Article
Biochemistry & Molecular Biology
Dallas R. Fonseca, Madison B. Loppnow, Leslie A. Day, Elisa L. Kelsey, Mohd Farid Abdul Halim, Kyle C. Costa
Summary: Natural transformation is an important evolutionary driver in microbial populations, but its mechanism is mainly characterized in bacteria. In this study, we identified a catalog of genes necessary for transformation in Methanococcus maripaludis, expanding our understanding of natural transformation in archaea. We found several transformation-associated candidate genes, including those encoding components of the type IV-like pilus, transcription/translation associated genes, putative membrane-bound transport proteins, and genes with unknown functions. Furthermore, we confirmed the importance of these genes for transformation using allelic replacement mutagenesis, and identified a conserved mechanism for DNA transfer in multiple archaea.
MOLECULAR GENETICS AND GENOMICS
(2023)
Article
Biochemistry & Molecular Biology
Shimei Lan, Zhangcheng Li, Huafang Hao, Shuang Liu, Zhicheng Huang, Yutong Bai, Yanzhao Li, Xinmin Yan, Pengcheng Gao, Shengli Chen, Yuefeng Chu
Summary: In this study, a fluorescent transposon mutant library of Mycoplasma bovis was constructed to identify adhesion-related genes. The surface-localized lipoprotein LppB was identified as a key factor for adhesion and invasion of host cells by the bacterium. The study suggests that LppB could be a potential therapeutic and vaccine target for Mycoplasma species.
Article
Biochemistry & Molecular Biology
Sarah L. Price, Derek Thibault, Taylor M. Garrison, Amanda Brady, Haixun Guo, Thomas E. Kehl-Fie, Sylvie Garneau-Tsodikova, Robert D. Perry, Tim van Opijnen, Matthew B. Lawrenz
Summary: Nutritional immunity involves limiting the availability of essential transition metals to invading pathogens. Yersinia pestis, the causative agent of plague, secretes a molecule called yersiniabactin to acquire iron and zinc during infection. This study identified the mechanism of yersiniabactin secretion, which has remained elusive for over 30 years, and demonstrated its importance for bacterial virulence.
Article
Food Science & Technology
Hui Wang, Kai Ma, Jiawei Shen, Mengcheng Fang, Hao Pei, Yun Li, Chengfeng Zhu, Fang Shu, Bingbing Li, Ting Xue
Summary: This study determined potential genes related to desiccation stress in Staphylococcus aureus (S. aureus) using transposon random mutagenesis. Eight mutants with different mutation sites were screened from a mutant library, showing lower survival rates under desiccation stress compared to the wild-type strain. These mutation sites were identified as potential desiccation-tolerant related genes. The study provides valuable information for controlling S. aureus in low water activity foods and their production environments.
FOOD RESEARCH INTERNATIONAL
(2023)
Article
Microbiology
Helen C. Neale, Michelle T. Hulin, Richard J. Harrison, Robert W. Jackson, Dawn L. Arnold
Summary: Bacterial canker of Prunus, caused by Pseudomonas syringae, affects economically important stone fruit crops like cherry, peach, apricot, and plum. Strains from two pathovars of P.s. have evolved to infect Prunus convergently, with mutations in virulence genes leading to changes in pathogenicity.
Article
Biotechnology & Applied Microbiology
Martyna Gongerowska-Jac, Marcin Jan Szafran, Dagmara Jakimowicz
Summary: This study introduces a novel approach to identify regulatory proteins that control transcription in Streptomyces. The experimental results demonstrate that the SCO4804 gene positively influences the transcription of topA, revealing a new player in the control of chromosome topology in these bacteria.
MICROBIAL CELL FACTORIES
(2021)
Article
Medicine, Research & Experimental
Yuning J. J. Tang, Emily G. G. Shuldiner, Saswati Karmakar, Monte M. M. Winslow
Summary: The vast number of genomic and molecular alterations in cancer present a significant challenge in understanding the mechanisms of tumor formation and identifying targets for treatment. High-throughput functional genomic methods in genetically engineered mouse models allow for rapid and systematic investigation of cancer driver genes. This review discusses the concepts and tools for investigating functionally important cancer genes in vivo using autochthonous cancer models, highlights emerging technical advances, potential opportunities for future research, and outlines a vision for integrating genetic perturbations with molecular analyses to advance our understanding of cancer genetics and molecular basis.
COLD SPRING HARBOR PERSPECTIVES IN MEDICINE
(2023)
Article
Immunology
Fan Yin, Yan Hu, Zixuan Bu, Yuying Liu, Hui Zhang, Yawen Hu, Ying Xue, Shaowen Li, Chen Tan, Xiabing Chen, Lu Li, Rui Zhou, Qi Huang
Summary: In this study, a transposon (Tn) mutagenesis library and a mouse infection model were used to identify important genes involved in the in vivo fitness of porcine ExPEC. Several genes, including Delta fimG, were found to be critical for in vivo fitness and adhesion to host cells. Additionally, metabolic genes and regulatory genes were also identified as important determinants of in vivo fitness. This study provides insights into the pathogenicity of porcine ExPEC.
Article
Biotechnology & Applied Microbiology
Hai-yue Bao, Hui-jie Li, Yong-yong Zhang, Andreas Bechthold, Xiao-ping Yu, Zheng Ma
Summary: In this study, a transposon mutagenesis strategy was employed to identify an unknown gene involved in rimocidin biosynthesis in Streptomyces rimosus M527. The results showed that the genes rrt and hyp have a positive and negative impact on rimocidin production, respectively, without affecting cell growth.
WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Daniel P. Miller, David A. Scott
Summary: Proteases are essential virulence factors of Porphyromonas gingivalis, a pathogen associated with Alzheimer's disease, cancer, arthritis, and periodontitis. Transposon sequencing has been used to identify essential genes in various disease-relevant conditions, which may be potential therapeutic targets for controlling P. gingivalis infections.
TRENDS IN MICROBIOLOGY
(2021)
Article
Oncology
Xiaozhong Teng, Tetsu Hayashida, Takeshi Murata, Aiko Nagayama, Tomoko Seki, Maiko Takahashi, Yuko Kitagawa
Summary: A transposon mutagenesis screen identified TAB2-NF-κB pathway as a candidate gene for eribulin resistance in breast cancer. Down-regulation of TAB2 increased sensitivity to eribulin, while combination of NF-κB inhibitors with eribulin significantly reduced cell viability and increased drug cytotoxicity.
Article
Microbiology
Li Huang, Mafeng Liu, Aparna Viswanathan Ammanath, Dekang Zhu, Renyong Jia, Shun Chen, Xinxin Zhao, Qiao Yang, Ying Wu, Shaqiu Zhang, Juan Huang, Xumin Ou, Sai Mao, Qun Gao, Di Sun, Bin Tian, Friedrich Goetz, Mingshu Wang, Anchun Cheng
Summary: The study identified 8 essential genes for natural transformation in R. anatipestifer ATCC11845, with 4 of them having putative annotations in the NCBI database.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
William M. Matern, Harley T. Harris, Carina Danchik, Marissa McDonald, Gopi Patel, Aashish Srivastava, Thomas R. Ioerger, Joel S. Bader, Petros C. Karakousis
Summary: Mycobacterium tuberculosis, the causative agent of tuberculosis, displays antibiotic tolerance under nutrient-starved conditions. A forward genetic screen identified candidate genes associated with resistance to rifampin and isoniazid. These findings provide potential therapeutic targets for more effective tuberculosis treatment.
Article
Plant Sciences
Yuki Monden, Hirona Tanaka, Ryota Funakoshi, Seiya Sunayama, Kiyotaka Yabe, Eri Kimoto, Kentaro Matsumiya, Takanori Yoshikawa
Summary: This study identified two rice lines with higher protein content by analyzing the insertion sites of mPing transposons and the transcriptome. The results provide insights into the mechanism behind increased protein content in rice and contribute to solving malnutrition and health problems by improving rice protein content.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Engineering, Biomedical
Neety Sahu, Pranay Agarwal, Fiorella Grandi, Michela Bruschi, Stuart Goodman, Derek Amanatullah, Nidhi Bhutani
Summary: The study demonstrates that co-culturing patient-derived OA cartilage explants with alginate-encapsulated MSC microbeads can lead to improved proteoglycan distribution, increased sGAG content, cell proliferation, elevated levels of cytokines such as IL-10, HGF, and sFAS, increased TIMP1 levels, and a decrease in apoptotic cells. This indicates that the paracrine factors secreted by MSC microbeads create a conducive microenvironment for anabolic, proliferative, and anti-apoptotic processes in patient-derived OA cartilage, ultimately promoting endogenous regeneration.
ADVANCED HEALTHCARE MATERIALS
(2021)
Article
Oncology
Xiaorong Zhou, Barrett L. Updegraff, Yabin Guo, Michael Peyton, Luc Girard, Jill E. Larsen, Xian-Jin Xie, Yunyun Zhou, Tae Hyun Hwang, Yang Xie, Jaime Rodriguez-Canales, Pamela Villalobos, Carmen Behrens, Ignacio I. Wistuba, John D. Minna, Kathryn A. O'Donnell
Article
Genetics & Heredity
Scott A. Keith, Sarah K. Maddux, Yayu Zhong, Meghna N. Chinchankar, Annabel A. Ferguson, Arjumand Ghazi, Alfred L. Fisher
Article
Genetics & Heredity
Yabin Guo, Yin Zhang, Kaishun Hu
Article
Cell Biology
Barrett L. Updegraff, Xiaorong Zhou, Yabin Guo, Mahesh S. Padanad, Pei-Hsuan Chen, Chendong Yang, Jessica Sudderth, Carla Rodriguez-Tirado, Luc Girard, John D. Minna, Prashant Mishra, Ralph J. DeBerardinis, Kathryn A. O'Donnell
Article
Genetics & Heredity
Kaishun Hu, Yu Li, Wenjing Wu, Hengxing Chen, Zhen Chen, Yin Zhang, Yabin Guo, Yin Dong
Article
Biochemistry & Molecular Biology
Kaishun Hu, Wenjing Wu, Yu Li, Lehang Lin, Dong Chen, Haiyan Yan, Xing Xiao, Hengxing Chen, Zhen Chen, Yin Zhang, Shuangbing Xu, Yabin Guo, H. Phillip Koeffler, Erwei Song, Dong Yin
Article
Biotechnology & Applied Microbiology
Jiawen Yang, Bin Yuan, Yu Wu, Meiyu Li, Jian Li, Donglin Xu, Zeng-hong Gao, Guangwei Ma, Yiting Zhou, Yachao Zuo, Jin Wang, Yabin Guo
Article
Genetics & Heredity
Yiting Zhou, Guangwei Ma, Jiawen Yang, Zenghong Gao, Yabin Guo
Summary: Recent study showed that Sleeping Beauty transposon can integrate into non-TA sites, mainly through aberrant integrations. The consensus sequence of the non-TA target sites corresponds to the transposon end sequence.
FRONTIERS IN GENETICS
(2021)
Article
Virology
Yujin Cui, Yabin Guo
Summary: This study analyzed the integration of the Tf1 retrotransposon in Schizosaccharomyces pombe and found a palindromic pattern in its integration sites, indicating interaction with subunits of the integrase oligomer. Furthermore, the study showed that Tf1 integration favors regions with nucleosome depletion.
Article
Biochemistry & Molecular Biology
Ying Liu, Guangwei Ma, Zenghong Gao, Jian Li, Jin Wang, Xiangping Zhu, Ruowu Ma, Jiawen Yang, Yiting Zhou, Kaishun Hu, Yin Zhang, Yabin Guo
Summary: Chromosome rearrangement plays significant roles in development, carcinogenesis, and evolution, but its mechanisms and subsequent effects are not fully understood. In this study, CRISPR-Cas9 was used to induce DNA double-strand breaks in human cells, resulting in global chromosome rearrangement. The rearranged genomes exhibited typical patterns observed in tumor genomes, and the epigenetic and transcriptomic landscapes were reshaped. Gene expressions related to p53 pathway, DNA repair, cell cycle, and apoptosis were greatly altered. This study provides a new application of CRISPR-Cas9 and a practical approach for global chromosome rearrangement in complex mammalian genomes.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Feng Li, Michael Lee, Caroline Esnault, Katie Wendover, Yabin Guo, Paul Atkins, Mikel Zaratiegui, Henry L. Levin
Summary: Retroelements can retain insertion activity in the absence of integrase by using an IN-independent pathway, possibly through single-strand annealing and noncanonical homologous recombination.
Meeting Abstract
Oncology
Xiaorong Zhou, Barrett L. Updegraff, Yabin Guo, Michael Peyton, Luc Girard, Jill E. Larsen, Xian-Jin Xie, Yunyun Zhou, Tae Hyun Hwang, Yang Xie, Jaime Rodriguez-Canales, Pamela Villalobos, Carmen Behrens, Wistuba I. Ignacio, John D. Minna, Kathryn A. O'Donnell
Article
Genetics & Heredity
Yabin Guo