Article
Chemistry, Multidisciplinary
Helal Abujubara, Jie Yang, A. Birsen Otyakmaz, Anais F. M. Noisier, Werngard Czechtizky, Malin Lemurell, Alesia A. A. Tietze
Summary: We report a mild ionic liquid (IL)-mediated thiolation technique using 1,3-ethyl-methyl imidazolium acetate as a solvent and precursor to generate activated IL for the conjugation reaction of small molecules and peptides. Interestingly, a bifunctional active IL could also be successfully employed as a linker for peptides lacking cysteine. This study lays the foundation for further investigation of the use of active ILs in modifying larger and more complex therapeutic modalities.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Biotechnology & Applied Microbiology
Garima Jain, Helga Ertesvag
Summary: In this study, the homologous recombination method in Rhodococcus opacus was improved by constructing and evaluating a conjugative, conditional suicide plasmid based on a replicon derived from Corynebacterium glutamicum. The low recombination frequency issue was successfully solved. It was also discovered that mycolic acid is essential for the viability of R. opacus.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Article
Genetics & Heredity
Emily L. L. Bean, Calvin Herman, Mary E. E. Anderson, Alan D. D. Grossman
Summary: Author summaryHorizontal gene transfer plays a crucial role in microbial evolution, allowing bacteria to acquire new genes and traits rapidly. Integrative and conjugative elements (ICEs) are mobile genetic elements that reside in a bacterial host chromosome and are significant drivers of horizontal gene transfer. This study investigated the determinants of transfer efficiencies by making and utilizing hybrid ICEs. The findings showed that there are species-specific interactions that help determine the efficiencies of stable acquisition. Furthermore, these hybrid elements can be useful in genetic engineering and synthetic biology to move genes and pathways into different bacterial species with greater efficiencies than naturally occurring ICEs.
Article
Engineering, Environmental
Houpu Zhang, Jiajin Song, Zhiruo Zheng, Tongxin Li, Nan Shi, Yuling Han, Luqing Zhang, Yunlong Yu, Hua Fang
Summary: Co-pollution of soil with pesticide residues and antibiotic resistance genes (ARGs) is increasing due to the substantial usage of pesticides and organic fertilizers in greenhouse-based agricultural production. Non-antibiotic stresses, including those from agricultural fungicides, are potential co-selectors for the horizontal transfer of ARGs, but the underlying mechanism remains unclear.
Article
Biochemistry & Molecular Biology
Eric Moeglin, Lina Barret, Bruno Chatton, Mariel Donzeau
Summary: This study describes a method for site-specific labeling of nanobodies using two co-assembling peptide tags, E3 and K3. The method provides a simple and robust approach for associating VHH and fluorescent probes, and demonstrates the potential application of these molecular probes in cell immuno-staining.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Microbiology
Lucia Giacone, M. Marcela Cameranesi, Rocio I. Sanchez, Adriana S. Limansky, Jorgelina Moran-Barrio, Alejandro M. Viale
Summary: By using various experimental approaches, it was found that plasmids in two closely related A. baumannii strains coexisting in the hospital environment generate structural diversity through site-specific recombination. The reversible plasmid genome rearrangements reported here represent an ancient mechanism for rapid adaptation of bacterial hosts to changing environments, and have played an important role in the evolution and dissemination of Acinetobacter plasmids and the acquisition of bla(OXA-58) genes in both Acinetobacter and non-Acinetobacter populations residing in the hospital niche.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Microbiology
Ruben L. L. Sanchez-Nieves, Changyi Zhang, Rachel J. J. Whitaker
Summary: This study investigates a plasmid-mediated mechanism of gene transfer in Sulfolobus islandicus that leads to high frequency recombination within the chromosome. Through genomic analysis, the researchers establish the distribution of recombinant tracts and identify distal non-selected recombination events. This study reveals the molecular factors governing gene transfer and recombination in crenarchaea.
FRONTIERS IN MICROBIOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Xueying Tian, Bin Zhou
Summary: SSRs are crucial genome engineering tools that have greatly advanced our understanding of gene functions and cell lineage relationships in biomedical research. To meet the increasing complexity of research, new site-specific genetic recombination technologies are being developed, including innovative strategies such as combining different recombinase systems and creating chemical- and light-inducible genetic systems.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Chemistry, Medicinal
Qun Zhou, Josephine Kyazike, Ekaterina Boudanova, Michael Drzyzga, Denise Honey, Robert Cost, Lihui Hou, Francis Duffieux, Marie-Priscille Brun, Anna Park, Huawei Qiu
Summary: By designing and introducing free cysteine residues into specific regions of antibodies, conjugates with high efficiency and selectivity can be generated.
Article
Chemistry, Multidisciplinary
Chao Dong, Guangqi Wu, Chen Chen, Xia Li, Rui Yuan, Liang Xu, Hui Guo, Jay Zhang, Hua Lu, Feng Wang
Summary: Researchers have developed a novel biocompatible selenopolypeptide and site-specifically conjugated it with A1AT, demonstrating that this strategy can improve the pharmacological properties of A1AT and potentially be applied to other oxidation-sensitive biotherapeutics.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Review
Biochemistry & Molecular Biology
Qun Zhou
Summary: As antibody-drug conjugates have become crucial for cancer therapy, various approaches have been developed to achieve selective and homogeneous molecules. These methods involve engineering antibodies to introduce specific amino acids or peptides for coupling. In addition to cytotoxic compounds, these techniques can also be applied to conjugate non-cytotoxic compounds, proteins/peptides, glycans, lipids, and nucleic acids. The resulting site-specific antibody conjugates offer potential for proof-of-concept studies and the development of novel therapeutic options.
Article
Biochemistry & Molecular Biology
Joel Sharbrough, Laura Bankers, Emily Cook, Peter D. Fields, Joseph Jalinsky, Kyle E. McElroy, Maurine Neiman, John M. Logsdon, Jeffrey L. Boore
Summary: Recent advances in long-read sequencing technology have allowed for direct investigation of mitochondrial genome architecture and recombination. Using PacBio sequencing, mitochondrial genomes of two species of New Zealand freshwater snails were reassembled, revealing a previously undetected structure and evidence of recombination. These findings raise questions about the origins and commonness of inverted repeats in cytoplasmic genomes and their role in mitochondrial genome evolution.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Microbiology
Laetitia Van Wonterghem, Matteo De Chiara, Gianni Liti, Jonas Warringer, Anne Farewell, Natalie Verstraeten, Jan Michiels
Summary: This study focused on bacterial host factors that assist in the transfer of conjugative plasmids, observing significant differences in conjugation efficiency among donor Escherichia coli strains. Through genome-wide association studies, candidate genes involved in conjugation were identified, with the roles of some genes confirmed by validating defects in single-gene deletion mutants. The study suggests that factors such as motility, energy supply, intracellular pH or salinity of the donor may affect the efficiency of plasmid transfer.
Article
Microbiology
Amy S. Gargis, Lori M. Spicer, Alyssa G. Kent, Wenming Zhu, Davina Campbell, Gillian McAllister, Thomas O. Ewing, Valerie Albrecht, Valerie A. Stevens, Mili Sheth, Jasmine Padilla, Dhwani Batra, J. Kristie Johnson, Alison Laufer Halpin, J. Kamile Rasheed, Christopher A. Elkins, Maria Karlsson, Joseph D. Lutgring
Summary: Enterococcus faecalis and faecium isolates with resistance to daptomycin and/or linezolid have become increasingly prevalent worldwide. This study presents the genomic characterization of daptomycin- and linezolid-resistant E. faecalis and E. faecium isolates from the United States between 2013 and 2016. The majority of daptomycin-resistant E. faecium isolates belonged to the emerging ST736 clone and contained mutations previously associated with resistance. However, some isolates did not contain these mutations. Linezolid resistance was rare, but two linezolid-resistant E. faecium isolates also exhibited resistance to daptomycin and vancomycin. The resistance mechanisms were identified and characterized through long-read sequencing.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
David Bartee, Kellie D. Nance, Jordan L. Meier
Summary: This study reports the synthesis and biophysical characterization of ac4C in its endogenous eukaryotic sequence context, establishing a chemical foundation for understanding the function of a universally conserved nucleobase in biology and disease.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Microbiology
Donghai Peng, Jian Lin, Qiong Huang, Wen Zheng, Guoqiang Liu, Jinshui Zheng, Lei Zhu, Ming Sun
ENVIRONMENTAL MICROBIOLOGY
(2016)
Article
Microbiology
Pengxia Wang, Qian Zhu, Hui Shang, Yiguang Zhu, Ming Sun
JOURNAL OF BASIC MICROBIOLOGY
(2016)
Article
Biotechnology & Applied Microbiology
Shouyong Ju, Jian Lin, Jinshui Zheng, Shaoying Wang, Hongying Zhou, Ming Sun
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2016)
Article
Biochemistry & Molecular Biology
Jinbo Huang, Zeyuan Guan, Liting Wan, Tingting Zou, Ming Sun
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2016)
Article
Biotechnology & Applied Microbiology
Shouyong Ju, Jinshui Zheng, Jian Lin, Ce Geng, Lei Zhu, Ziyu Guan, Ziqiang Zheng, Ming Sun
JOURNAL OF BIOTECHNOLOGY
(2016)
Article
Biotechnology & Applied Microbiology
Zhaoxia Dong, Junhua Li, Jinshui Zheng, Ce Geng, Donghai Peng, Ming Sun
JOURNAL OF BIOTECHNOLOGY
(2016)
Article
Biotechnology & Applied Microbiology
Yueying Wang, Jingjing Fu, Qian Zhu, Lei Zhu, Jinshui Zheng, Hualin Liu, Donghai Peng, Lifang Ruan, Ming Sun
JOURNAL OF BIOTECHNOLOGY
(2016)
Article
Microbiology
Bingyue Xin, Jinshui Zheng, Hualin Liu, Junhua Li, Lifang Ruan, Donghai Peng, Muhammad Sajid, Ming Sun
FRONTIERS IN MICROBIOLOGY
(2016)
Article
Biochemistry & Molecular Biology
Cuiying Du, Shiyun Cao, Xiangyu Shi, Xiangtao Nie, Jinshui Zheng, Yun Deng, Lifang Ruan, Donghai Peng, Ming Sun
JOURNAL OF BIOLOGICAL CHEMISTRY
(2017)
Article
Biotechnology & Applied Microbiology
Ziqiang Zheng, Jinshui Zheng, Donghai Peng, Ming Sun
JOURNAL OF BIOTECHNOLOGY
(2017)
Review
Biochemistry & Molecular Biology
Chaohua Zhu, Gang Guo, Qiqi Ma, Fengjuan Zhang, Funing Ma, Jianping Liu, Dao Xiao, Xiaolin Yang, Ming Sun
PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY
(2017)
Article
Multidisciplinary Sciences
Ce Geng, Xiangtao Nie, Zhichao Tang, Yuyang Zhang, Jian Lin, Ming Sun, Donghai Peng
SCIENTIFIC REPORTS
(2016)
Article
Microbiology
Jianwei Shi, Fengjuan Zhang, Ling Chen, Alejandra Bravo, Mario Soberon, Ming Sun
Summary: PFTs are pore-forming toxins used by bacterial pathogens to establish infections, causing localized pore formation in gut cells of nematodes but systemic mitochondrial damage in distal regions. These toxins affect the activity of mitochondrial respiratory chain complex I, leading to loss of mitochondrial membrane potential and fragmentation, ultimately increasing sensitivity to PFTs. Inhibition of mitochondrial fission or increase of mitochondrial content improves survival of animals treated with PFTs, highlighting the importance of mitochondrial changes in PFT-mediated toxicity.
ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Biochemical Research Methods
Hualin Liu, Jinshui Zheng, Dexin Bo, Yun Yu, Weixing Ye, Donghai Peng, Ming Sun
Summary: Bacillus thuringiensis (Bt) toxin genes have been widely utilized in genetically modified crops for pest control. The web-based tool BtToxin_Digger efficiently mines toxin genes from large-scale sequence data, enabling accurate prediction and downstream analysis and testing. This versatile tool can also be used to mine other targeting genes from genome and metagenome data with database replacement.
Article
Microbiology
Guoqiang Liu, Yingying Kong, Hualin Liu, Donghai Peng, Lifang Ruan, Yiming Wu, Ming Sun
FEMS MICROBIOLOGY LETTERS
(2017)