Article
Biochemistry & Molecular Biology
Takahito Mukai
Summary: The study analyzed the SelB genes of Rhizobiales species and found overlapping tRNA(Sec) sequences in some Alphaproteobacteria and Sinorhizobium meliloti SelB genes. It was hypothesized that once the tRNA(Sec) is processed, the expression of full-length SelB may be repressed. This is the first report of a nested tRNA gene within a protein ORF in bacteria.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Virology
Hugo de Paula Oliveira, Ethiane R. dos Santos, Robert L. Harrison, Bergmann Morais Ribeiro, Daniel M. P. Ardisson-Araujo
Summary: In this study, a large-scale in silico search was conducted to identify putative tRNA genes in baculovirus genomes. The analysis revealed diverse tRNA genes with variations in structure, location, and anti-codon identity. Some genes showed a bias for the codons specified by the tRNAs present in their genomes. Additionally, evidence of transcription and modification of viral tRNA genes was found through analysis of small RNA deep sequencing data. Further research is required to understand the expression and functionality of these viral tRNAs.
Article
Genetics & Heredity
Takahito Mukai, Kazuaki Amikura, Xian Fu, Dieter Soell, Ana Crnkovic
Summary: This study provides a comprehensive bioinformatic analysis of the diversity of indirect cysteine encoding systems. The results shed new light on the variations in SepRS and SepCysS enzymes, adaptation to lifestyle and habitat, and provide new information on the evolution of the genetic code.
FRONTIERS IN GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Navid Ahmadinejad, Shayna Troftgruben, Junwen Wang, Pramod B. Chandrashekar, Valentin Dinu, Carlo Maley, Li Liu
Summary: Understanding intratumor heterogeneity is crucial for studying tumorigenesis and designing personalized treatments. This study presents a novel algorithm, MAGOS, that successfully identifies subclones in tumors sequenced at low depths and outperforms existing methods in terms of decomposition accuracy, minimum sequencing depth, and computation efficiency. The analysis of late-stage liver cancers using MAGOS revealed that a high subclone count in a tumor is a significant risk factor for poor prognosis.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Review
Biochemical Research Methods
Zhaoqian Liu, Jingtong Feng, Bin Yu, Qin Ma, Bingqiang Liu
Summary: Bacterial genomes are recognized to closely interact with cellular processes. Researchers focus on uncovering organizational mechanisms of bacterial genomes to reveal potential cellular activities. Advances in experimental techniques and computational models provide opportunities for understanding these mechanisms, including local structures such as operons/transcription units and global constraints shaping bacterial genomes.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Xiao-Dong Xu, Jia-Yin Guan, Zi-Yi Zhang, Yu-Rou Cao, Kenneth B. Storey, Dan-Na Yu, Jia-Yong Zhang
Summary: Gene rearrangements have been discovered in several mantodea mitochondrial genomes, primarily concentrated in the region of CR-I-Q-M-ND2. These rearrangements may serve as shared characteristics for different groups within the Mantidae family.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Review
Oncology
Stephen L. DeAngelo, Balazs Gyorffy, Markos Koutmos, Yatrik M. Shah
Summary: This article reviews the biological function of selenium and highlights the role of selenoproteins in cellular antioxidant capacity. It also emphasizes the potential of targeting selenoproteins and the biogenesis of selenocysteine for therapeutic intervention in cancer.
Review
Plant Sciences
Yong Feng, Mengyun Jiang, Weichang Yu, Jiannan Zhou
Summary: The increasing recognition of the roles of short/small open reading frames (sORFs) in recent years is attributed to the development and application of the Ribo-Seq technique, which allows for the identification of sORFs in various organisms. However, caution should be exercised when using RPFs to identify sORFs in plants, particularly for polyploidy species, due to the small size and complexity of the plant genome. This study compares different approaches to the identification of plant sORFs, discusses their advantages and disadvantages, and provides a guide for researchers in choosing the appropriate method for plant sORF studies.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Gyuhyeok Cho, Jangmin Lee, Jungwook Kim
Summary: The uridine at the 34th position of tRNA can be modified to affect decoding properties during translation. MnmC enzyme in bacteria like Escherichia coli converts cmnm(5)(s(2))U to mnm(5)(s(2))U, while MnmM enzyme in Bacillus subtilis converts nm(5)(s(2))U to mnm(5)(s(2))U.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Chemistry, Multidisciplinary
Rebecca Notis Dardashti, Shay Laps, Jacob S. Gichtin, Norman Metanis
Summary: Human selenoprotein H, the only selenocysteine-containing protein located in the cell's nucleolus, is suggested to be involved in DNA binding, reactive oxygen species consumption, and cancer prevention. In this study, a semi-synthetic approach was used to obtain a mutated selenoprotein H and it was demonstrated to have sub-micromolar affinity for DNA binding using biolayer interferometry. The developed semi-synthetic approach can be applied for producing biologically and therapeutically relevant proteins.
Article
Biochemistry & Molecular Biology
Fatemeh Sharifi, Yuzhen Ye
Summary: Reverse transcriptases (RTs) play various roles in different systems in prokaryotes, but there is a lack of computational tools for their identification and characterization. Researchers developed a tool called myRT to identify and classify prokaryotic RTs, providing genomic neighborhood information.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biology
Zijun Xiong, Ding He, Xuanming Guang, Qiye Li
Summary: This study presents the complete mitochondrial genomes of three Poneroid ants and reveals novel gene rearrangements. It also reports the duplication of tRNA genes for the first time in Formicidae. Phylogenetic analyses support the monophyly of the Poneroid clade and the sister group relationship between the subfamilies Paraponerinae and Amblyoponinae.
Article
Biochemistry & Molecular Biology
Leighton J. Payne, Sean Meaden, Mario R. Mestre, Chris Palmer, Nicolas Toro, Peter C. Fineran, Simon A. Jackson
Summary: Most bacteria and archaea possess multiple antiviral defence systems, and the PADLOC web server provides a convenient resource for analyzing and detecting these systems.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biotechnology & Applied Microbiology
T. Jeffrey Cole, Jennifer K. Parker, Aaron L. Feller, Claus O. Wilke, Bryan W. Davies
Summary: Class II microcins are small bacteriocins produced by Gram-negative bacteria in the Enterobacteriaceae, playing a role in interbacterial competition. Despite limited direct evidence, they show a diverse array of molecular functionalities and target specificities, suggesting untapped potential for discovering peptide antibiotics.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Plant Sciences
Zhenjun Li, Yongsheng Tian, Bo Wang, Rihe Peng, Jing Xu, Xiaoyan Fu, Hongjuan Han, Lijuan Wang, Wenhui Zhang, Yongdong Deng, Yu Wang, Zehao Gong, Jianjie Gao, Quanhong Yao
Summary: This study successfully redirected selenium flow in rice by overexpressing the genes encoding selenocysteine lyase and selenocysteine methyltransferase. Transgenic plants showed lower sensitivity to selenium stress and increased tolerance to selenate and selenite, as well as improved selenium elimination capabilities. These findings suggest that genetically modified plants have the potential to restore selenium-contaminated environments.
JOURNAL OF PLANT PHYSIOLOGY
(2022)
Article
Multidisciplinary Sciences
Francois Aguet, Alvaro N. Barbeira, Rodrigo Bonazzola, Andrew Brown, Stephane E. Castel, Brian Jo, Silva Kasela, Sarah Kim-Hellmuth, Yanyu Liang, Princy Parsana, Elise Flynn, Laure Fresard, Eric R. Gamazon, Andrew R. Hamel, Yuan He, Farhad Hormozdiari, Pejman Mohammadi, Manuel Munoz-Aguirre, Kristin G. Ardlie, Alexis Battle, Rodrigo Bonazzola, Christopher D. Brown, Nancy Cox, Emmanouil T. Dermitzakis, Barbara E. Engelhardt, Diego Garrido-Martin, Nicole R. Gay, Gad Getz, Roderic Guigo, Andrew R. Hamel, Robert E. Handsaker, Yuan He, Paul J. Hoffman, Farhad Hormozdiari, Hae Kyung Im, Brian Jo, Silva Kasela, Seva Kashin, Sarah Kim-Hellmuth, Alan Kwong, Tuuli Lappalainen, Xiao Li, Yanyu Liang, Daniel G. MacArthur, Pejman Mohammadi, Stephen B. Montgomery, Manuel Munoz-Aguirre, John M. Rouhana, Farhad Hormozdiari, Hae Kyung Im, Sarah Kim-Hellmuth, Kristin G. Ardlie, Gad Getz, Roderic Guigo, Hae Kyung Im, Tuuli Lappalainen, Stephen B. Montgomery, Hae Kyung Im, Tuuli Lappalainen, Tuuli Lappalainen, Shankara Anand, Stacey Gabriel, Gad Getz, Aaron Graubert, Kane Hadley, Robert E. Handsaker, Katherine H. Huang, Seva Kashin, Xiao Li, Daniel G. MacArthur, Samuel R. Meier, Jared L. Nedzel, Brunilda Balliu, Don Conrad, Daniel J. Cotter, Sayantan Das, Olivia M. de Goede, Eleazar Eskin, Tiffany Y. Eulalio, Nicole M. Ferraro, Diego Garrido-Martin, Nicole R. Gay, Gad Getz, Aaron Graubert, Roderic Guigo, Kane Hadley, Andrew R. Hamel, Robert E. Handsaker, Yuan He, Paul J. Hoffman, Farhad Hormozdiari, Lei Hou, Katherine H. Huang, Hae Kyung Im, Brian Jo, Silva Kasela, Seva Kashin, Manolis Kellis, Sarah Kim-Hellmuth, Alan Kwong, Tuuli Lappalainen, Xiao Li, Xin Li, Yanyu Liang, Daniel G. MacArthur, Serghei Mangul, Samuel R. Meier, Pejman Mohammadi, Stephen B. Montgomery, Manuel Munoz-Aguirre, Daniel C. Nachun, Jared L. Nedzel, Duyen Y. Nguyen, Andrew B. Nobel, YoSon Park, Ferran Reverter, Chiara Sabatti, Ashis Saha, Ayellet Segre, Matthew Stephens, Benjamin J. Strober, Nicole A. Teran, Ellen Todres, Ana Vinuela, Gao Wang, Xiaoquan Wen, Fred Wright, Valentin Wucher, Yuxin Zou, Pedro G. Ferreira, Gen Li, Marta Mele, Esti Yeger-Lotem, Mary E. Barcus, Debra Bradbury, Tanya Krubit, Jeffrey A. McLean, Liqun Qi, Karna Robinson, Nancy Roche, Anna M. Smith, David E. Tabor, Anita Undale, Jason Bridge, Lori E. Brigham, Barbara A. Foster, Bryan M. Gillard, Richard Hasz, Marcus Hunter, Christopher Johns, Mark Johnson, Ellen Karasik, Gene Kopen, William F. Leinweber, Alisa McDonald, Michael T. Moser, Kevin Myer, Kimberley D. Ramsey, Brian Roe, Saboor Shad, Jeffrey A. Thomas, Gary Walters, Michael Washington, Joseph Wheeler, Scott D. Jewell, Daniel C. Rohrer, Dana R. Valley, David A. Davis, Deborah C. Mash, Philip A. Branton, Leslie Sobin, Laura K. Barker, Heather M. Gardiner, Maghboeba Mosavel, Laura A. Siminoff, Paul Flicek, Maximilian Haeussler, Thomas Juettemann, W. James Kent, Christopher M. Lee, Conner C. Powell, Kate R. Rosenbloom, Magali Ruffier, Dan Sheppard, Kieron Taylor, Stephen J. Trevanion, Daniel R. Zerbino, Nathan S. Abell, Joshua Akey, Lin Chen, Kathryn Demanelis, Jennifer A. Doherty, Andrew P. Feinberg, Kasper D. Hansen, Peter F. Hickey, Lei Hou, Farzana Jasmine, Lihua Jiang, Rajinder Kaul, Manolis Kellis, Muhammad G. Kibriya, Jin Billy Li, Qin Li, Shin Lin, Sandra E. Linder, Stephen B. Montgomery, Meritxell Oliva, Yongjin Park, Brandon L. Pierce, Lindsay F. Rizzardi, Andrew D. Skol, Kevin S. Smith, Michael Snyder, John Stamatoyannopoulos, Hua Tang, Meng Wang, Latarsha J. Carithers, Ping Guan, Susan E. Koester, A. Roger Little, Helen M. Moore, Concepcion R. Nierras, Abhi K. Rao, Jimmie B. Vaught, Simona Volpi
Article
Biochemical Research Methods
Manuel Munoz-Aguirre, Vasilis F. Ntasis, Santiago Rojas, Roderic Guigo
PLOS COMPUTATIONAL BIOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Adam Frankish, Mark Diekhans, Irwin Jungreis, Julien Lagarde, Jane E. Loveland, Jonathan M. Mudge, Cristina Sisu, James C. Wright, Joel Armstrong, If Barnes, Andrew Berry, Alexandra Bignell, Carles Boix, Silvia Carbonell Sala, Fiona Cunningham, Tomas Di Domenico, Sarah Donaldson, Ian T. Fiddes, Carlos Garcia Giron, Jose Manuel Gonzalez, Tiago Grego, Matthew Hardy, Thibaut Hourlier, Kevin L. Howe, Toby Hunt, Osagie G. Izuogu, Rory Johnson, Fergal J. Martin, Laura Martinez, Shamika Mohanan, Paul Muir, Fabio C. P. Navarro, Anne Parker, Baikang Pei, Fernando Pozo, Ferriol Calvet Riera, Magali Ruffier, Bianca M. Schmitt, Eloise Stapleton, Marie-Marthe Suner, Irina Sycheva, Barbara Uszczynska-Ratajczak, Maxim Y. Wolf, Jinuri Xu, Yucheng T. Yang, Andrew Yates, Daniel Zerbino, Yan Zhang, Jyoti S. Choudhary, Mark Gerstein, Roderic Guigo, Tim J. P. Hubbard, Manolis Kellis, Benedict Paten, Michael L. Tress, Paul Flicek
Summary: The GENCODE project annotates human and mouse genes and transcripts with high accuracy, using experimental data and bioinformatic tools, and continues to improve annotation infrastructure and tools for the human and mouse genomes. This includes manual annotation for the mouse reference genome, targeted improvements for SARS-CoV-2 related genes, collaborative projects for reference annotation databases, and the first GENCODE supervised automated annotation of lncRNAs.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Genetics & Heredity
Silvia Perez-Lluch, Cecilia C. Klein, Alessandra Breschi, Marina Ruiz-Romero, Amaya Abad, Emilio Palumbo, Lyazzat Bekish, Carme Arnan, Roderic Guigo
Article
Multidisciplinary Sciences
Diego Garrido-Martin, Beatrice Borsari, Miquel Calvo, Ferran Reverter, Roderic Guigo
Summary: Alternative splicing is a fundamental step in eukaryotic mRNA biogenesis, and the comprehensive catalog of splicing QTLs in the human genome generated through analysis of the GTEx dataset provides insight into splicing regulation mechanisms and disease mechanisms.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Bertrand Fouks, Philipp Brand, Hung N. Nguyen, Jacob Herman, Francisco Camara, Daniel Ence, Darren E. Hagen, Katharina J. Hoff, Stefanie Nachweide, Lars Romoth, Kimberly K. O. Walden, Roderic Guigo, Mario Stanke, Giuseppe Narzisi, Mark Yandell, Hugh M. Robertson, Nikolaus Koeniger, Panuwan Chantawannakul, Michael C. Schatz, Kim C. Worley, Gene E. Robinson, Christine G. Elsik, Olav Rueppell
Summary: This study compared the genomes of three different subgenera of honey bees and revealed a complex gene regulation pattern and the role of positive selection in adaptive evolution among honey bee species.
Article
Multidisciplinary Sciences
Svetlana Kalmykova, Marina Kalinina, Stepan Denisov, Alexey Mironov, Dmitry Skvortsov, Roderic Guigo, Dmitri Pervouchine
Summary: The ability of nucleic acids to form double-stranded structures is essential for all living systems, with long-range RNA structures containing conserved complementary regions abundant in human protein-coding genes. PCCRs, mainly located within introns, have a distinct splicing pattern and may affect splicing widely.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Beatrice Borsari, Pablo Villegas-Miron, Silvia Perez-Lluch, Isabel Turpin, Hafid Laayouni, Alba Segarra-Casas, Jaume Bertranpetit, Roderic Guigo, Sandra Acosta
Summary: The study explored the correlation between the genomic location of active enhancers and tissue-specific gene expression, revealing that tissue-specific enhancers are enriched in intronic regions and control genes involved in tissue-specific functions. The results suggest that the genomic location of active enhancers is crucial for the tissue-specific control of gene expression, with the transition from developmental to adult stages showing a continuum of intergenic to intronic enhancers.
Article
Clinical Neurology
Natalia Vilor-Tejedor, Iacopo Ciampa, Gregory Operto, Carles Falcon, Marc Suarez-Calvet, Marta Crous-Bou, Mahnaz Shekari, Eider M. Arenaza-Urquijo, Marta Mila-Aloma, Oriol Grau-Rivera, Carolina Minguillon, Gwendlyn Kollmorgen, Henrik Zetterberg, Kaj Blennow, Roderic Guigo, Jose Luis Molinuevo, Juan Domingo Gispert
Summary: This study found that in the asymptomatic stages of the Alzheimer's continuum, ePVS in the CS region is specifically associated with tau pathophysiology, neurodegeneration, and synaptic dysfunction, while there is no association with ePVS in the BG region.
ALZHEIMERS RESEARCH & THERAPY
(2021)
Article
Genetics & Heredity
Iacopo Ciampa, Gregory Operto, Carles Falcon, Carolina Minguillon, Manuel Castro de Moura, David Pineyro, Manel Esteller, Jose Luis Molinuevo, Roderic Guigo, Arcadi Navarro, Juan Gispert, Natalia Vilor-Tejedor
Summary: The study revealed a significant association between the BIN1-rs744373 polymorphism and ePVS in the centrum semiovale, showing increased risk for G allele carriers, particularly in APOE-epsilon 4 carriers. This suggests that genetic predisposition for Alzheimer's disease may influence the enlargement of perivascular spaces in the brain.
Review
Biochemistry & Molecular Biology
Didac Santesmasses, Vadim N. Gladyshev
Summary: Selenium is incorporated into selenoproteins as the 21st amino acid selenocysteine (Sec). There are 25 selenoproteins encoded in the human genome, and their synthesis requires a dedicated machinery. Most selenoproteins are oxidoreductases with important functions in human health. Deficiencies in selenoproteins can lead to various disorders, with mutations in selenoprotein genes or Sec machinery genes being common causes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Petra A. Tsuji, Didac Santesmasses, Byeong J. Lee, Vadim N. Gladyshev, Dolph L. Hatfield
Summary: Selenium is an essential element in the diet and has many health benefits, such as preventing heart disease and cancer, supporting male reproduction, and boosting the immune system. It plays important roles in the molecular biology of organisms and its incorporation into proteins is a unique feature. Research has focused on selenium's role in cancer prevention and its potential involvement in various diseases.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Genetics & Heredity
Anna Vlasova, Toni Hermoso Pulido, Francisco Camara, Julia Ponomarenko, Roderic Guigo
Summary: Functional annotation is essential for enhancing the biological relevance of predicted features in genomic sequences, and improving gene structural annotation. The pipeline FA-nf, implemented in Nextflow, integrates various annotation approaches for producing multiple files and reports efficiently. It can be easily parallelized and deployed in a Linux computational environment, ensuring full reproducibility through software containerization.
Article
Biochemistry & Molecular Biology
Didac Santesmasses, Vadim N. Gladyshev
Summary: Through analysis of the co-essentiality network, this study identified functional partners of selenoproteins and Sec machinery proteins. The key role of selenium is to support the functions of GPX4 and TXNRD1, with further functional links to PRDX6 and SCD.
Article
Cell Biology
Nina Khera, Didac Santesmasses, Csaba Kerepesi, Vadim N. Gladyshev
Summary: Research shows that COVID-19 mortality rate in children follows a U-shaped curve, reaching its minimum at ages 3-10 and then increasing with age. Childhood mortality rates from COVID-19 are considerably lower than from other diseases, indicating that children are better protected at youngest ages.