Article
Biochemical Research Methods
Taner Arslan, Yanbo Pan, Georgios Mermelekas, Mattias Vesterlund, Lukas M. Orre, Janne Lehtio
Summary: The subcellular localization of a protein is crucial for understanding its functions. In this study, a mass spectrometry- and bioinformatics-based pipeline was developed to generate a comprehensive resource for protein subcellular localization in multiple human cancer cell lines. The protocol includes a detailed wet-lab procedure, quantitative MS-data analysis, machine learning-based classification, and visualization of the output. The pipeline was evaluated using different peptide pre-fractionation approaches and proved to be straightforward and robust, with the entire process being completed within 1-2 weeks.
Article
Plant Sciences
Noman Shoaib, Nishbah Mughal, Lun Liu, Ali Raza, Leiyang Shen, Guowu Yu
Summary: This study provides insights into the importance of phosphorylation in the regulation of starch biosynthesis, specifically in Zea mays PHO1. The results suggest that phosphorylation at the S566 residue within the L80 region plays a crucial role in modulating or enhancing PHO1 activity. These findings contribute to a better understanding of starch biosynthesis regulation and offer potential targets for optimizing crop yield.
Article
Biochemistry & Molecular Biology
Guowu Yu, Yuewei Mou, Noman Shoaib, Xuewu He, Lun Liu, Runze Di, Nishbah Mughal, Na Zhang, Yubi Huang
Summary: This study identified and characterized the phosphorylation site of the AGPase large subunit in maize. Mutations mimicking phosphorylation and dephosphorylation were created to investigate the impact on AGPase activity. The findings suggest that phosphorylation enhances AGPase activity, providing a potential strategy for improving starch biosynthesis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Cell Biology
Chowdhury S. Abdullah, Richa Aishwarya, Shafiul Alam, Naznin Sultana Remex, Mahboob Morshed, Sadia Nitu, Sumitra Miriyala, Manikandan Panchatcharam, Brandon Hartman, Judy King, Mohammad Alfrad Nobel G. Bhuiyan, James Traylor, Christopher Kevil, A. Wayne Orr, Shenuarin Bhuiyan
Summary: This study reveals the localization of Sigmar1 on mitochondrial membranes in cardiomyocytes and its essential role in maintaining mitochondrial respiratory homeostasis.
Article
Multidisciplinary Sciences
Xiaoyu Guo, Xue Ding, Juan Dong
Summary: In this study, the authors found that BSL proteins in Arabidopsis have different functions in the cell cortex and nucleus, regulating stomatal formation through the activation or deactivation of different signaling pathways.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Yiming Li, Min Zeng, Fuhao Zhang, Fang-Xiang Wu, Min Li
Summary: In this study, DeepCellEss, a sequence-based interpretable deep learning framework, is proposed for cell line-specific essential protein predictions. By utilizing convolutional neural networks, bidirectional long short-term memory, and multi-head self-attention mechanism, DeepCellEss achieves effective prediction performance for different cell lines and outperforms existing methods and metrics.
Article
Biology
Alexis Diaz-Vegas, Dougall M. Norris, Sigrid Jall-Rogg, Kristen C. Cooke, Olivia J. Conway, Amber S. Shun-Shion, Xiaowen Duan, Meg Potter, Julian van Gerwen, Harry J. M. Baird, Sean J. Humphrey, David E. James, Daniel J. Fazakerley, James Burch
Summary: This study introduces a high-content imaging platform for studying endogenous GLUT4 translocation in intact adipocytes, enabling accurate analysis of GLUT4 responses to specific perturbations and the study of other trafficking proteins and lipid droplet morphology. The study found that Vps45 and Rab14 are selective regulators of GLUT4, while knockdown of Trarg1, Stx6, Stx16, Tbc1d4, and Rab10 affects both GLUT4 and TfR translocation. Additionally, Kif13A, a Rab10 binding molecular motor, was identified as a novel regulator of GLUT4 traffic.
LIFE SCIENCE ALLIANCE
(2022)
Article
Entomology
Xian Zhang, Qiao-Ran Wang, Qian Wu, Jun Gu, Li-Hua Huang
Summary: FK506 inhibits insect molting and metamorphosis by blocking FKBPs, specifically cytoplasmic FKBPs such as FKBP45 and FKBP12b which regulate the nuclear localization of EcR and the 20E signaling pathway.
Article
Biochemistry & Molecular Biology
Sheng Yan, Bin Peng, Shifeng Kan, Guangcan Shao, Zhikai Xiahou, Xiangyan Tang, Yong-Xiang Chen, Meng-Qiu Dong, Xiao Liu, Xingzhi Xu, Jing Li
Summary: This article investigates the impact of O-GlcNAc transferase (OGT) on PLK1, and finds that OGT can modify PLK1 through O-GlcNAcylation. Further research reveals that the T291A and T291N mutations increase the stability of PLK1 and lead to chromosome segregation defects and uterine carcinoma. The findings suggest that OGT exerts its mitotic function partially through O-GlcNAcylation of PLK1, which may contribute to tumorigenesis by elevating O-GlcNAc levels.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Lingran Zhang, Ning Zhang, Sisheng Wang, Hongyan Tian, Lu Liu, Dan Pei, Xiaodong Yu, Lei Zhao, Feng Chen
Summary: The study revealed that TaSnRK1 alpha regulates cold tolerance in wheat by phosphorylating TaPAP6L and identified key phosphorylation sites. In addition, TaPAP6L positively modulates cold tolerance by increasing jasmonic acid synthesis and suppressing degradation.
Article
Microbiology
Liyao Deng, Jieyu Wan, Anchun Cheng, Mingshu Wang, Bin Tian, Ying Wu, Qiao Yang, Xumin Ou, Sai Mao, Di Sun, Shaqiu Zhang, Dekang Zhu, Renyong Jia, Shun Chen, Mafeng Liu, Xinxin Zhao, Juan Huang, Qun Gao, Yanling Yu, Ling Zhang, Leichang Pan
Summary: This study revealed that DPV UL47 protein is a phosphorylated substrate of US3 protein, and the phosphorylation regulates the cytoplasmic localization of UL47. Additionally, US3 protein promotes the cytoplasmic localization of UL47 during DPV infection.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Tamar Szoke, Nitsan Albocher, Sutharsan Govindarajan, Anat Nussbaum-Shochat, Orna Amster-Choder
Summary: TmaR, a previously unannotated protein in E. coli, localizes to the cell pole when phosphorylated on a tyrosine residue and controls the subcellular localization and activity of Enzyme I (EI) by binding and polar sequestration. The absence of TmaR leads to detrimental effects on cell survival in mild acidic conditions and affects the ability of cells to enter stationary phase, demonstrating the importance of TmaR in regulating cellular processes.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Agronomy
Guowu Yu, Noman Shoaib, Yang Yang, Lun Liu, Nishbah Mughal, Yuewei Mou, Yubi Huang
Summary: This study investigated the impact of point mutations at phosphorylation sites on the subcellular localization and activity of AGPase in maize, and found that these mutations did not affect subcellular localization, but significantly modulated AGPase activity. This provides crucial insights into the role of point mutations in enhancing AGPase activity and improving starch biosynthesis in maize.
Article
Biochemistry & Molecular Biology
Jianyu Lu, Zhenhui Wang, Jinxi Li, Qian Zhao, Fan Qi, Fu Wang, Chunxiao Xiaoyang, Guofei Tan, Hanlu Wu, Michael K. Deyholos, Ningning Wang, Yingnan Liu, Jian Zhang
Summary: Flax is an important cash crop with multiple commercial uses. This study focuses on the Growth Regulatory Factor (GRF) gene family in flax, identifying and predicting the regulation of LuGRF genes. The study also explores the chromosomal locations, gene promoters, protein structure, and expression patterns of these genes. The findings provide a foundation for understanding the function of LuGRF genes and improving flax breeding.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Cell Biology
Eugene N. Kozlov, Roman V. Deev, Elena V. Tokmatcheva, Anna Tvorogova, Zaur M. Kachaev, Rudolf A. Gilmutdinov, Mariya Zhukova, Elena V. Savvateeva-Popova, Paul Schedl, Yulii V. Shidlovskii
Summary: Intracellular trafficking plays a critical role in the functioning of highly polarized cells, such as neurons. Transport of mRNAs, proteins, and other molecules to synaptic terminals maintains contact between neurons and ensures the transmission of nerve impulses. Cytoplasmic polyadenylation element binding (CPEB) proteins play an essential role in long-term memory (LTM) formation by regulating local translation in synapses.
Article
Neurosciences
Song Wu, Guangming Gan, Zhiping Zhang, Jie Sun, Qifu Wang, Zhongbao Gao, Meixiang Li, Shan Jin, Juan Huang, Ulrich Thomas, Yong-hui Jiang, Yan Li, Rui Tian, Yong Q. Zhang
JOURNAL OF NEUROSCIENCE
(2017)
Article
Cell Biology
Weihui Xu, Juan Huang, Baohua Li, Jiayang Li, Yonghong Wang
Article
Genetics & Heredity
Juan Huang, Wenke Zhou, Annie M. Watson, Yuh-Nung Jan, Yang Hong
Article
Genetics & Heredity
Juan Huang, Pallavi Ghosh, Graham F. Hatfull, Yang Hong
Article
Cell Biology
Juan Huang, Lynn Huang, Yi-Jiun Chen, Erin Austin, Caitlin E. Devor, Fabrice Roegiers, Yang Hong
JOURNAL OF CELL SCIENCE
(2011)
Article
Multidisciplinary Sciences
Juan Huang, Wenke Zhou, Wei Dong, Annie M. Watson, Yang Hong
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2009)
Article
Biochemistry & Molecular Biology
Ya Wang, Rui Xu, Yiwei Cheng, Haowei Cao, Zibin Wang, Tianyu Zhu, Jiayin Jiang, Hao Zhang, Chang Wang, Lin Qi, Mingxi Liu, Xuejiang Guo, Juan Huang, Jiahao Sha
JOURNAL OF GENETICS AND GENOMICS
(2019)
Article
Multidisciplinary Sciences
Liuze Gao, Shuhui Chang, Wenjuan Xia, Xiaolin Wang, Chenwang Zhang, Liping Cheng, Xu Liu, Liang Chen, Qinghua Shi, Juan Huang, Eugene Yujun Xu, Ge Shan
