Article
Plant Sciences
Xuan Feng, Qingzhi Zhang, David J. Clarke, Hai Deng, David O'Hagan
Summary: 3'-O-ss-Glucosyl-4',5'-didehydro-5'-deoxyadenosine 13 is a natural product of Streptomyces calvus and Streptomyces virens, and can also be generated in vitro by the enzyme NucGT. Experimental results using oxygen-18 and deuterium isotopes confirm that 13 is not a biosynthetic precursor to nucleocidin 1.
JOURNAL OF NATURAL PRODUCTS
(2023)
Article
Microbiology
Balaji Sundararaman, Matthew D. Sylvester, Varvara K. Kozyreva, Zenda L. Berrada, Russell B. Corbett-Detig, Richard E. Green
Summary: Genomic epidemiology uses pathogens' whole-genome sequences to understand and manage the spread of infectious diseases. We developed a cost-effective method called CNERs to generate whole-genome enrichment probes, which successfully enriched Mycobacterium tuberculosis DNA and demonstrated its utility for lineage identification and drug-resistance characterization.
Article
Biochemistry & Molecular Biology
Sarah Fischer, Nicolas Spath, Mohamed Hamed
Summary: The heterogeneity of lung tumor nodules can be studied through the analysis of phenotypic characteristics in radiological images combined with transcriptome expression levels. By constructing a radiogenomic association map, potential links between gene and miRNA expression and image phenotypes were discovered. The study also found a correlation between gene regulatory networks and the formation of texture in lung tumors. Radiogenomic approaches have the potential to identify image biomarkers for genetic variation and expand our understanding of tumor heterogeneity.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Agricultural Engineering
Shengnan Li, Mingsi Gao, Heng Dong, Yuxin Jiang, Wanting Liang, Jiwei Jiang, Shih-Hsin Ho, Fengxiang Li
Summary: This study found that bio-electro-Fenton systems can efficiently remove antibiotics from wastewater and control the production of antibiotic resistance genes (ARGs). The most prevalent type of ARG was found to be fluoroquinolone antibiotic genes, and Proteobacteria were identified as the dominant bacteria carrying ARGs.
BIORESOURCE TECHNOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Jeff K. Kerkovius, Andrea Stegner, Aneta Turlik, Pik Hoi Lam, Kendall N. Houk, Sarah E. Reisman
Summary: (+)-Matrine and (+)-isomatrine, tetracyclic alkaloids derived from Sophora flavescens, are synthesized through a biosynthetic pathway involving (-)-lysine and the intermediacy of Delta 1-piperidine. A new dearomative annulation reaction using pyridine as a stable surrogate for Delta 1-piperidine allows for the efficient synthesis of matrine alkaloids. Isomatrine, synthesized in four steps from inexpensive commercially available chemicals, serves as the precursor to other lupin alkaloids.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Multidisciplinary Sciences
Annalisa Pisciotta, Alessia Maria Sampino, Alessandro Presentato, Marco Galardini, Angel Manteca, Rosa Alduina
Summary: DNA methylation is an epigenetic modification that has been detected in both prokaryotic and eukaryotic genomes. This study focused on the role of cytosine methylation in Streptomyces coelicolor and found that it affects gene expression, growth, and antibiotic biosynthesis. The researchers identified methylated cytosines and methylation motifs in the genome, and demonstrated that cytosine methylation influences gene transcription. This study provides new insights into the role of cytosine methylation in controlling bacterial gene expression.
SCIENTIFIC REPORTS
(2023)
Article
Biotechnology & Applied Microbiology
Jia Zhou, Yan Chen, Wan-Xia Li, Jian-Hang Qu, Tian Chen, Yi-Ping Wang, Ning-Yu Geng
Summary: Excessive use of chloramphenicol (CAP) and its residues poses a potential threat to human health and ecological safety. This study investigates the interactions of microbial community with antibiotic resistance genes (ARGs) during the treatment of CAP wastewater, revealing a potential antibiotic resistance mechanism. The treatment shows excellent performance, removing 95.5% of CAP by enriching the core genera of Candidatus Competibacter and Hydrogenophaga, which possess strong antibiotic resistance and adaptability. The findings highlight the importance of the efflux pump mechanism in combating CAP pressure.
INTERNATIONAL BIODETERIORATION & BIODEGRADATION
(2023)
Review
Plant Sciences
Zhihua Hua
Summary: Protein ubiquitylation is a common post-translational modification process in plants, and it has been predicted that around 5% of the Arabidopsis proteome is involved in this system. However, only a small fraction of this system has been functionally characterized. In this review, the author discusses the current status, issues, and new approaches in studying protein ubiquitylation in plant biology, including bioinformatics, proteomics, functional genomics, and evolutionary biology. The author also proposes a new model for the expansion of the F-box gene superfamily and suggests focusing future studies on the core and active groups of ubiquitin E3 ligase genes.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Chemistry, Multidisciplinary
Julia Krumbholz, Keishi Ishida, Martin Baunach, Jonna E. Teikari, Magdalena M. Rose, Severin Sasso, Christian Hertweck, Elke Dittmann
Summary: In this study, two cell density-dependent chemical mediators in the symbiotic model strain Nostoc punctiforme were discovered and their pronounced impact on the regulation of specialized metabolism was demonstrated. Through transcriptional, bioinformatic, and labeling studies, two adjacent biosynthetic gene clusters were assigned to the biosynthesis of these two polyketide mediators. These findings provide insight into the orchestration of specialized metabolite production and offer lessons for the genomic mining and high-titer production of cyanobacterial bioactive compounds.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Multidisciplinary
Anja Greule, Thierry Izore, Daniel Machell, Mathias H. Hansen, Melanie Schoppet, James J. De Voss, Louise K. Charkoudian, Ralf B. Schittenhelm, Jeffrey R. Harmer, Max J. Cryle
Summary: Cytochrome P450 enzymes are enzymes that can perform oxidative reactions using heme. However, some of these enzymes can be damaged by oxidation, leading to decreased enzyme activity. Research has shown that the heme orientation in the active site of certain cytochrome P450 enzymes may contribute to this oxidative damage.
FRONTIERS IN CHEMISTRY
(2022)
Article
Biotechnology & Applied Microbiology
Zerlina G. Wuisan, I. Dewa M. Kresna, Nils Boehringer, Kim Lewis, Till F. Schaeberle
Summary: Darobactin A (DAR) is a promising antibiotic targeting Gram-negative bacteria, initially identified in bacteria from several genera. It targets the outer membrane protein BamA and has shown convincing in vivo activities in mouse infection models. By establishing a heterologous production and engineering platform, DAR production yield can be improved and structure modification approaches can be facilitated. Only two genes are necessary for the heterologous production of this RiPP antibiotic.
METABOLIC ENGINEERING
(2021)
Article
Chemistry, Organic
Li Rao, Guan-Yin Yuan, Xing-Yue Chen, Jia-Ling Ran, Yi Zou
Summary: In this study, two versatile fungal CYP450s capable of performing diverse oxidations on seven PQST scaffolds were discovered, resulting in the generation of 20 unique products. This significantly expands the diversity of oxidized PQST scaffolds and provides important biocatalysts for the selective oxidation of inert carbons of terpenoids in future research.
Article
Biology
Bing-Bing Ma, Chen-Fan Sun, Jing-Yi Zhou, Shuai-Lei Gu, Xin-Yi Dai, Yan-Zhen Chen, Qing-Wei Zhao, Xu-Ming Mao
Summary: Protein post-translational modifications (PTMs) with various acyl groups in Streptomyces can be further modified, known as post-PTM modification (PPM). By oxidizing the crotonyl groups of an acetyl-CoA synthetase Acs, the protein LimB in Streptomyces roseosporus regulates crotonylation level, morphological development, and antibiotic production.
COMMUNICATIONS BIOLOGY
(2023)
Article
Microbiology
Christoph H. R. Senges, Jennifer J. Stepanek, Michaela Wenzel, Nadja Raatschen, Uemran Ay, Yvonne Maertens, Pascal Prochnow, Melissa Vazquez Hernandez, Abdulkadir Yayci, Britta Schubert, Niklas B. M. Janzing, Helen L. Warmuth, Martin Kozik, Jens Bongard, John N. Alumasa, Bauke Albada, Maya Penkova, Tadeja Lukezic, Nohemy A. Sorto, Nicole Lorenz, Reece G. Miller, Bingyao Zhu, Martin Benda, Joerg Stuelke, Sina Schaekermann, Lars Leichert, Kathi Scheinpflug, Heike Broetz-Oesterhelt, Christian Hertweck, Jared T. Shaw, Hrvoje Petkovic, Jean M. Brunel, Kenneth C. Keiler, Nils Metzler-Nolte, Julia E. Bandow
Summary: This study introduces a proteomic approach for rapid classification of new antibiotics, aiming to accelerate antibiotic research. Comparison of proteomic responses allows quick identification of antibiotics with dual mechanisms, and helps generate hypotheses on mechanisms of action. Proteomic profiling also reveals the impact of antibiotics on bacterial physiology.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2021)
Article
Materials Science, Multidisciplinary
Caiyao Yang, Pingchuan Shen, Qi Ou, Qian Peng, Shuyao Zhou, Jinshi Li, Zhirong Liu, Zujin Zhao, Anjun Qin, Zhigang Shuai, Ben Zhong Tang, Xuefeng Guo
Summary: The realization of functional molecular devices relies on a deep understanding of the structure-property relationship of molecules. However, due to limited detection sensitivity and temporal resolution of current methods, there are few reports on real-time probing of dynamic changes in molecular stereostructures at the single-molecule level. In this study, we present a thorough investigation of the dynamic stereostructures of a single aggregation-induced emission molecule using molecular junctions. The results provide new insights into the development of ultra-sensitive devices and suggest that further integration with optical measurements can enable synchronous monitoring of single-molecule photochemistry and photophysics.
Article
Multidisciplinary Sciences
Oksana Bilyk, Markiyan Samborskyy, Peter F. Leadlay
Article
Plant Sciences
Wilaiwan Koomsiri, Yuki Inahashi, Kantinan Leetanasaksakul, Kazuro Shiomi, Yoko Takahashi, Satoshi Omura, Markiyan Samborskyy, Peter F. Leadlay, Pakorn Wattana-Amorn, Arinthip Thamchaipenet, Takuji Nakashima
JOURNAL OF NATURAL PRODUCTS
(2019)
Article
Chemistry, Multidisciplinary
Samantha L. Kilgour, Robert Jenkins, Manuela Tosin
CHEMISTRY-A EUROPEAN JOURNAL
(2019)
Article
Chemistry, Physical
Rory Little, Fernanda C. R. Paiva, Robert Jenkins, Hui Hong, Yuhui Sun, Yuliya Demydchuk, Markiyan Samborskyy, Manuela Tosin, Finian J. Leeper, Marcio V. B. Dias, Peter F. Leadlay
Article
Chemistry, Multidisciplinary
Samantha L. Kilgour, David P. A. Kilgour, Panward Prasongpholchai, Peter B. O'Connor, Manuela Tosin
CHEMISTRY-A EUROPEAN JOURNAL
(2019)
Article
Biochemical Research Methods
Fernanda C. R. de Paiva, Karen Chan, Markiyan Samborskyy, Ariel M. Silber, Peter F. Leadlay, Marcio V. B. Dias
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2020)
Article
Immunology
Andrii Rabets, Galyna Bila, Roman Grytsko, Markian Samborskyy, Yuriy Rebets, Sandor G. Vari, Quentin Pagneux, Alexandre Barras, Rabah Boukherroub, Sabine Szunerits, Rostyslav Bilyy
Summary: Studies have shown that antibodies developed during SARS-CoV-2 infection can potentially recognize and mitigate the severity of other coronaviral infections such as MERS-CoV. The high homology in the spike protein domain indicates that coronaviral infections may produce cross-reactive antibodies effective against SARS-CoV-2. These findings open up new possibilities in fighting coronaviral infections and developing vaccines that remain effective even after viral mutations.
ARCHIVUM IMMUNOLOGIAE ET THERAPIAE EXPERIMENTALIS
(2021)
Article
Biotechnology & Applied Microbiology
Olena Tigunova, Markiyan Samborskyy, Viacheslav Bratishko, Oleksandr Balabak, Liubov Zelena, Sergiy Shulga
Summary: The rapid development of new molecular methods and sequencing technologies has provided new insights into bacterial genomes. In this study, the entire genome of the producing strain Clostridium sp. UCM B-7570 was sequenced and characterized, and the genes encoding enzymes involved in butanol fermentation were found and analyzed. The strain was identified as C. pasteurianum and suggested for metabolic engineering purposes.
JOURNAL OF APPLIED GENETICS
(2023)
Article
Chemistry, Multidisciplinary
Y. T. Candace Ho, Joe A. Kaczmarski, Julien Tailhades, Thierry Izore, David L. Steer, Ralf B. Schittenhelm, Manuela Tosin, Colin J. Jackson, Max J. Cryle
Summary: Nonribosomal peptide synthetases play a significant role in producing essential peptide natural products, with carrier proteins as their core component. By replacing the CP substrate thioesters with stabilized ester analogues, active condensation domain complexes are formed, while amide stabilization leads to non-functional complexes.
CHEMICAL COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Daniel J. Leng, Anja Greule, Max J. Cryle, Manuela Tosin
Summary: Chemical probes were used to capture biosynthetic intermediates generated in the nonribosomal peptide formation of vancomycin in vivo. The putative intercepted intermediates were characterised via HR-LC-MS2, providing insights into the timing of the first chlorination of the peptide backbone by the halogenase VhaA. This information is significant for enzyme engineering towards the production of novel glycopeptides.
CHEMICAL COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Hui Hong, Markiyan Samborskyy, Yongjun Zhou, Peter F. Leadlay
CELL CHEMICAL BIOLOGY
(2019)
Article
Microbiology
Luciana Gonzaga de Oliveira, Renata Sigrist, Bruno Sachetto Paulo, Markyian Samborskyy
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2019)
Article
Chemistry, Multidisciplinary
Fabrizio Alberti, Daniel J. Leng, Ina Wilkening, Lijiang Song, Manuela Tosin, Christophe Corre
Article
Microbiology
Taicia Pacheco Fill, Jessica Fernanda Baretta, Luiz Gonzaga Paula de Almeida, Iran Malavazi, Louise Teixeira Cerdeira, Markiyan Samborskyy, Ana Tereza Ribeiro de Vasconcelos, Peter Leadlay, Edson Rodrigues-Filho
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2018)
Article
Chemistry, Multidisciplinary
Alexander M. Prophet, Kritanjan Polley, Gary J. Van Berkel, David T. Limmer, Kevin R. Wilson
Summary: The oxidation kinetics of iodide by ozone at the air-water interface is studied in single microdroplets. Molecular simulations and kinetic modeling are used to understand the underlying multiphase mechanism.
Article
Chemistry, Multidisciplinary
Rong Zhang, Jiajing Lan, Fei Wang, Shumei Chen, Jian Zhang
Summary: By utilizing 1,1'-ferrocene dicarboxylic acid as a chelating and surface protection ligand, we have synthesized multi-nuclear indium oxide clusters with varying nuclear sizes, including heptanuclear and thirteen-nuclear clusters. These clusters possess labile coordination sites, allowing for structural modification and self-assembly, resulting in the formation of various cluster structures.
Article
Chemistry, Multidisciplinary
Hui Wang, Hui Liu, Mingsen Wang, Jiaheng Hou, Yongjun Li, Yuancheng Wang, Yingjie Zhao
Summary: Two supramolecular complexes were prepared using CBs and M1, and their single-crystal structures were analyzed by SCXRD. The unexpected 1:2 self-assembly structure between M1 and CB[8] was discovered for the first time. These complexes exhibit unique photophysical properties and provide valuable information about the structure and photophysical properties of supramolecular complexes.
Article
Chemistry, Multidisciplinary
Chang-Hee Lee, Sookil Park, Sanggil Kim, Ji Young Hyun, Hyun Soo Lee, Injae Shin
Summary: The epidermal growth factor receptor (EGFR) is a cell-surface glycoprotein involved in cell proliferation and tumor development. This study used a fluorescently labeled EGFR to investigate its time-dependent endocytosis in live cells and found that appended glycans affect EGFR internalization. Additionally, the study detected sialic acid residues attached to EGFR on the live cell surface using FRET-based imaging. This research provides valuable insights into the cellular functions of EGFR.
Article
Chemistry, Multidisciplinary
Subhankar Sahu, Lokesh Kumar, Sumita Das, Dipti Gupta, Ruchi Anand
Summary: This study proposes a strategy that combines organic electronics with biosensor scaffolds to create a compact device for monitoring environmental aromatic pollution. By coupling biosensing protein MopR with an organic electrochemical transistor (OECT), a sensor module capable of efficient detection of phenol was designed. Exclusive phenol detection with minimal loss of sensitivity could be achieved in complex pollutant mixtures and real environmental samples.
Review
Chemistry, Multidisciplinary
Changseok Lee, Hyung-Joon Kang, Sungwoo Hong
Summary: The formation of C-N bonds through hydroamination reactions catalyzed by nickel hydrides has been a topic of recent interest. This approach offers a way to efficiently transform a variety of alkene and alkyne substrates into compounds enriched with C-N bonds. The review provides a concise overview of the underlying reaction mechanisms and aims to stimulate further progress in NiH-catalytic techniques and catalyst design.
Article
Chemistry, Multidisciplinary
Yueci Wu, Lu-Lu Sun, Hai-Hao Han, Xiao-Peng He, Weiguo Cao, Tony D. James
Summary: Drug-induced liver injury (DILI) is a common cause of acute liver failure in the USA and Europe, but most cases can be recovered or prevented by discontinuing the offending drug. Recent research has found that peroxynitrite (ONOO-) can be used as a potential indicator for early diagnosis of DILI, and there is an urgent need to establish a method to detect and track peroxynitrite in DILI cases. In this study, a FRET-based nano fluorescent probe CD-N-I was developed, which showed high selectivity and sensitivity in detecting peroxynitrite. The probe successfully detected exogenous peroxynitrite in live cells and endogenous peroxynitrite in APAP-induced liver injury of HepG2 cells.
Article
Chemistry, Multidisciplinary
Dmitry L. Lipilin, Mikhail O. Zubkov, Mikhail D. Kosobokov, Alexander D. Dilman
Summary: This article describes a direct photocatalytic method for the thiolation of unprotected acids, which was previously challenging. By using a thionocarbonate reagent with an N-O bond, the efficient conversion of carboxylic acids to thiols is achieved.
Article
Chemistry, Multidisciplinary
Jason Malenfant, Lucille Kuster, Yohann Gagne, Kouassi Signo, Maxime Denis, Sylvain Canesi, Mathieu Frenette
Summary: Raman microscopy can reveal compound-specific vibrational fingerprints without sample preparation. The combination of efficient theoretical calculations and a user-friendly software can accurately predict peak positions and provide match scores to assist with structure determination.
Article
Chemistry, Multidisciplinary
Jayoh A. Hernandez, Paul S. Micus, Sean Alec Lois Sunga, Luca Mazzei, Stefano Ciurli, Gabriele Meloni
Summary: Essential trace metals play crucial roles in the survival and virulence of bacterial pathogens. Helicobacter pylori requires nickel for colonization and persistence in the stomach, and NixA is an essential nickel transporter in this process. This study characterizes the selectivity and electrogenic nature of NixA-mediated nickel transport.
Article
Chemistry, Multidisciplinary
Tarali Devi, Kuheli Dutta, Jennifer Deutscher, Stefan Mebs, Uwe Kuhlmann, Michael Haumann, Beatrice Cula, Holger Dau, Peter Hildebrandt, Kallol Ray
Summary: This study emphasizes the importance of subtle electronic changes and secondary interactions in the stability of biologically relevant metal-dioxygen intermediates. It also shows that the role of the chloride ligand in stabilizing the Fe-III-(OOBu)-Bu-t moiety can extend to other anions, including the thiolate ligand.
Article
Chemistry, Multidisciplinary
Jacqueline R. Santhouse, Jeremy M. G. Leung, Lillian T. Chong, W. Seth Horne
Summary: By studying the folding kinetics and mechanism of the BdpA sequence, researchers found that altering the backbone connectivity can affect protein folding. This suggests that protein mimetic chains have a significant degree of plasticity in transitioning between unfolded and folded states.
Article
Chemistry, Multidisciplinary
Divanshu Gupta, Ralf Einholz, Holger F. Bettinger
Summary: This study presents the first direct spectroscopic evidence of a cyclic seven-membered iminoborane. Compared to linear amino-iminoboranes, this cyclic iminoborane exhibits weakened bond strength and lower Lewis acidity value. The study suggests that the reduced ring strain of cyclic iminoborane prevents nitrogen fixation but allows facile (2 + 2) cycloaddition reaction with C2H4.
Article
Chemistry, Multidisciplinary
Renny Mathew, Aniruddha Mazumder, Praveen Kumar, Julie Matula, Sharmarke Mohamed, Petr Brazda, Mahesh Hariharan, Brijith Thomas
Summary: This study reveals the packing arrangement of partially disordered nitro-perylenediimide (NO2-PDI) using a synergistic approach that combines 3D ED, ssNMR, and DFT techniques. By overcoming these challenges, this methodology opens up new avenues for material characterization, driving exciting advancements in the field.
