Article
Biochemistry & Molecular Biology
Mariia Dimova, Andrii Tugai, Tetiana Tugai, Galyna Iutynska, Dani Dordevic, Ivan Kushkevych
Summary: Comamonas testosteroni is a common human pathogen that can cause various infections and inflammatory bowel disease. This study found that these strains have a strong ability to degrade hexachlorobenzene in contaminated soil, and the chemical substances produced during the reaction differed from the control group.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Victor Barozi, Thommas Mutemi Musyoka, Olivier Sheik Amamuddy, Ozlem Tastan Bishop
Summary: This study explored the effects of 11 high confidence mutations in the Mtb KatG protein on tuberculosis treatment, revealing significant changes in structure and residue network communication patterns. Mutant proteins exhibited increased loop flexibility around the heme binding pocket and showed asymmetric behavior compared to the wild-type protein.
Article
Microbiology
Allexa Dow, Preeti Sule, Timothy J. O'Donnell, Andrew Burger, Joshua T. Mattila, Brandi Antonio, Kevin Vergara, Endrei Marcantonio, L. Garry Adams, Nicholas James, Philip G. Williams, Jeffrey D. Cirillo, Sladjana Prisic
Summary: This study suggests that zinc ion availability may influence the bacterial heterogeneity of Mycobacterium tuberculosis, leading to changes in gene expression patterns and increased resistance to oxidative stress in vivo. This could have implications for host-pathogen interactions and the ability of Mtb to adapt to different environmental conditions.
Review
Immunology
Rinako Nakagawa, Dinis Pedro Calado
Summary: Germinal centers play a crucial role in the production of high-affinity antibody secreting plasma cells and memory-B cells for vaccination. The positive selection process in GCs guides B cell fates towards becoming either PCs, MBCs or persistent GC-B cells, with each cell type playing a specific role in the immune response.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Immunology
Xiao-Yong Zhan, Gao-Feng Zha, Yulong He
Summary: The ongoing outbreak of human monkeypox (hMPX) in 2022 is a serious global threat. Understanding the evolution of the monkeypox virus (MPXV) at the gene level may provide insights into the unique aspects of the current outbreak, including human-to-human transmission. Analysis of MPXV coding genes revealed that while most genes were subjected to negative selection, there were a few genes that showed evidence of positive Darwinian selection, which may play a crucial role in viral adaptation, virulence, and transmission.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Biology
Samira Bnikkou, Abdellatif Laknifli, Khalid Majourhat, Sara Jalili, Jose Antonio Hernandez, Pedro Martinez-Gomez, Pedro Jose Martinez-Garcia
Summary: An integrated molecular and biochemical approach was used to compare Moroccan and Spanish argan ecotypes, revealing similarities in genetic diversity and response to water stress. Both ecotypes showed increased POX and SOD activities under drought stress, with higher SOD activity in the Spanish ecotype in an inland area. This suggests a potential tolerance to drought stress.
Article
Plant Sciences
Hilda Samson Bachwenkizi, Gladness Elibariki Temu, Deusdedith Rugaihukamu Mbanzibwa, Margareth Daudi Lupembe, Stephan Ngailo, Fred Donati Tairo, Deogracious Protas Massawe
Summary: Using HTS and Sanger sequencing techniques, this study detected and analyzed the genetic diversity, recombination events, and evolutionary selection pressure of SPLCVs in Tanzania. The results showed high genetic diversity of the detected SPLCVs and their close relationship with other similar viruses. In addition, recombination events were found in SPLCVs and different evolutionary selection pressures were observed in their genes.
PHYSIOLOGICAL AND MOLECULAR PLANT PATHOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Donald C. Dearborn, Sophie Warren, Frank Hailer
Summary: Pathogen-mediated selection and sexual selection are important drivers of evolution. The major histocompatibility complex (MHC) genes play a crucial role in these processes. However, previous research has shown a lack of emphasis on the class II MHC gene, MHC-IIA, in infectious disease and sexual selection studies. In this study, MHC-IIA sequence data from 50 vertebrate species were analyzed, revealing high levels of polymorphism and positive selection in MHC-IIA. Fish species exhibited stronger positive selection on MHC-IIA compared to other surveyed vertebrate groups. These findings highlight the importance of MHC-IIA as a target of selection and suggest the need for further characterization of MHC-IIA at both allelic and genomic levels.
Article
Multidisciplinary Sciences
Yuwen Pan, Panhong Liu, Fang Wang, Peng Wu, Fanjun Cheng, Xin Jin, Shuhua Xu
Summary: The ACE2 gene shows diversity, with ACE2-hg1 in East Asians being positively correlated with COVID-19 severity and ACE2-hg2 being negatively correlated. East Asians have a significant loss of common ACE2 variations compared to other populations. Additionally, ACE2-hg2 exhibits strong positive selection, which may be related to past viral epidemics.
NATIONAL SCIENCE REVIEW
(2022)
Article
Agriculture, Dairy & Animal Science
Heidi Signer-Hasler, Lucas Casanova, Alex Barenco, Blaise Maitre, Alessandro Bagnato, Mario Vevey, Beate Berger, Mojca Simcic, Denis Boichon, Aurelien Capitan, Ivica Medugorac, Joern Bennewitz, Gabor Meszaros, Johann Soelkner, Cord Droegemueller, Christine Flury
Summary: We analyzed genome-wide SNP data from 18 local cattle breeds from the Alpine region to understand their population structure and identify genomic regions involved in positive selection. Different breeds like Evolener, Eringer, Valdostana Pezzata Nera, and Valdostana Castana showed distinct genetic differences compared to other Alpine breeds. We found selection signatures on chromosome 6 near genes related to coat color and body size, and identified 47 genome regions with ROH islands using high-density SNP data. The results provide insights into adaptation to the alpine environment and specific characteristics in local Alpine cattle breeds.
Article
Biotechnology & Applied Microbiology
B. Falcao, N. Dsouza, K. Gokarn
Summary: This study investigates the mechanism of key enzymes involved in drug interaction in tuberculosis. The findings suggest that mutations can impact the structure of the protein and its binding pattern with the drug, potentially leading to increased drug resistance in Mycobacterium tuberculosis.
RESEARCH JOURNAL OF BIOTECHNOLOGY
(2022)
Article
Veterinary Sciences
Mohammad Al Abri, Ahmad Alfoudari, Zainab Mohammad, Faisal Almathen, Waleed Al-Marzooqi, Salim Al-Hajri, Mahmood Al-Amri, Hussain Bahbahani
Summary: This study analyzed the whole autosomal data of dromedary camels from the Southeast Arabian Peninsula, revealing genetic distinctions between populations and candidate regions with signatures of positive selection. These candidate regions contain genes related to immune response, lipid metabolism, energy expenditure, optical and auditory functions, and long-term memory. The findings have implications for genomic breeding programs and conservation of the species.
FRONTIERS IN VETERINARY SCIENCE
(2023)
Article
Immunology
John T. Loh, Jennifer H. B. Shuman, Aung Soe Lin, Natalie Favret, M. Blanca Piazuelo, Simon Mallal, Abha Chopra, Mark S. McClain, Timothy L. Cover
Summary: Gastric inflammation was found to increase the activity of Cag T4SS in Helicobacter pylori, resulting in mutations in the katA gene. These mutations led to increased production of catalase, which enhanced the bacterium's resistance to hydrogen peroxide.
INFECTION AND IMMUNITY
(2022)
Article
Plant Sciences
Cristina C. Bastias, Barbara Carvalho, Silvia Matesanz, Lydia de la Cruz-Amo, Andres Bravo-Oviedo, Cyrille Violle, Fernando Valladares, Raquel Benavides
Summary: The study demonstrates that tree diversity can have a positive impact on community biomass at the seedling stage, with certain tree species playing a crucial role. Drought conditions limit above-ground biomass production without interacting with species richness. This work emphasizes the need for integrated approaches to understanding biodiversity-biomass relationships.
JOURNAL OF VEGETATION SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Stefan Hofbauer, Marcello Pignataro, Marco Borsari, Carlo Augusto Bortolotti, Giulia Di Rocco, Gianina Ravenscroft, Paul G. Furtmuller, Christian Obinger, Marco Sola, Gianantonio Battistuzzi
Summary: The autosomal dominant striated muscle disease myoglobinopathy is caused by a single point mutation in human myoglobin, leading to increased reactivity towards hydrogen peroxide, enhanced tendency to form high-molecular-weight aggregates, and accelerated heme bleaching. These effects contribute to impaired oxygen binding capacity and faster heme dissociation, ultimately impacting the pathological symptoms of myoglobinopathy.
Article
Biochemistry & Molecular Biology
Marcelo Pedrosa Gomes, Rafael Shinji Akiyama Kitamura, Raizza Zorman Marques, Marcello Locatelli Barbato, Marcel Zamocky
Summary: We investigated the individual and combined contributions of two distinct heme proteins, ascorbate peroxidase (APX) and catalase (CAT), on the tolerance of Lemna minor plants to antibiotics. Our results showed that APX activity was crucial for the plant's tolerance to amoxicillin, while CAT activity played an important role in protecting against oxidative damage caused by ciprofloxacin. Both enzymes were also important for the plant's tolerance to erythromycin. Molecular kinetic approaches to enhance APX and/or CAT scavenging activities could improve the use of L. minor plants for antibiotic reclamation from water bodies.
Editorial Material
Biochemistry & Molecular Biology
Christian Obinger
Summary: This paper presents the first purification and characterization of a manganese peroxidase, demonstrating its ability to oxidize various compounds using hydrogen peroxide and Mn(II). This discovery in 1985 laid the foundation for extensive research on the structure-function relationships, ecological roles, and industrial applications of manganese peroxidases.
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
(2022)
Article
Biochemistry & Molecular Biology
Marcel Zamocky, Jana Harichova
Summary: We reconstructed the molecular phylogeny of heme containing peroxygenases, revealing high diversity and conserved sequence motifs. The genes coding for these peroxygenases were detected mainly in fungi, but also in other lower eukaryotes. The phylogenetic analysis can be useful for designing modified peroxygenases for future biotech applications.
Article
Biology
Marcel Zamocky, Milos Musil, Maksym Danchenko, Peter Ferianc, Katarina Chovanova, Peter Barath, Andrej Poljovka, David Bednar
Summary: This study presents a detailed bioinformatics analysis of Hybrid B heme peroxidases in the fungal family Sclerotiniaceae. The research reveals the evolutionary pattern of these peroxidases in phytopathogens and identifies similar peroxidase sequences in different fungal species. The study also highlights minor yet important modifications in the active center architecture of these peroxidases.
Article
Biochemistry & Molecular Biology
Douglas Jardim-Messeder, Marcel Zamocky, Gilberto Sachetto-Martins, Marcia Margis-Pinheiro
Summary: This article analyzes and discusses the origin, evolution, and function of the APX family. The study found that APX originated as a soluble enzyme and evolved to have targeting sequences for chloroplasts and mitochondria. Independent gene duplications and neofunctionalization events in certain angiosperm groups resulted in the development of APX isoforms localized in different subcellular compartments. The complexity of APX isoforms contributes to the adaptation of diverse plant species to changing environmental conditions.
Article
Biochemistry & Molecular Biology
Anja Wagner, Edgar Galicia-Andres, Magdalena Teufl, Lukas Gold, Christian Obinger, Peter Sykacek, Chris Oostenbrink, Michael W. Traxlmayr
Summary: By screening a mutated EGFR library, previously unknown activating mutations in EGFR were discovered. These mutations are not only located in the kinase domain of EGFR, but also in other regions, including the extracellular and transmembrane domains.
Article
Biochemistry & Molecular Biology
Daniel Schmidt, Nikolaus Falb, Ilenia Serra, Marzia Bellei, Vera Pfanzagl, Stefan Hofbauer, Sabine Van Doorslaer, Gianantonio Battistuzzi, Paul G. Furtmuller, Christian Obinger
Article
Biochemistry & Molecular Biology
Daniel R. Ramos, Paul G. Furtmueller, Christian Obinger, Angeles Pena-Gallego, Ignacio Perez-Juste, J. Arturo Santaballa
Summary: Electronic structure calculations using DFT were conducted to examine the influence of water molecules and protonation on the heme group of peroxidases in different redox and spin states. The study discusses shared geometries, spectroscopic properties, and thermodynamics of peroxidases. Computed Gibbs free energies suggest that the corresponding aquo complexes are not thermodynamically stable, supporting the five-coordinate Fe(III) center in native ferric peroxidases with a non-bonding water molecule. Protonation of the ferryl oxygen of compound II is found to be necessary and computed Gibbs free energies reveal pK(a) values of approximately 8.5-9.0 for compound II.
Article
Biochemistry & Molecular Biology
Douglas Jardim-Messeder, Andreia Caverzan, Natalia Balbinott, Paloma K. Menguer, Ana L. S. Paiva, Moaciria Lemos, Juliana R. Cunha, Marcos L. Gaeta, Miguel Costa, Marcel Zamocky, Nelson J. M. Saibo, Joaquim A. G. Silveira, Rogerio Margis, Marcia Margis-Pinheiro
Summary: This study found that silencing the OsAPX7 gene in rice does not affect plant growth, redox state, or photosynthesis parameters. However, silenced plants (APX7i) show higher tolerance to drought stress, with a higher ability to maintain stomata aperture and photosynthesis performance compared to non-transformed plants. RNA-seq analyses indicate that the silencing of OsAPX7 does not alter the global expression of genes related to reactive oxygen species metabolism. Additionally, the drought-induced regulation of genes related to proteasome pathway, nitrogen metabolism, and carotenoid metabolism is impaired in APX7i plants. On the other hand, genes associated with flavonoid and tyrosine metabolism are upregulated, while genes related to phytohormone signal transduction and nicotinate and nicotinamide metabolism are downregulated in APX7i during drought stress. These results suggest that OsAPX7 may be involved in signaling transduction pathways related to drought stress response in rice, providing insights into the physiological role of chloroplast APX isoforms.
Editorial Material
Biochemistry & Molecular Biology
Marcel Zamocky
Article
Biology
Douglas Jardim-Messeder, Ygor de Souza-Vieira, Lucas Correa Lavaquial, Daniela Cassol, Vanessa Galhego, Gabriel Afonso Bastos, Thais Felix-Cordeiro, Regis Lopes Correa, Marcel Zamocky, Marcia Margis-Pinheiro, Gilberto Sachetto-Martins
Summary: Climate changes threaten agriculture and plants need to cope with different environmental conditions, including reactive oxygen species (ROS). The ascorbate-glutathione cycle, composed of APX, MDAR, DHAR, and GR enzymes, is the main antioxidant pathway in plants. This study identified and classified these genes in multiple plant species, predicted their subcellular localization, and contributed to understanding their evolutionary history. The expression pattern of these genes in response to drought stress in castor bean was also analyzed. Overall, this study provides important insights into the regulation of ROS metabolism in drought tolerance.
Article
Biochemistry & Molecular Biology
Zuzana Farkas, Andrea Puskarova, Alena Opalkova Siskova, Andrej Poljovka, Marcel Zamocky, Eva Vadkerti, Martin Urik, Bence Farkas, Maria Buckova, Lucia Krakova, Domenico Pangallo
Summary: Two different biocleaning techniques were investigated for stamp removal from handmade and machine-made paper samples. The cellulose content in handmade paper and the lignin content in machine-made paper were analyzed. The effectiveness of the biocleaning methods was determined using spectrophotometer measurements and microstructural analysis. The study found that the EEM-based approaches were the most suitable for stamp removal, as they were less time-consuming and easy to produce.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Biochemistry & Molecular Biology
Andrej Poljovka, Milos Musil, David Bednar, Katarina Chovanova, Vladena Bauerova-Hlinkova, Jana Bellova, Lenka Kohutova, Peter Barath, Marcel Zamocky
Summary: The study found that the catalase-peroxidases from thermophilic and mesophilic fungi have similar active center structures and peroxidase activity, while the thermophilic variant CthedisKatG showed enhanced manganese peroxidase activity at higher temperatures. Two constructed mutations completely abolished catalatic activity and altered the peroxidase activity, suggesting the potential biotech applications of bifunctional heme enzymes with variable reactivity.
Article
Biochemistry & Molecular Biology
Marcel Zamocky, Peter Ferianc
Summary: This study demonstrates the deep evolutionary origin of the conserved animal serum amyloid A (SAA) apolipoprotein family, which also leads to the occurrence of highly similar SAA-like sequences in certain bacterial genomes. Horizontal gene transfer of corresponding genes between gut bacteria and non-vertebrate animals was discovered in the phylogenetic tree analysis. The study discusses the conserved sequence motifs and structural fold of the SAA protein family and their potential biological functions.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)