequencing. A patient with severe disease was found to have a spike protein amino acid mutation W152L, located within a neutralizing epitope. Monitoring of serial specimens is important in identifying hotspots of mutations, especially those occurring at neutralizing epitopes which may affect therapeutic efficacy of monoclonal antibodies.
CLINICAL MICROBIOLOGY AND INFECTION
(2021)
Article
Biochemistry & Molecular Biology
Wentian Luo, Alison B. Hickman, Pavol Genzor, Rodolfo Ghirlando, Christopher M. Furman, Anna Menshikh, Astrid Haase, Fred Dyda, Matthew H. Wilson
Summary: This study reveals the regulation and structural features of the piggyBac transposon system in mammalian cells using biochemical and cell-based assays, AlphaFold modeling, and protein redesign. The study demonstrates that phosphorylation of the transposase N-terminus and the need for asymmetric transposon ends negatively regulate piggyBac transposition. These findings expand the potential use of piggyBac transposase for genomic applications.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Agriculture, Multidisciplinary
Hideyuki Suzuki, Asuka Sasabu
Summary: Although the purified Escherichia coli gamma-glutamyltranspeptidase exhibits higher transpeptidation activity than hydrolysis activity, most of the gamma-glutamyltranspeptidase activity in vivo is hydrolysis activity when measured using whole cells. By employing specific anchor proteins, E. coli cells were able to express gamma-glutamyltranspeptidase on the extracellular surface, resulting in higher transpeptidation activity compared to hydrolysis activity in the presence of NaCl. These cells were also used successfully to produce a kokumi compound, gamma-Glu-Val-Gly.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Editorial Material
Cell Biology
Lan Jiang, Tianyun Shen, Xinyuan Wang, Lunzhi Dai, Kefeng Lu, Huihui Li
Summary: Posttranslational modification plays a crucial role in regulating protein functions. The functions and mechanisms of N-terminal acetylation, which occurs on the first amino acids of proteins, in the field of macroautophagy/autophagy are not well understood. Recent studies have shown that the N-terminal acetyltransferase NatB is essential for autophagy and it modifies actin cytoskeleton constituent Act1 and dynamin-like GTPase Vps1, promoting the formation and fusion of autophagosomes.
Article
Cell Biology
Emilie Ma, Laurent Maloisel, Lea Le Falher, Raphael Guerois, Eric Coic
Summary: Rad52 SUMOylation or mutations disrupting the Rad52-Rad51 interaction can suppress Rad51 filament toxicity, while mutations in the Rad52 N-terminal domain can also reduce DNA damage sensitivity of Srs2-deficient cells. These mutations affect the Rad52 oligomeric ring structure and play a crucial role in protecting Rad51 filaments from Srs2, but they may also increase Rad51 filament stability and toxicity in Srs2-deficient cells. The stabilization function of Rad52 ring structure is distinct from its mediator and annealing activities.
Article
Multidisciplinary Sciences
Mark L. Blaxter
Summary: The Earth Biogenome Project aims to sequence the genomes of all eukaryotic life on earth, and the Darwin Tree of Life Project focuses on delivering high-quality genome sequences for the British and Irish islands. The collaboration between biodiversity organizations and genomics institutes has established a workflow that collects specimens, performs sequencing, generates curated assemblies, and openly releases the data for global use in future scientific and conservation efforts.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Biochemical Research Methods
Dohun Yi, Jin-Wu Nam, Hyobin Jeong
Summary: Structural variants (SVs) are diverse genomic rearrangements that accumulate in the genome during cell development and aging, potentially impacting cancer development. Detecting somatic SVs is challenging but crucial for understanding their functional implications. This review summarizes recent advances in whole-genome sequencing (WGS)-based approaches for somatic SV detection, including computational algorithms for bulk WGS data and cutting-edge single-cell techniques. The advantages and limitations of bulk and single-cell approaches are discussed, along with their potential for linking somatic SVs to functional readouts.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Charlotte L. Frankling, Megan F. Downes, Angray S. Kang, Ewan R. G. Main
Summary: Many gram-negative bacteria use a protein nanomachine called the Type Three Secretion System (T3SS) to infect. This system transports bacterial toxins using a proteinaceous channel that links the bacteria and host cell. In this study, the specificity of the binding interfaces of the translocator-chaperone complexes from Pseudomonas aeruginosa was investigated.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Biochemical Research Methods
Zhenmiao Zhang, Chao Yang, Werner Pieter Veldsman, Xiaodong Fang, Lu Zhang
Summary: This paper comprehensively evaluates 19 commonly used assembly tools on metagenomic sequencing datasets from simulation, mock communities, and human gut microbiomes. It finds that long-read assemblers generate high contig contiguity but fail to reveal some medium- and high-quality metagenome-assembled genomes (MAGs). Linked-read assemblers obtain the highest number of overall near-complete MAGs from the human gut microbiomes. Hybrid assemblers using both short- and long-read sequencing are promising methods to improve both total assembly length and the number of near-complete MAGs. The paper also discusses the running time and memory consumption of these assembly tools and provides practical guidance for selecting them.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Virology
Merike Somera, Erkki Truve
ARCHIVES OF VIROLOGY
(2015)
Review
Virology
Merike Somera, Cecilia Sarmiento, Erkki Truve
News Item
Plant Sciences
M. Somera, M. Gantsovski, E. Truve, P. Soovali
Article
Virology
Grete Nummert, Merike Somera, Gabriela Uffert, Erik Abner, Erkki Truve
News Item
Plant Sciences
M. Somera, E. Truve, P. Soovali
Article
Plant Sciences
Merike Somera, Anders Kvarnheden, Cecile Desbiez, Dag-Ragnar Blystad, Pille Soovali, Jiban Kumar Kundu, Mark Gantsovski, Jim Nygren, Herve Lecoq, Eric Verdin, Carl Spetz, Lucie Tamisier, Erkki Truve, Swbastien Massart
Article
Microbiology
Merike Somera, Sebastien Massart, Lucie Tamisier, Pille Soovali, Kanitha Sathees, Anders Kvarnheden
Summary: The study used high-throughput sequencing to survey different species of barley and cereal yellow dwarf viruses in Estonian cereal fields, revealing a new BYDV-OYV species closely related to BYDV-PAV-CN. By analyzing complete genome sequences, the study found genetic relationships between BYDV-OYV and BYDV-PAV-CN, both meeting the species criteria of the Luteovirus genus. Update of diagnostic primers based on genomic information is essential for accurate detection and surveillance of YDVs.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Merike Somera, Denis Fargette, Eugenie Hebrard, Cecilia Sarmiento
Summary: The family Solemoviridae consists of viruses with icosahedral particles, a genome of 4-6 kb positive- sense, monopartite, polycistronic RNA, and a narrow host range. Transmission methods vary among different genera within the family.
JOURNAL OF GENERAL VIROLOGY
(2021)
Correction
Microbiology
Merike Somera, Sebastien Massart, Lucie Tamisier, Pille Soovali, Kanitha Sathees, Anders Kvarnheden
FRONTIERS IN MICROBIOLOGY
(2021)
Review
Genetics & Heredity
Francesco Guarino, Angela Cicatelli, Stefano Castiglione, Dolores R. Agius, Gul Ebru Orhun, Sotirios Fragkostefanakis, Julie Leclercq, Judit Dobranszki, Eirini Kaiserli, Michal Lieberman-Lazarovich, Merike Somera, Cecilia Sarmiento, Cristina Vettori, Donatella Paffetti, Anna M. G. Poma, Panagiotis N. Moschou, Mateo Gasparovic, Sanaz Yousefi, Chiara Vergata, Margot M. J. Berger, Philippe Gallusci, Dragana Miladinovic, Federico Martinelli
Summary: Crop adaptation to climate change is influenced by epigenetic mechanisms, which are still poorly understood in non-model plants. This review summarizes the recent findings on crop epigenetic responses to climate change and presents a speculative viewpoint on the underlying epigenetic mechanisms. Understanding these mechanisms will facilitate the design and cultivation of crop varieties with diverse tolerance/resistance to stresses.
FRONTIERS IN GENETICS
(2022)
Review
Plant Sciences
Ferenz Sustek-Sanchez, Odd Arne Rognli, Nils Rostoks, Merike Somera, Kristina Jaskune, Mallikarjuna Rao Kovi, Grazina Statkeviciute, Cecilia Sarmiento
Summary: To meet the growing demand for food and adapt to climate change, there is a need for high-yielding crops that can withstand abiotic stresses. Genome editing, particularly using the CRISPR-Cas system, has shown promise in developing stress-resistant plants. This review focuses on the application of genome editing in improving forage grasses' resilience to drought, salt, heat, and cold stresses.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Virology
Martin Frei, Cecilia Sarmiento, Kairi Kaerblane, Annette Niehl, Merike Somera
Summary: In this study, we sequenced four historical isolates of CnMoV from different hosts and locations. The CnMoV genome ranged from 4417 to 4419 nt and encoded five ORFs. Phylogenetic analysis showed that CnMoV belongs to the Sobemovirus genus. We found high similarity in nucleotide and amino acid sequences among the sequenced CnMoV isolates. Amino acid changes in the coat protein were associated with serological differences.
ARCHIVES OF VIROLOGY
(2023)
Article
Virology
A. Shchetynina, I. Budzanivska, O. Pereboychuk, M. Somera, E. Truve
Article
Virology
Merike Somera, Erkki Truve
ARCHIVES OF VIROLOGY
(2017)
