Article
Microbiology
Ireneusz Sobolewski, Katarzyna Adamowicz, Anna Struck, Agnieszka Zylicz-Stachula, Piotr M. Skowron
Summary: DNA purification methods are important tools in molecular biology, but currently available techniques may not be effective for certain specialized applications. We have developed a method that uses silica columns and mini-scale isolation to efficiently purify bacteriophage genomic DNA from concentrated phage preparations, without the need for removing CsCl solutions.
Article
Biotechnology & Applied Microbiology
Ryota Kurashiki, Kosuke Koyama, Yukina Sakaguchi, Yuta Okumura, Takashi Ohshiro, Hirokazu Suzuki
Summary: Through studying Geobacillus kaustophilus HTA426, we discovered a robust promoter for efficient recombinant protein production at high temperatures, and successfully applied it to other strains with satisfactory yields. Additionally, we developed a simple purification method for extracting recombinant proteins from both intracellular and extracellular fractions.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Review
Microbiology
Beata Lubkowska, Joanna Jezewska-Frackowiak, Ireneusz Sobolewski, Piotr M. Skowron
Summary: Bacteriophages of thermophiles play important roles in biogeochemical, ecological processes, and biotechnology applications. Despite being underrepresented in the known prokaryotic virosphere, there is considerable potential for discovering novel bacteriophage-host systems in various environments.
Article
Microbiology
Daniela Pinto, Raquel Goncalo, Mariana Louro, Marta Sousa Silva, Guillem Hernandez, Tiago N. Cordeiro, Carlos Cordeiro, Carlos Sao-Jose
Summary: The occurrence of endolysin genes encoding two polypeptide isoforms by in-frame overlapping ORFs and their organization as enzymatic complexes is more common than previously thought, challenging the established view of endolysins. The discovery of a heteromeric endolysin with a 1:5 subunit stoichiometry provides new insights and has possible implications in the design of alternative antibacterials.
MICROBIOLOGY SPECTRUM
(2022)
Article
Multidisciplinary Sciences
Elina Cernooka, Janis Rumnieks, Nikita Zrelovs, Kaspars Tars, Andris Kazaks
Summary: Endolysins are enzymes encoded by bacteriophages that have the potential to treat multidrug-resistant bacterial infections. The study found that the endolysin encoded by Hafnia phage Enc34 has an unusual structure and exhibits activity against peptidoglycan from different bacteria. The research also reveals the evolutionary relationship between Enc34 endolysin and other enzymes at the molecular level.
SCIENTIFIC REPORTS
(2022)
Article
Chemistry, Multidisciplinary
Catrina Nguyen, Lauren M. Yearwood, Michelle E. McCully
Summary: Using molecular dynamics simulations, research on three-helix bundle structures in thermophilic proteins revealed stabilization strategies such as shortening and rigidification of loops, which can enhance the thermostability of proteins. Additionally, specific structural elements, like buried disulfide bonds and salt bridges, were found to provide stability for proteins.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2022)
Article
Environmental Sciences
Xinyu Zhang, Ying Li, Kexin Zhang, Yansong Yin, Jie Wang, Luocheng Wang, Zhexing Wang, Ruiling Zhang, Haijun Wang, Zhong Zhang
Summary: Graphene oxide (GO) is widely used in various fields and its release into the environment is increasing. It has been found that GO leads to bacterial overgrowth and affects bacteriophage infection. The presence of GO expands biofilms and hinders the ability of bacteriophages to kill bacteria and reproduce. Additionally, adding GO to sewage increases bacterial diversity and richness.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Biochemistry & Molecular Biology
Jeffrey A. Purslow, Jolene N. Thimmesch, Valeria Sivo, Trang T. Nguyen, Balabhadra Khatiwada, Rochelle R. Dotas, Vincenzo Venditti
Summary: Enzyme I (EI) of the bacterial phosphotransferase system (PTS) is a master regulator of bacterial metabolism and a potential target for broad-spectrum antibiotics. Research shows that the activity of EI is influenced by the conformational dynamics within the N-terminal domain (EIN), and engineering hybrid mesophilic/thermophilic chimeras can modulate these dynamics to affect enzyme activity. This study provides insights into the dynamics/function relationship in proteins and opens new possibilities in biophysics research.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Xymena Stachurska, Krzysztof Cendrowski, Kamila Pachnowska, Agnieszka Piegat, Ewa Mijowska, Pawel Nawrotek
Summary: Little is known about the interactions between non-filamentous, complex-structured lytic phages and free, non-ordered nanoparticles. This study investigated the influence of various nanoparticles on a T4-like phage, revealing that the charge of the nanoparticles is crucial for the specific attachment of the phage, and most nanoparticles positively affected the phage lytic performance.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Genetics & Heredity
Yajiao Wang, Yu Liu, Yuxing Wu, Nan Wu, Wenwen Liu, Xifeng Wang
Summary: In this study, the diversity and interactions of bacteriophages and their host bacteria in soils from three typical rice agroecosystems in China were analyzed using metagenomic sequencing. The results showed that the diversity and predicted functions of soil bacteria and viruses varied among the different agroecosystems.
ENVIRONMENTAL MICROBIOME
(2022)
Article
Microbiology
Vincent Somerville, Thibault Schowing, Helene Chabas, Remo S. Schmidt, Ueli von Ah, Remy Bruggmann, Philipp Engel
Summary: This study focuses on the diversity and distribution of bacterial defense mechanisms in cheese-associated communities. The researchers found that nearly identical bacterial strains in these communities possess diverse and highly variable innate and adaptive immune systems, indicating rapid turnover. The abundance of CRISPR spacers correlated with the abundance of matching target sequences, suggesting functional and selective defense repertoires. However, CRISPR spacers only covered a subset of the phages identified in cheese, indicating that innate immune mechanisms may have complementary roles. The findings highlight the dynamic nature of bacterial defense mechanisms and their ecological and molecular processes in low complexity communities, such as those found in cheese.
Article
Virology
Nora Halgasova, Daniela Krajcikova, Daniel Kraus, Gabriela Bukovska
Summary: The gp43 replication protein consists of a prim-pol domain and a helicase-like C-terminal domain. Mutants with varying truncations showed that the N-terminal and C-terminal regions have significant impacts on ATPase and helicase activities. The N-terminal 38 amino acids may modulate DNA binding and oligomerization, while the 87 C-terminal residues are crucial for binding to DNA substrates.
Article
Biochemistry & Molecular Biology
Yusuke Fujino, Takero Miyagawa, Masayuki Torii, Masao Inoue, Yuki Fujii, Hiroki Okanishi, Yoshikatsu Kanai, Ryoji Masui
Summary: A study found that a thermophilic Ser/Thr protein kinase completely unfolds at high temperatures, but is significantly stabilized by its natural ligands ATP and ADP, increasing the melting temperature to 80 degrees Celsius. This striking effect of a substrate on the thermostability of thermophilic proteins has not been reported before.
Review
Microbiology
Gabriel Valiente
Summary: This article provides a systematic review of available virus-host protein-protein interaction database resources, evaluating their specificity, the number of interactions included, and functionality. It also analyzes the overlap of the databases and the structure of the interaction network across viruses and hosts.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Beata Lubkowska, Edyta Czajkowska, Ireneusz Sobolewski, Natalia Krawczun, Agnieszka Zylicz-Stachula, Piotr M. Skowron
Summary: In this study, a method for rapid concentration and purification of an enzyme from a diluted crude cell lysate was developed using a novel capsule glycosylase-depolymerase (TP84_26 GD) from bacteriophage TP-84. A modified polyethyleneimine (PEI)-based purification method was used to efficiently purify the enzyme, and its properties were characterized.
Article
Virology
Geng Yang, Jiajia Wang, Tao Luo, Xiaobo Zhang
Article
Biochemistry & Molecular Biology
Siyuan Zhang, Xiaobo Zhang
Article
Fisheries
Yuechao Sun, Xiaobo Zhang
FISH & SHELLFISH IMMUNOLOGY
(2019)
Article
Biochemistry & Molecular Biology
Yuechao Sun, Yu Zhang, Xiaobo Zhang
Article
Cell & Tissue Engineering
Fan Yang, Pei Cui, Yu Lu, Xiaobo Zhang
STEM CELL RESEARCH & THERAPY
(2019)
Article
Fisheries
Wenlin Wu, Congjie Dai, Xunwei Duan, Cuifang Wang, Xiaosi Lin, Jiaying Ke, Yixuan Wang, Xiaobo Zhang, Haipeng Liu
FISH & SHELLFISH IMMUNOLOGY
(2019)
Article
Oncology
Yi Gong, Geng Yang, Qizhi Wang, Yumeng Wang, Xiaobo Zhang
MOLECULAR CANCER RESEARCH
(2020)
Article
Cell & Tissue Engineering
Wenlin Wu, Chenxi Xu, Xiaobo Zhang, An Yu, Le Shu
STEM CELL RESEARCH & THERAPY
(2020)
Article
Microbiology
Xumei Sun, Junyi Yang, Minhui Zheng, Xiaobo Zhang
Summary: The study developed a biocoenosis generator that continuously released methane on the 1000-m deep-sea floor of the South China Sea, artificially constructing a deep-sea ecosystem biocoenosis. It was found that deep-sea biocoenosis consisted of anaerobic methane-oxidizing archaea, symbiotic archaea, bacteria, and animals, with viruses coexisting during the origin of the ecosystem.
ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Medicine, Research & Experimental
Yalei Cui, Haitao Wan, Xiaobo Zhang
Summary: The study identified shrimp miR-34 as a potential antiviral miRNA against WSSV infection and suppressor of cancer progression, suggesting that animal antiviral miRNAs may have anti-tumor activity in humans.
MOLECULAR THERAPY-NUCLEIC ACIDS
(2021)
Article
Cell Biology
Chenxi Xu, Jianjian Zhuang, Xiaobo Zhang
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2020)
Article
Multidisciplinary Sciences
Siyuan Zhang, Fan Xin, Xiaobo Zhang
Summary: Compounds packaged in virions of white spot syndrome virus can trigger the viral life cycle by enhancing host glycolysis, leading to virus infection. This process involves the binding of palmitic amide to triosephosphate isomerase and the upregulation of HIF-1, enhancing glycolysis and promoting virus infection.
Review
Fisheries
Yi Gong, Xiaobo Zhang
Summary: Shrimp have developed innate immunity to fight against more than 20 viruses, with RNA interference (RNAi) playing a key role. Short interfering RNAs (siRNAs) and microRNAs (miRNAs) are important in virus-host interactions. The non-seed sequence in miRNAs is essential for their targeting function in regulating virus-host interactions.
DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY
(2021)
Article
Cell & Tissue Engineering
Mengqi Chu, Haitao Wan, Xiaobo Zhang
Summary: The study revealed that hnRNP A2B1 is significantly upregulated in melanoma stem cells, playing an important role in promoting the expression of anti-apoptosis genes and suppressing pro-apoptosis genes by regulating their splicing. This ultimately leads to cell cycle arrest in G2 phase and apoptosis of melanoma stem cells, highlighting the crucial requirement of hnRNP A2B1 in tumorigenesis and providing novel insights into the role of hnRNPs in cancer stem cells.
STEM CELL RESEARCH & THERAPY
(2021)
Article
Chemistry, Analytical
Jianjian Zhuang, Haitao Wan, Xiaobo Zhang
Summary: A biosensor using AuNP-modified AuE and CPs was developed for the detection of miR-100 in GC patients' sera. The biosensor showed high specificity and sensitivity in distinguishing miR-100 variants, with a detection range from 100 aM to 10 pM and a LOD of 100 aM. The cutoff for gastric cancer detection was determined to be 5 fM based on testing 100 human sera samples.
