Article
Biochemistry & Molecular Biology
Zheng Zhang, Tong Liu, Hangyan Dong, Jian Li, Haofan Sun, Xiaohong Qian, Weijie Qin
Summary: RNA-protein interactions are crucial in biological regulation, and the development of the PP method for RNA tagging and RNP enrichment has enabled successful screening and analysis of RBPs.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Chemistry, Analytical
Bianbian Huo, Yuanyuan Liu, Lingjun Li, Weijie Qin
Summary: The study developed a novel chemical enrichment method (AFT-OCAP) for simultaneous analysis of O-GlcNAc chromatin-associated proteins (OCAPs) and mapping their binding DNA, providing valuable tools for understanding the functions of OCAPs and the regulatory machinery of O-GlcNAcylation on gene transcription.
Article
Medicine, Research & Experimental
Asfa Alli-Shaik, Beiying Qiu, Siew Li Lai, Ning Cheung, Gavin Tan, Suat Peng Neo, Alison Tan, Chiu Ming Gemmy Cheung, Wanjin Hong, Tien Yin Wong, Xiaomeng Wang, Jayantha Gunarathne
Summary: Diabetic retinopathy (DR) is a major complication of diabetes mellitus, and anti-vascular endothelial growth factor (VEGF) therapy is commonly used for treatment. However, many DR patients do not respond well to this treatment. This study used proteome profiling to identify dysregulations in metabolic, signaling, and immune networks in the vitreous humor of PDR patients. The impaired ADAM10-AXL axis was proposed as a driver of retinal angiogenesis, and restoring aberrant ectodomain shedding was suggested as a potential treatment strategy for PDR.
Article
Immunology
Shuxin Yang, Wenjuan Zhao, Muchun Zhu, Huijuan Hu, Weijie Wang, Zhongsheng Zang, Meiling Jin, Jiacheng Bi, Jiandong Huang, Chenli Liu, Xuefei Li, Peng Yin, Nan Li
Summary: The engineered obligate anaerobic Salmonella typhimurium strain YB1 has the potential to repress tumor growth and metastasis, with a distinct immune response identified through temporal proteome profiling. This includes the activation of innate immune responses, phagocytosis, and recruitment of T cells leading to tumor shrinkage. Temporal proteome profiling can systematically reveal the YB1 induced immune responses in tumors, showing great promise for elucidating the mechanism of bacteria-mediated cancer immunotherapy.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Lin Bai, Guojian Yang, Zhaoyu Qin, Jiacheng Lyu, Yunzhi Wang, Jinwen Feng, Mingwei Liu, Tongqing Gong, Xianju Li, Zhengyang Li, Jixi Li, Jun Qin, Wenjun Yang, Chen Ding
Summary: This study used a novel method to analyze the binding activity of transcription factors under DNA modifications and identified potential readers for 5fC-modified DNA. By quantifying the modified DNA-binding activity of 1039 TFs, it revealed the hierarchical networks between the transcriptional protein machinery and modified DNA.
Article
Multidisciplinary Sciences
Martin Steger, Vadim Demichev, Mattias Backman, Uli Ohmayer, Phillip Ihmor, Stefan Mueller, Markus Ralser, Henrik Daub
Summary: By combining improved sample preparation, data-independent acquisition mass spectrometry and deep learning, the researchers developed a robust and precise workflow for quantitative ubiquitinome profiling, enabling the characterization of USP7 deubiquitinase targets and inhibitor effects. Their method not only improves system-level understanding of ubiquitin signaling but also increases the identification numbers of ubiquitinated peptides, while dissecting the scope of USP7 action through high temporal resolution analysis.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Dustin T. King, Jesus E. Serrano-Negron, Yanping Zhu, Christopher L. Moore, Matthew D. Shoulders, Leonard J. Foster, David J. Vocadlo
Summary: Posttranslational modifications can alter protein stability and cellular physiology. This study presents an unbiased proteome-wide approach to explore the influence of protein modifications on thermodynamic stability. Using this approach, the authors identify a set of proteins that are destabilized by O-GlcNAc modification and form distinct macromolecular complexes.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Plant Sciences
Waltraud X. Schulze, Michael Altenbuchinger, Mingjie He, Markus Kraenzlein, Christian Zoerb
Summary: The study revealed that drought affects protein abundance of multiple pathways in plants, including starch metabolism, aquaporin abundance, PSII proteins, and histones. Additionally, drought has a significant effect on nutrient assimilation, especially sulfur metabolism.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2021)
Article
Cell Biology
Jinjian Xu, Xue Cai, Zelei Miao, Yan Yan, Danyu Chen, Zhen-xiao Yang, Liang Yue, Wei Hu, Laibao Zhuo, Jia-ting Wang, Zhangzhi Xue, Yuanqing Fu, Ying Xu, Ju-Sheng Zheng, Tiannan Guo, Yu-ming Chen
Summary: The role of circulatory proteomics in osteoporosis is unclear, but proteome-wide profiling holds the potential to offer mechanistic insights into osteoporosis. Through the study of two Chinese cohorts, several proteins associated with osteoporosis were identified and used to generate the biological age of bone, showing a significant correlation with bone mineral density. The findings uncovered new mechanistic insights into osteoporosis, indicating that serum proteomics could be a crucial indicator for evaluating bone aging.
Article
Chemistry, Analytical
Guoli Wang, Yang Li, Ting Wang, Jun Wang, Jun Yao, Guoquan Yan, Ying Zhang, Haojie Lu
Summary: O-GlcNAcylation, a simple but essential protein post-translational modification, plays critical roles in cellular processes and is closely associated with various diseases. However, the low stoichiometry and reversibility properties of O-GlcNAcylation pose challenges for system-wide research. In this study, a novel method combining multi-comparative thermal proteome profiling was developed for O-GlcNAc transferase (OGT) substrate discovery. By profiling and comparing the melting curves of proteins under different treatments, proteins with significantly altered stabilities induced by OGT and uridine-5'-diphosphate N-acetylglucosamine were identified and new O-GlcNAcylated proteins were uncovered.
ANALYTICAL CHEMISTRY
(2023)
Article
Biotechnology & Applied Microbiology
Ping Lin, Hui-ru Bai, Ling He, Qiu-xiang Huang, Qin-han Zeng, Yuan-zhi Pan, Bei-bei Jiang, Fan Zhang, Lei Zhang, Qing-Lin Liu
Summary: This study analyzed the proteome-wide and lysine crotonylation in chrysanthemum under low-temperature stress, revealing insights into the mechanisms of crotonylation in positively regulating APX activity to mitigate oxidative damage caused by low temperatures. These findings provide a basis for studying crotonylation to regulate antioxidant enzyme activity in response to low-temperature stress and offer new research ideas for molecular breeding of chilling-tolerance and freezing-tolerance chrysanthemums.
Article
Biochemistry & Molecular Biology
Yu Jin, Yi Zhou, Wenfeng Deng, Yuchen Wang, Richard J. Lee, Yanna Liu, Nahel Elias, Yangcheng Hu, Min-Hua Luo, Rumin Liu, Bowen Guan, Jian Geng, Jian Xu, Junfeng Ma, Jiapeng Zhou, Na Liu, Michael L. Blute, Robert B. Colvin, Chin-Lee Wu, Yun Miao
Summary: Chronic BK polyomavirus (BKPyV) infection is considered a potential oncogenic factor for urothelial carcinoma (UC) in renal transplant recipients. Integration sites between human and BKPyV genomes were enriched with microhomologies, and viral insertional integration led to fusion sequences of 75 human genes, with 15 genes showing statistical association with UC based on expression analysis. These findings suggest a potential mechanism of viral-driven carcinogenesis in BKPyV-related UC.
Article
Chemistry, Analytical
Pierre Sabatier, Christian M. Beusch, Zhaowei Meng, Roman A. Zubarev
Summary: The ResT-PISA assay enables quantification of the lifetime of drug-target interaction by monitoring temporal protein solubility profiles after drug removal. It combines affinity and residence time assessments into a single proteomic analysis and improves target prioritization with a combined scoring system. This method is valuable in drug development and precision medicine.
ANALYTICAL CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Haizhu Zhang, Zhaoyu Qin, Xuetong Yue, Yang Liu, Xiaogang Sun, Jinwen Feng, Ziyan Xu, Jiangyan Zhao, Kai Li, Jiange Qiu, Wenjun Yang, Fuchu He, Chen Ding
Summary: ATAC-MS is a method to identify transcriptional protein complexes assembled on accessible chromatin, providing insight into the protein machinery in open chromatin. Combined with ATAC-seq, it allows for high-resolution profiling of chromatin-transcriptional machinery. Additionally, the fusion protein ctATAC-MS enables systematic pinpointing of the transcriptional machinery at specific open chromatin regions.
Article
Immunology
Wenbing Zhi, Xia Du, Ye Li, Chunliu Wang, Tingting Sun, Shiyu Zong, Qiqi Liu, Kai Hu, Yang Liu, Hong Zhang
Summary: The research shows that SPC has a therapeutic effect on asthma, reducing inflammation and pathological damage by targeting multiple key points. Proteomic and molecular docking screening results indicate that SPC acts on a variety of critical targets, making it a potential drug for treating asthma.
INTERNATIONAL IMMUNOPHARMACOLOGY
(2021)
Article
Oncology
Sanne Lokkegaard, Daniel Elias, Carla L. Alves, Martin V. Bennetzen, Anne-Vibeke Laenkholm, Martin Bak, Morten F. Gjerstorff, Lene E. Johansen, Henriette Vever, Christina Bjerre, Tove Kirkegaard, Bo Nordenskjoeld, Tommy Fornander, Olle Stal, Linda S. Lindstroem, Laura J. Esserman, Anne E. Lykkesfeldt, Jens S. Andersen, Rikke Leth-Larsen, Henrik J. Ditzel
Summary: MCM3 plays a crucial role in influencing endocrine resistance in ER+ breast cancer, acting as an independent prognostic marker and a predictive marker of response to endocrine treatment.
Article
Obstetrics & Gynecology
Franz S. Gruber, Zoe C. Johnston, Neil R. Norcross, Irene Georgiou, Caroline Wilson, Kevin D. Read, Ian H. Gilbert, Jason R. Swedlow, Sarah Martins da Silva, Christopher L. R. Barratt
Summary: This study utilized a high-throughput screening platform to identify compounds that can enhance sperm motility, providing a promising starting point for male fertility drug discovery.
HUMAN REPRODUCTION
(2022)
Article
Chemistry, Medicinal
Adam G. Bond, Conner Craigon, Kwok-Ho Chan, Andrea Testa, Athanasios Karapetsas, Rotimi Fasimoye, Thomas Macartney, J. Julian Blow, Dario R. Alessi, Alessio Ciulli
Summary: This study describes the design and development of a new protein degradation system utilizing a variant of the Brd4 bromodomain as a degradation tag. The system effectively degrades BromoTagged proteins in a fast, selective manner, showing favorable pharmacokinetic profile in mice. This system expands the arsenal of chemical genetic degradation tools for manipulating protein levels and exploring therapeutic potential in cells and in vivo.
JOURNAL OF MEDICINAL CHEMISTRY
(2021)
Editorial Material
Biotechnology & Applied Microbiology
Philip S. Jones, Steven van Helden, Volkhart Min-Jian Li, Ton Vries, Jon S. B. de Vlieger
Summary: The European Lead Factory combines assets and experience from major pharma with innovation and agility of academia and SMEs in a collaborative platform to expand access to high-throughput screening. With many successes heading towards the clinic, the organization is broadening its approach to screening and partnering.
NATURE REVIEWS DRUG DISCOVERY
(2022)
Article
Biochemistry & Molecular Biology
Maria Gockert, Manfred Schmid, Lis Jakobsen, Marvin Jens, Jens S. Andersen, Torben Heick Jensen
Summary: This study investigates the consequences of acute losses of the adaptors NEXT and PAXT, as well as core exosome components, revealing a specific intron degradation phenotype in long-term NEXT depletion samples and an alternative mode of RNA decay independent of the core exosome.
NUCLEIC ACIDS RESEARCH
(2022)
Review
Developmental Biology
Zoe C. Johnston, Franz S. Gruber, Sean G. Brown, Neil R. Norcross, Jason Swedlow, Ian H. Gilbert, Christopher L. R. Barratt
Summary: Despite recent advances, there is still incomplete understanding of male infertility and male non-hormonal contraceptives. Direct observation of compounds' effects on sperm function can increase knowledge and advance the field.
Article
Biochemistry & Molecular Biology
Ilaria Volpi, Peter J. Gillespie, Gaganmeet Singh Chadha, J. Julian Blow
Summary: Treslin/Ticrr is essential for DNA replication initiation and forms a complex with MTBP. DDK and CDK activities cooperate to regulate the interaction of Treslin-MTBP, which is crucial for selecting replication origins. This study provides insights into the mechanisms behind replication initiation regulation.
Letter
Biochemical Research Methods
Xiaopeng Zhu, Yang Zhang, Yuchuan Wang, Dechao Tian, Andrew S. Belmont, Jason R. Swedlow, Jian Ma
Article
Multidisciplinary Sciences
Alexander J. Ropelewski, Megan A. Rizzo, Jason R. Swedlow, Jan Huisken, Pavel Osten, Neda Khanjani, Kurt Weiss, Vesselina Bakalov, Michelle Engle, Lauren Gridley, Michelle Krzyzanowski, Tom Madden, Deborah Maiese, Meisha Mandal, Justin Waterfield, David Williams, Carol M. Hamilton, Wayne Huggins
Summary: Recent advances in fluorescence microscopy techniques and tissue clearing, labeling, and staining have provided unprecedented opportunities for studying brain structure and function. Consistent annotation of metadata is crucial for understanding, reusing, and integrating these data.
Review
Biology
Peter J. Gillespie, J. Julian Blow
Summary: To ensure genetic stability, cells must duplicate their complement of chromosomes prior to cell division. This process involves replicating chromosomal DNA and re-establishing the chromatin environment. The duplication of chromatid pairs must remain coupled until cell division to ensure equal segregation of genetic material. Cyclin-dependent kinases (CDK) control the regulation of chromosome duplication. CDK also activates Dbf4-dependent kinase (DDK), which facilitates DNA replication activation and coordination with chromatin re-establishment and chromatid coupling. This review discusses the outsourcing of these activities by CDK to DDK to ensure chromosome maintenance during cell division.
Article
Biochemistry & Molecular Biology
Narcis A. Petriman, Marta Loureiro-Lopez, Michael Taschner, Nevin K. Zacharia, Magdalena M. Georgieva, Niels Boegholm, Jiaolong Wang, Andre Mourao, Robert B. Russell, Jens S. Andersen, Esben Lorentzen
Summary: Cilia are essential organelles for cellular functions such as motility, signaling, and sensory reception. In this study, the researchers used Alphafold to model the structure of the IFT-B complex, which is involved in cilium formation. The results provide insights into the assembly and function of the IFT-B complex.
Correction
Multidisciplinary Sciences
Federico Pelisch, Remi Sonneville, Ehsan Pourkarimi, Ana Agostinho, J. Julian Blow, Anton Gartner, Ronald T. Hay
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Jerome O. Rouviere, Anna Salerno-Kochan, Soren Lykke-Andersen, William Garland, Yuhui Dou, Om Rathore, Ewa Smidova Molska, Guifen Wu, Manfred Schmid, Andrii Bugai, Lis Jakobsen, Kristina Zumer, Patrick Cramer, Jens S. Andersen, Elena Conti, Torben Heick Jensen
Summary: The RNA-binding ARS2 protein is involved in both early RNA polymerase II (RNAPII) transcription termination and transcript decay. It binds to ZC3H4 to recruit it to chromatin for RNAPII termination and forms a direct connection to the NEXT complex for rapid degradation of the RNA. ARS2 functions differently at CPA-instructed termination sites.
Article
Biochemistry & Molecular Biology
Niels Boegholm, Narcis A. Petriman, Marta Loureiro-Lopez, Jiaolong Wang, Miren Itxaso Santiago Vela, Beibei Liu, Tomoharu Kanie, Roy Ng, Peter K. Jackson, Jens S. Andersen, Esben Lorentzen
Summary: Cilia are important cellular organelles for signaling and motility and are constructed via intraflagellar transport (IFT). RabL2 localizes to the basal body of cilia via an interaction with CEP19 before downstream association with the IFT machinery. Reconstituted pentameric IFT complex containing IFT81/74 enhances the GTP hydrolysis rate of RabL2. Structural models of RabL2-containing IFT complexes validate the architectural understanding of RabL2 incorporation into the IFT complex.
Article
Cell Biology
Patrik Polak, William Garland, Om Rathore, Manfred Schmid, Anna Salerno-Kochan, Lis Jakobsen, Maria Gockert, Piotr Gerlach, Toomas Silla, Jens S. Andersen, Elena Conti, Torben Heick Jensen
Summary: The RNA exosome is a versatile ribonuclease that functions in the nucleoplasm of mammalian cells. It is assisted by the nuclear exosome targeting (NEXT) complex and the poly(A) exosome targeting (PAXT) connection. The PAXT pathway targets short adenylated RNAs through the ZFC3H1 component, which interacts directly with ARS2. In addition, ZC3H18 competes with PAXT and antagonizes its activity.
