Article
Agronomy
Marlene Lachaux, Emilie Thomas, Adam J. Bogdanove, Boris Szurek, Mathilde Hutin
Summary: We identified and characterized TalD and TalI as two African Xoo TALEs with avirulence activity on IR64 and CT13432 respectively. Resistance of CT13432 against African Xoo results from the combination of two mechanisms, one relying on the TalI-mediated induction of an unknown executor gene and the other on an Xa1-like gene or allele.
Article
Multidisciplinary Sciences
Ting-Sung Hsieh, Victor A. Lopez, Miles H. Black, Adam Osinski, Krzysztof Pawlowski, Diana R. Tomchick, Jen Liou, Vincent S. Tagliabracci
Summary: During infection, bacterial pathogens can manipulate host cellular membranes by utilizing a self-organizing system involving bacterial kinases and phosphatases, such as the Legionella effector MavQ. This mechanism allows bacteria to hijack host cellular structures for survival by driving rapid turnover of phosphoinositides and inducing vesicle and tubule budding.
Review
Plant Sciences
Melania Figueroa, Diana Ortiz, Eva C. Henningsen
Summary: Fungal pathogens can secrete hundreds of effectors that promote host susceptibility, posing a challenge for researchers due to biological complexity and lack of genetic tools in some fungi. Recent advancements have shed light on how these pathogens manipulate plant physiology using similar strategies. Breakthroughs have also been made in identifying effectors from challenging systems and introducing concepts such as the 'iceberg model' to explain the suppression of plant immunity by certain effectors.
CURRENT OPINION IN PLANT BIOLOGY
(2021)
Article
Plant Sciences
Ayaka Yoshihisa, Satomi Yoshimura, Motoki Shimizu, Sayaka Sato, Shogo Matsuno, Akira Mine, Koji Yamaguchi, Tsutomu Kawasaki
Summary: In this study, the researchers discovered that OsERF101 is a transcription factor that interacts with Xa1, and it can regulate the recognition of TAL effectors by Xa1 and act as a positive regulator of Xa1-mediated immunity. Additionally, OsERF101 negatively regulates another Xa1-mediated immune pathway.
Article
Biochemistry & Molecular Biology
Daisylyn Senna Tan, Shun Lai Cheung, Ya Gao, Maike Weinbuch, Haoqing Hu, Liyang Shi, Shih-Chieh Ti, Andrew P. Hutchins, Vlad Cojocaru, Ralf Jauch
Summary: Oct4 is found to bind to a compact palindromic DNA element with a methylated CpG core (CpGpal) in alternative states of pluripotency and during cellular reprogramming towards induced pluripotent stem cells (iPSCs). This binding is Oct4-specific and driven by its POU-homeodomain. The POU-specific domain is detached from DNA during the binding process.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Biochemistry & Molecular Biology
Naohiro Yano, Alexey V. Fedulov
Summary: Aberrant DNA hypermethylation is observed in various diseases, and therapeutic DNA demethylation has the potential to elucidate the importance of epigenetic alterations and open new avenues for treatment. However, current methods are limited in their ability to target specific epimutations. Gene-specific epigenetic editing, using DNA-binding molecules and demethylases, offers a critical approach for re-activating silenced genes. Challenges, such as the need for transgenesis, need to be addressed. This review explores gene-specific DNA demethylation as an innovative therapeutic strategy.
Article
Chemistry, Physical
Kwang-Im Oh, Ho-Seong Jin, Thananjeyan Balasubramaniyam, Ji-Yeon Shin, Seo-Ree Choi, Young Jun Seo, Byeong-Seon Kim, Yeo-Jin Seo, Seung-Ryong Kwon, Nak-Kyoon Kim, Joon-Hwa Lee
Summary: Developing chemical modifications of DNA to find drug targets is challenging. In this study, double-methylated guanosine was incorporated into DNA and its solution structure was determined. The flexible Z-DNA formed as a result showed slow conformational exchange and a novel helical structure. The transition from Z-DNA to tBZ provides new insights into structural diversity and may serve as a potential drug target.
JOURNAL OF MOLECULAR LIQUIDS
(2023)
Article
Biochemistry & Molecular Biology
Haixia Wang, Shumei Wang, Wei Wang, Lin Xu, Lydia R. J. Welsh, Marek Gierlinski, Stephen C. Whisson, Piers A. Hemsley, Petra C. Boevink, Paul R. J. Birch
Summary: Cytoplasmic RXLR effectors from Phytophthora infestans enter plant host cells via clathrin-mediated endocytosis. Transient silencing of clathrin heavy chain or the endosome marker gene attenuated P. infestans infection and reduced translocation of RXLR effectors into host cells. Co-localization of RXLR effectors with clathrin-coated vesicles and immunoprecipitation experiments confirmed the uptake of RXLR effectors via clathrin-mediated endocytosis.
Article
Biochemical Research Methods
Zhenxing Guo, Andrew M. Shafik, Peng Jin, Zhijin Wu, Hao Wu
Summary: In this work, a novel statistical method is developed to identify mRNA epigenetic modification regions from MeRIP-seq data, based on an empirical Bayesian hierarchical model. This method accounts for various sources of variations in the data through rigorous modeling and applies shrinkage estimation by borrowing information from transcriptome-wide data to stabilize the parameter estimation, showing higher accuracy, robustness, and efficiency compared to existing peak calling methods in simulation and real data analyses.
Article
Biochemistry & Molecular Biology
Franziska Wimmer, Ioannis Mougiakos, Frank Englert, Chase L. Beisel
Summary: This study applies cell-free transcription-translation systems to accelerate the characterization of multi-subunit CRISPR effectors and transposons. It uncovers different types of effectors and investigates targeting rules for transposons, providing convenience and methods for studying and utilizing the diversity of CRISPR-Cas systems and transposons.
Article
Genetics & Heredity
Olga Taryma-Lesniak, Tina E. Kjeldsen, Lise Lotte Hansen, Tomasz K. Wojdacz
Summary: Unequal amplification of templates in pyrosequencing can significantly affect its sensitivity and dynamic range, highlighting the importance of assessing the effect before using the technology.
Article
Spectroscopy
Amir Amiri Sadeghan, Hossein Soltaninejad, Mehdi Dadmehr, Amir Ali Hamidieh, Mohammad Ali Asadollahi, Morteza Hosseini, Mohammad Reza Ganjali, Saman Hosseinkhani
Summary: This method utilizes a fluorescence turn-on strategy to detect the methylation state of DNA, eliminating the need for labor-intensive chemical or enzymatic treatments. It shows a linear relationship within the detection limit range, exhibits quenching effect on unmethylated DNA, and has high specificity.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2021)
Article
Biochemical Research Methods
Hongfei Li, Yue Gong, Yifeng Liu, Hao Lin, Guohua Wang
Summary: Transcription factors (TFs) are proteins involved in gene expression regulation, and recent studies have shown that some TFs can interact with methylated DNA fragments. This study presents a machine learning-based approach to quickly identify TFs that can bind to methylated DNA. The proposed model, based on tripeptide word vector feature and recurrent neural network, achieves high accuracy in predicting TFs and their binding to methylated DNA.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Plant Sciences
Alvaro L. Perez-Quintero, R. Luis M. Rodriguez, Sara Cuesta-Morrondo, Eliska Hakalova, Daniela Betancurt-Anzola, Laura Carolina Camelo Valera, Luis Alberto Chica Cardenas, Luisa Matiz-Ceron, Jonathan M. Jacobs, Veronica Roman-Reyna, Alejandro Reyes Munoz, Adriana Jimena Bernal Giraldo, Ralf Koebnik
Summary: Strains of Xanthomonas citri pv. malvacearum cause bacterial blight of cotton, posing a serious threat to cotton production worldwide. The activity of TAL effectors is associated with the development of disease symptoms, and the pathogen exhibits genetic diversity and variation in TAL effector genes. Pseudogenization of TAL effector genes is observed, which may be related to resistance genes.
Article
Biochemistry & Molecular Biology
Suman Abhishek, Naveen Kumar Nakarakanti, Waghela Deeksha, Eerappa Rajakumara
Summary: UHRF1 SRA can recognize non-mCpG DNA, with contrasting mechanisms for hemi-mCpG and fully-mCpHpG DNA recognition. While the binding affinity for fully-mCpG is weaker, UHRF1 SRA exhibits higher affinity for fully-mCpHpG.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Review
Biochemistry & Molecular Biology
Leia Colin, Felix Ruhnow, Jian-Kang Zhu, Chunzhao Zhao, Yang Zhao, Staffan Persson
Summary: Salt stress causes ionic toxicity, osmotic stress, and oxidative stress, directly affecting plant growth and development. Plants perceive salt stress through the cell wall and coordinate effective responses. Some mechanisms underlying these processes have been elucidated.
Article
Plant Sciences
Mingjing Wang, Hailong Zhang, Xiaonan Zhao, Jingwen Zhou, Guochen Qin, Yuqi Liu, Xiaoyue Kou, Zhenjie Zhao, Tao Wu, Jian-Kang Zhu, Xianzhong Feng, Lixin Li
Summary: The gene AtSYP81 in Arabidopsis thaliana plays a critical role in root growth and development by regulating peroxisome- and peroxidase-mediated ROS homeostasis. Knockdown of AtSYP81 resulted in reduced root meristem activity and disruption of root stem cell niche identity. Transcriptome analysis revealed changed expression of class III peroxidases, adding evidence of the regulatory role of AtSYP81 in ROS signaling.
Article
Multidisciplinary Sciences
Ying Huang, Jing An, Sanchari Sircar, Clara Bergis, Chloe Dias Lopes, Xiaoning He, Barbara Da Costa, Feng-Quan Tan, Jeremie Bazin, Javier Antunez-Sanchez, Maria Florencia Mammarella, Ravi-sureshbhai Devani, Rim Brik-Chaouche, Abdelhafid Bendahmane, Florian Frugier, Chongjing Xia, Christophe Rothan, Aline V. Probst, Zouine Mohamed, Catherine Bergounioux, Marianne Delarue, Yijing Zhang, Shaojian Zheng, Martin Crespi, Sotirios Fragkostefanakis, Magdy M. Mahfouz, Federico Ariel, Jose Gutierrez-Marcos, Cecile Raynaud, David Latrasse, Moussa Benhamed
Summary: This study examines the changes in chromatin and gene expression in response to heat stress in tomato. They found that heat stress rapidly alters chromatin structure and leads to the formation of temporary contacts between promoters and enhancers, which drive the expression of genes responsive to heat stress. The researchers also discovered that this spatial reorganization of chromatin requires the transcription factor HSFA1a.
NATURE COMMUNICATIONS
(2023)
Review
Biochemical Research Methods
Ahmed Ghouneimy, Ahmed Mahas, Tin Marsic, Rashid Aman, Magdy Mahfouz
Summary: The COVID-19 pandemic has highlighted the need for decentralized Point of Care (POC) solutions in the diagnostic field. CRISPR-based diagnostics have emerged as promising tools that could revolutionize molecular diagnostics, but there are obstacles to their use in POC applications.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Wenjun Jiang, Rashid Aman, Zahir Ali, Magdy Mahfouz
Summary: Rapid, specific, and robust diagnostic strategies are needed for the development of sensitive biosensors to control contamination and disease transmission. The Bio-SCAN V2 platform, a ligand-responsive CRISPR-Cas system, provides a rapid and ultrasensitive detection platform for theophylline with a limit of detection up to 2 μM in just 15 minutes.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
Tian Xie, Guangjun Xu, Yun Liu, Bradley Quade, Weichun Lin, Xiao-chen Bai
Summary: MuSK is a receptor tyrosine kinase that is essential for the neuromuscular junction. Its activation requires both agrin and LRP4 coreceptors. This study presents the cryo-EM structure of the extracellular ternary complex of agrin/LRP4/MuSK, revealing how LRP4 recruits agrin and MuSK to activate MuSK receptor.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Multidisciplinary Sciences
Fenghua Yang, Tong Bian, Xiechao Zhan, Zhe Chen, Zhihan Xing, Nicolas A. A. Larsen, Xiaofeng Zhang, Yigong Shi
Summary: The authors report the high-resolution structures of two assembly precursors of human U2 snRNP and reveal that the RNA helicases DDX42 and DDX46 are mutually exclusive in terms of SF3B1-binding. The N-terminal sequences of DDX42 and DDX46 anchor on SF3B1, but their helicase domains have different interactions with U2 snRNA and TAT-SF1. Mutations in SF3B1 directly target the residues in the RNA path that interact with DDX42 and DDX46.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Shahid Chaudhary, Zahir Ali, Muhammad Tehseen, Evan F. Haney, Aaron Pantoja-Angles, Salwa Alshehri, Tiannyu Wang, Gerard J. Clancy, Maya Ayach, Charlotte Hauser, Pei-Ying Hong, Samir M. Hamdan, Robert E. W. Hancock, Magdy Mahfouz
Summary: This study demonstrates the efficient production of bioactive amidated AMPs through transient expression in Nicotiana benthamiana line expressing the mammalian enzyme peptidylglycine alpha-amidating mono-oxygenase. The AMPs purified from plants exhibit robust killing activity against highly virulent and antibiotic-resistant pathogens, and can prevent their biofilm formation when used in combination with antibiotics. The techno-economic analysis also shows the potential economic advantages and scalability for industrial use of this platform.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Tian Xie, Peng Liu, Xinyue Wu, Feitong Dong, Zike Zhang, Jian Yue, Usha Mahawar, Faheem Farooq, Hisham Vohra, Qi Fang, Wenchen Liu, Binks W. Wattenberg, Xin Gong
Summary: The researchers elucidated the molecular mechanism of ceramide sensing by the SPT-ORMDL complex, which is tightly regulated by cellular sphingolipid levels. They found that the ORM/ORMDL family proteins can bind to specific sites of the serine palmitoyltransferase (SPT) complex after modifying cellular sphingolipids, leading to the inhibition of its activity. Furthermore, they discovered that mutations in the SPTLC1 subunit in childhood amyotrophic lateral sclerosis (ALS) patients impair ceramide sensing.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Peng Liu, Tian Xie, Xinyue Wu, Gongshe Han, Sita D. Gupta, Zike Zhang, Jian Yue, Feitong Dong, Kenneth Gable, Somashekarappa Niranjanakumari, Wanyuan Li, Lin Wang, Wenchen Liu, Ruifeng Yao, Edgar B. Cahoon, Teresa M. Dunn, Xin Gong
Summary: This study reveals the structure of the serine palmitoyltransferase (SPT) complex and its interaction with ORM/ORMDL proteins. ORM1 acts as a negative regulator of SPT by binding to a small molecule derived from steroid degradation, thereby controlling lipid synthesis and homeostasis. This has implications for plant responses to microbial attacks.
Article
Food Science & Technology
Khalid Sedeek, Andrea Zuccolo, Alice Fornasiero, Annika M. Weber, Krishnaveni Sanikommu, Sangeetha Sampathkumar, Luis F. Rivera, Haroon Butt, Saule Mussurova, Abdulrahman Alhabsi, Nurmansyah Nurmansyah, Elizabeth P. Ryan, Rod A. Wing, Magdy M. Mahfouz
Summary: In this study, genome assemblies of 5 pigmented rice varieties were generated and the genetic variation among 51 pigmented rice varieties was evaluated. Phylogenetic analysis divided the pigmented varieties into four groups. Metabolomics and ionomics profiling revealed that black rice varieties are rich in aromatic secondary metabolites. A regeneration and transformation system was established and CRISPR-Cas9 was used to create an early maturing, shorter-stature black rice variety. This study provides a multi-omics resource for understanding and improving Asian pigmented rice.
Article
Chemistry, Analytical
Wenjun Jiang, Rashid Aman, Zahir Ali, Gundra S. Rao, Magdy Mahfouz
Summary: This study presents a new peptide nucleic acid (PNA)-based nucleic acid detection toolkit, PNA-Pdx, which provides accurate and rapid detection of specific nucleic acid sequences, including pathogens and genomic sequences, such as SARS-CoV-2, in clinical samples.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Tin Marsic, Sivakrishna Rao Gundra, Qiaochu Wang, Rashid Aman, Ahmed Mahas, Magdy M. Mahfouz
Summary: Programmable site-specific nucleases have a wide range of applications in basic biology research, biotechnology, and gene therapy. Using peptide nucleic acids (PNAs), we have developed a technology called PNA-assisted pAgo editing (PNP editing) that enables prokaryotic Argonaute proteins to introduce site-specific double-strand breaks (DSBs) independent of the target sequence. This technology has the potential for in vitro and in vivo applications, including genome editing.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biology
Yini Li, Lu Tian, Ying Zhang, Yigong Shi
Summary: In Caenorhabditis elegans (C. elegans), programmed cell death is initiated by the activation of CED-3 through the assembly of the CED-4 apoptosome. Cryo-EM structures of the CED-4 apoptosome and different CED-4/CED-3 complexes reveal the distinct stages of CED-3 activation. The dynamic organization of the CED-4 apoptosome regulates the initiation of programmed cell death.
LIFE SCIENCE ALLIANCE
(2023)
Article
Chemistry, Analytical
Wenjun Jiang, Rashid Aman, Zahir Ali, Gundra S. Rao, Magdy Mahfouz
Summary: PNA-Pdx is a novel peptide nucleic acid (PNA)-based nucleic acid detection toolkit that can accurately and rapidly detect specific nucleic acid sequences. It can also invade double-stranded DNA to produce single-stranded DNA for precise detection of genomic SNPs.
ANALYTICAL CHEMISTRY
(2023)
