Article
Biochemistry & Molecular Biology
Jinfu Tian, Jiahui Zhang, Frederic Francis
Summary: In this study, 2469 VQ genes from 56 plant species were identified and their molecular and evolutionary features were analyzed. The study found that amino acids are highly conserved in the VQ domain, while other positions are relatively variable. Most VQ genes encode small proteins and do not have introns. The VQ proteins can be divided into nine subgroups and in gymnosperms, they are classified into 11 groups with similar motifs in each group.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Loni Klaus, Bernardo P. de Almeida, Anna Vlasova, Filip Nemcko, Alexander Schleiffer, Katharina Bergauer, Lorena Hofbauer, Martina Rath, Alexander Stark
Summary: All multicellular organisms rely on differential gene expression, which is regulated by regulatory DNA elements and DNA-binding transcription factors. This study focuses on the less-studied repressors and develops a high-throughput method called repressive-domain (RD)-seq to systematically identify repressive domains (RDs) in complex DNA-fragment libraries. By screening more than 200,000 fragments in Drosophila melanogaster, the researchers identify 195 RDs in known repressors and proteins not previously associated with repression. They find that many RDs contain recurrent short peptide motifs that are conserved between fly and human and are functionally important. Moreover, they show that different RDs interact with and depend on different co-repressors (CoRs). These findings provide valuable insights into the sequences and functional impact of repressors and should benefit further studies.
Article
Plant Sciences
Ridhi Khurana, Sanchi Bhimrajka, Gundra Sivakrishna Rao, Vibha Verma, Neelima Boora, Gautam Gawande, Meenu Kapoor, Khareedu Venkateswara Rao, Sanjay Kapoor
Summary: OsMADS29 is a seed-specific transcription factor involved in embryo and endosperm development and starch filling during seed development in rice. The upstream regulatory region of OsMADS29 contains both positive and negative regulatory elements, as well as auxin-responsive elements, which guide its development-dependent and spatial expression.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Livia Pagano, Valeria Pennacchietti, Awa Diop, Daniele Santorelli, Paola Pietrangeli, Lucia Marcocci, Caterina Nardella, Francesca Malagrino, Angelo Toto, Stefano Gianni
Summary: In this study, the folding properties of the multidomain protein Grb2 were analyzed, revealing the interaction between the SH2 and C-SH3 domains during folding. These findings contribute to a better understanding of multidomain protein folding.
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
(2022)
Article
Multidisciplinary Sciences
Ilka Erven, Elena Abraham, Thomas Hermanns, Ulrich Baumann, Kay Hofmann
Summary: Distinct families of eukaryotic deubiquitinases (DUBs) are regulators of ubiquitin signaling. In addition to the known large tegument proteins of herpesviruses, a new class of DUBs has been identified in eukaryotes and bacteria. This class, named VTD (Viral tegument-like DUB), shows distant homology with the herpesvirus tegument proteins and has diverse specificity for different types of ubiquitin chains.
NATURE COMMUNICATIONS
(2022)
Article
Biology
Duanzhi Wu, Xin Fang, Kai Luan, Qijin Xu, Shiqi Lin, Shiying Sun, Jiaying Yang, Bingying Dong, Balachandran Manavalan, Zhijun Liao
Summary: In this study, SH2 domain-containing proteins and non-SH2 domain-containing proteins were successfully identified using deep learning technology. The best performing 288-dimensional features were obtained. Additionally, a new motif, YKIR, in the SH2 domain was discovered and its function in signal transduction was analyzed.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Biology
Zhiqing Wang, Peng Zeng, Bing Zhou
Summary: The study identified a mechanism for heme homeostasis in fruit flies, which is similar to that in mammals, suggesting that the fly model could serve as a valuable platform for heme research.
Article
Plant Sciences
Xue Feng, Qian Yu, Jianbin Zeng, Xiaoyan He, Wenxing Liu
Summary: In this study, 79 GATA genes were identified in wheat and classified into four subfamilies. The analysis of amino acid sequences and expression patterns revealed significant differences among these genes. Furthermore, comparisons with other plant genomes provided insights into the evolutionary characteristics. These findings are important for future gene function analysis, molecular breeding, and stress response research in wheat.
Article
Biochemistry & Molecular Biology
Farbod Sedaghat-Hamedani, Sabine Rebs, Ibrahim El-Battrawy, Safak Chasan, Tobias Krause, Jan Haas, Rujia Zhong, Zhenxing Liao, Qiang Xu, Xiaobo Zhou, Ibrahim Akin, Edgar Zitron, Norbert Frey, Katrin Streckfuss-Boemeke, Elham Kayvanpour
Summary: This study evaluated the pathogenicity of the SCN5a p.C335R variant in familial DCM and conduction disease using iPSC-CMs. The SCN5a p.C335R variant caused a loss of function of peak INa in DCM patients and coexistence of genetic variants in channels and structural genes increased the severity of the DCM phenotype.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Cell Biology
Szabolcs Sipeki, Kitti Koprivanacz, Tamas Takacs, Anita Kurilla, Loretta Laszlo, Virag Vas, Laszlo Buday
Summary: Signal transduction is essential for cells to perceive and respond to information, with subcellular hubs formed via protein interactions playing a central role. The SH2 and SH3 domains serve as prototypes for interaction domains that recognize proteins, lipids, nucleic acids, and small molecules. The lipid-binding properties of SH2 and SH3 domains are also important for modulating complex assembly.
Article
Biochemistry & Molecular Biology
Nhu Ngoc Quynh Vo, Yuhta Nomura, Kiyomi Kinugasa, Hiroshi Takagi, Shunji Takahashi
Summary: This study reports five drimenol synthases (DMSs) from marine bacteria and reveals the biosynthesis of drimane sesquiterpenes in bacteria. Protein structure modeling and biochemical analysis shed light on the catalytic mechanism of AsDMS and further elucidate the diversity of structure and function of terpene synthases.
ACS CHEMICAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Guang Yang, Hein J. Wijma, Henriette J. Rozeboom, Maria Laura Mascotti, Marco W. Fraaije
Summary: The thioredoxin pathway is an antioxidant system that involves electron transfer from a thioredoxin reductase to thioredoxin. Most thioredoxin reductases use NADPH as a reducing cofactor, but a new type called deazaflavin-dependent flavin-containing thioredoxin reductase (DFTR) was found in Archaea which utilizes a reduced deazaflavin cofactor (F420H2) instead. To understand the biochemistry of DFTRs, two other archaeal representatives were identified and characterized. These DFTRs showed high specificity for F420H2 but limited activity with NADPH, suggesting mechanistic similarities with NADPH-dependent thioredoxin reductases (NTRs). Structural analysis identified two key residues that determine cofactor specificity of DFTRs, leading to the identification and experimental characterization of a bacterial DFTR.
Article
Biotechnology & Applied Microbiology
Junjie Tao, Huimin Jia, Mengting Wu, Wenqi Zhong, Dongfeng Jia, Zupeng Wang, Chunhui Huang
Summary: In this study, the TIFY gene family in kiwifruit was identified and characterized, providing valuable insights into their evolution, gene structure, promoter cis-elements, and expression patterns. The results lay a foundation for understanding the function of TIFY genes in kiwifruit and offer a potential approach for preventing and treating kiwifruit bacterial spot disease.
Article
Biotechnology & Applied Microbiology
Wenqing Zheng, Liang Du
Summary: This study identified 88 DUB family genes in the woody model plant Populus trichocarpa, classified them based on phylogenetic analysis, and found that these genes may play important roles in plant stress response according to expression profiling.
Article
Biochemistry & Molecular Biology
Weigui Luo, Nian Xiao, Feiyan Wu, Beixin Mo, Wenwen Kong, Yu Yu
Summary: The expression patterns and functions of MmYUC genes in Mikania micrantha play a crucial role in understanding the growth and invasion mechanisms of this plant.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Jonathan A. Cooper, Tomonori Kaneko, Shawn S. C. Li
MOLECULAR AND CELLULAR BIOLOGY
(2015)
Article
Multidisciplinary Sciences
Xuan Cao, Tomonori Kaneko, Jenny S. Li, An-Dong Liu, Courtney Voss, Shawn S. C. Li
NATURE COMMUNICATIONS
(2015)
Article
Biochemical Research Methods
Arunas Kazlauskas, Constanze Schmotz, Tapio Kesti, Jussi Hepojoki, Iivari Kleino, Tomonori Kaneko, Shawn S. C. Li, Kalle Saksela
MOLECULAR & CELLULAR PROTEOMICS
(2016)
Article
Biochemistry & Molecular Biology
Yangyang Bian, Lei Li, Mingming Dong, Xuguang Liu, Tomonori Kaneko, Kai Cheng, Huadong Liu, Courtney Voss, Xuan Cao, Yan Wang, David Litchfield, Mingliang Ye, Shawn S-C Li, Hanfa Zou
NATURE CHEMICAL BIOLOGY
(2016)
Article
Biochemical Research Methods
Ran Wei, Tomonori Kaneko, Xuguang Liu, Huadong Liu, Lei Li, Courtney Voss, Eric Liu, Ningning He, Shawn S. -C. Li
MOLECULAR & CELLULAR PROTEOMICS
(2018)
Article
Biochemistry & Molecular Biology
Rui Wang, Pete Y. M. Leung, Feng Huang, Qingzhuang Tang, Tomonori Kaneko, Mei Huang, Zigang Li, Shawn S. C. Li, Yi Wang, Jiang Xia
Article
Biochemistry & Molecular Biology
Greg M. Findlay, Matthew J. Smith, Fredrik Lanner, Marilyn S. Hsiung, Gerald D. Gish, Evangelia Petsalaki, Katie Cockburn, Tomonori Kaneko, Haiming Huang, Richard D. Bagshaw, Troy Ketela, Monika Tucholska, Lorne Taylor, David D. Bowtell, Jason Moffat, Mitsuhiko Ikura, Shawn S. C. Li, Sachdev S. Sidhu, Janet Rossant, Tony Pawson
Article
Biochemistry & Molecular Biology
Gurpreet Kaur Dhami, Huadong Liu, Marek Galka, Courtney Voss, Ran Wei, Kimberly Muranko, Tomonori Kaneko, Sean P. Cregan, Lin Li, Shawn Shun-Cheng Li
Article
Chemistry, Analytical
Rui Wang, Mei Huang, Linting Li, Tomonori Kaneko, Courtney Voss, Liang Zhang, Jiang Xia, Shawn S. C. Li
ANALYTICAL CHEMISTRY
(2018)
Article
Biochemical Research Methods
Huadong Liu, Haiming Huang, Courtney Voss, Tomonori Kaneko, Wen Tao Qin, Sachdev Sidhu, Shawn S. -C. Li
MOLECULAR & CELLULAR PROTEOMICS
(2019)
Article
Biochemistry & Molecular Biology
Gianluca Veggiani, Haiming Huang, Bradley P. Yates, Jiefei Tong, Tomonori Kaneko, Rakesh Joshi, Shawn S. C. Li, Michael F. Moran, Gerald Gish, Sachdev S. Sidhu
Article
Medicine, Research & Experimental
Courtney Voss, Sally Esmail, Xuguang Liu, Michael J. Knauer, Suzanne Ackloo, Tomonori Kaneko, Lori Lowes, Peter Stogios, Almagul Seitova, Ashley Hutchinson, Farhad Yusifov, Tatiana Skarina, Elena Evdokimova, Peter Loppnau, Pegah Ghiabi, Taraneh Haijan, Shanshan Zhong, Husam Abdoh, Benjamin D. Hedley, Vipin Bhayana, Claudio M. Martin, Marat Slessarev, Benjamin Chin-Yee, Douglas D. Fraser, Ian Chin-Yee, Shawn S. C. Li
Summary: This study identified linear epitopes from SARS-CoV-2 proteins and demonstrated their ability to provide higher resolution antibody profiling compared to traditional antigens. The antibody responses to specific epitopes were found to be correlated with clinical severity and patient survival. Additionally, mutations in the coronavirus variant B.1.1.7 were shown to alter the specificity of corresponding epitopes.
Article
Biochemistry & Molecular Biology
Lyugao Qin, Xuan Cao, Tomonori Kaneko, Courtney Voss, Xuguang Liu, Guoping Wang, Shawn S-C Li
Summary: Cell migration is regulated by the interplay of two molecular switches, P-switch and T-switch, with P-switch being crucial for both initiation and continuation of migration induced by growth factors, while T-switch is only necessary to sustain cell migration. The interaction of the two switches facilitated by the interleukin-6-Janus kinase-STAT3 pathway governs a sequence of dynamic protein-protein interactions for sustained cell migration. The similar mechanism utilized by both normal and tumorigenic epithelial cells suggests that P-switch and T-switch are general regulators of epithelial cell migration and potential therapeutic targets.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Qi Zhang, Rober Abdo, Cristiana Iosef, Tomonori Kaneko, Matthew Cecchini, Victor K. Han, Shawn Shun-Cheng Li
Summary: Brain metastases (BrMs) are a common occurrence in lung cancer with poor prognosis. The tumor microenvironment in the brain undergoes extensive remodeling to create an immunosuppressive and fibrogenic niche for BrMs. Differential gene expression analysis identifies fibrosis and immune regulation as the major functional modules disrupted in both the lung and brain tumor microenvironments.
NATURE COMMUNICATIONS
(2022)