scholarly journals A protein–protein interaction underlies the molecular basis for substrate recognition by an adenosine-to-inosine RNA-editing enzyme

2018 ◽  
Vol 46 (18) ◽  
pp. 9647-9659 ◽  
Author(s):  
Suba Rajendren ◽  
Aidan C Manning ◽  
Haider Al-Awadi ◽  
Kentaro Yamada ◽  
Yuichiro Takagi ◽  
...  
Keyword(s):  
Rna Editing ◽  
Protein Interaction ◽  
Molecular Basis ◽  
Substrate Recognition ◽  
Protein Protein Interaction ◽  
Editing Enzyme

scholarly journals Molecular Basis of a Million-Fold Affinity Maturation Process in a Protein–Protein Interaction

2011 ◽  
Vol 411 (2) ◽  
pp. 321-328 ◽  
Author(s):  
Daniel A. Bonsor ◽  
Sandra Postel ◽  
Brian G. Pierce ◽  
Ningyan Wang ◽  
Penny Zhu ◽  
...  
Keyword(s):  
Protein Interaction ◽  
Molecular Basis ◽  
Affinity Maturation ◽  
Maturation Process ◽  
Protein Protein Interaction

scholarly journals Interactome of vertebrate GAF/ThPOK reveals its diverse functions in gene regulation and DNA repair

2019 ◽  
Author(s):  
Avinash Srivastava ◽  
Rakesh Mishra
Keyword(s):  
Dna Damage ◽  
Dna Repair ◽  
Protein Interaction ◽  
Cutaneous Melanoma ◽  
Molecular Basis ◽  
Gene Activation ◽  
Biological Significance ◽  
Protein Interaction Data ◽  
Protein Protein Interaction ◽  
Ribonucleoprotein Complexes

Evolutionary conservation and lineage-specific diversification of existing proteins forms the basis for evolving complexity of protein-protein interaction networks and presumably, thereby that of the organism. GAGA associated factor (GAF) belongs to BTB/POZ and zinc finger family of transcription factors and it is conserved from flies to humans. Emerging evidence shows indispensable roles of vertebrate GAF (vGAF a.k.a. ThPOK) in functionally divergent developmental processes like hematopoiesis, adipogenesis, and lactation. vGAF is a sequence-specific DNA binding transcription factor with multiple context-dependent roles in gene activation/repression, enhancer-blocking and more recently, it has shown to be the part of ribonucleoprotein complexes as well. In order to understand the molecular basis of these diverse functions, we analyzed the protein-protein interactome of vGAF. This analysis shows vGAF association with chromatin remodelers, RNA metabolic machinery, transcriptional activators/repressors, and components of DNA repair machinery, thereby provides a plausible explanation for the diverse molecular functions of vGAF. Our findings discern the novel role of vGAF in several molecular processes like DNA repair and RNA metabolism. We further tested the biological significance of our protein-protein interaction data and show a novel function of vGAF in DNA repair and cell survival after UV induced DNA damage. Consistent with these results, analysis of high-throughput RNA-seq data shows the downregulation of vGAF in samples of skin cutaneous melanoma for which the primary cause is UV induced DNA damage. These findings suggest vGAF as an early diagnostic biomarker for skin cutaneous melanoma. Taken together, our study reveals a molecular basis for the diverse functions of vGAF. We uncover its role in DNA repair and provide an explanation for key roles of such evolutionary conserved factors in processes like development and disease.

An efficient transient assays system using Agrobacterium-mediated transformation of onion (Allium cepa) epidermal cells

2020 ◽  
Vol 80 (03) ◽  
Author(s):  
Yu-Miao Zhang ◽  
Jun Wang ◽  
Tao Wu
Keyword(s):  
Subcellular Localization ◽  
Protein Interaction ◽  
Protein Interactions ◽  
Epidermal Cells ◽  
Cyclin Dependent Kinase ◽  
Protein Subcellular Localization ◽  
Protein Protein Interactions ◽  
Efficient System ◽  
Protein Protein Interaction ◽  
Onion Epidermal Cells

In this study, the Agrobacterium infection medium, infection duration, detergent, and cell density were optimized. The sorghum-based infection medium (SbIM), 10-20 min infection time, addition of 0.01% Silwet L-77, and Agrobacterium optical density at 600 nm (OD600), improved the competence of onion epidermal cells to support Agrobacterium infection at >90% efficiency. Cyclin-dependent kinase D-2 (CDKD-2) and cytochrome c-type biogenesis protein (CYCH), protein-protein interactions were localized. The optimized procedure is a quick and efficient system for examining protein subcellular localization and protein-protein interaction.

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