scholarly journals Characterization and analysis of some chilling-response WRKY transcription factors in tomato

2020 ◽  
Author(s):  
Yixuan Wang ◽  
Kunyang Zhuang ◽  
Qingwei Meng ◽  
Chen Meng
Keyword(s):  
Transcription Factors ◽  
Protein Interactions ◽  
Chilling Stress ◽  
Mrna Levels ◽  
Protein Protein Interactions ◽  
Biotic And Abiotic Stress ◽  
Wrky Transcription Factors ◽  
Promoter Regions ◽  
Cis Acting ◽  
Chilling Response

Abstract WRKY transcription factors play various important roles in biotic and abiotic stress. In present study, a total of 81 WRKYs in tomato (Solanum lycopersicum) was identified and their gene structure, phylogeny and sub-location were analyzed. Here, we further analyzed their expression and potential roles under chilling stress. Nevertheless, the predicted chloroplast-located WRKYs are failed to be detected in the chloroplast. Then, 27 SlWRKYs with high chilling-induced mRNA levels (more than 3 fold to the control) are selected from these WRKYs. Promoter analysis showed that some cold stress-related cis-acting elements (CBFs binding site) existed in many promoter regions of these chilling response WRKYs (WRKY2, WRKY50, WRKY59 etc.), implying that these WRKY transcription factors may participate in CBFs mediated pathway under chilling stress. The interaction proteins of WRKYs are essential to affect the DNA binding and transcription regulatory activities of WRKYs, thus controlling its downstream genes expression. Therefore, we predicted and analyzed the protein-protein interactions of those chilling related WRKY transcription factors and then speculated the complex regulatory and functional network of WRKY transcription factors under chilling stress. A better understanding of SlWRKYs would be helpful for providing a theoretical basis for further illustrating the regulatory mechanism of SlWRKYs under chilling stress.

scholarly journals Protein–Protein Interactions in the Regulation of WRKY Transcription Factors

2013 ◽  
Vol 6 (2) ◽  
pp. 287-300 ◽  
Author(s):  
Yingjun Chi ◽  
Yan Yang ◽  
Yuan Zhou ◽  
Jie Zhou ◽  
Baofang Fan ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Protein Interactions ◽  
Protein Protein Interactions ◽  
Wrky Transcription Factors

scholarly journals The detection of covariation of mRNA levels of large sets of genes across multiple human populations

2016 ◽  
Author(s):  
Yu Quan ◽  
Chao Xie ◽  
Rohan B. H. Williams ◽  
Peter F. R Little
Keyword(s):  
Protein Interactions ◽  
Large Scale ◽  
Human Populations ◽  
Mrna Levels ◽  
Batch Effects ◽  
Protein Protein Interactions ◽  
Promoter Regions ◽  
Biological Origin ◽  
Human Lymphoblastoid Cell ◽  
Large Sets

AbstractIn this study, we analyse RNA-Seq data from panels of human lymphoblastoid cell lines (LCLs) to identify covariation in the mRNA levels of large numbers of genes. Such large scale covariation may have biological origin or be due to technical variation in analysis (generally referred to as batch effects). We show that batch effects cannot explain this covariation by demonstrating reproducibility across different human populations and across different methods of analysis. This view is also supported by enrichment of single and combinations of transcription factors (TFs) binding to cognate promoter regions, enrichment of genes shown to be sensitive to the knockdown of individual TFs, enrichment of functional pathways, and finally enrichment of protein-protein interactions in proteins encoded by groups of covarying genes. The properties of the groups of covarying genes are therefore most readily explained by the influence of cumulative variations in the effectors of gene expression that act in trans on cognate genes. We suggest that covariation has functional outcomes by showing that covariation of 83 genes involved in the spliceosome pathway accounts for 8–16% of the variation in the alternative splicing patterns of genes expressed in human LCLs.

scholarly journals Zinc Oxide Nanoparticles Alleviate Chilling Stress in Rice (Oryza Sativa L.) by Regulating Antioxidative System and Chilling Response Transcription Factors

Molecules ◽  
2021 ◽  
Vol 26 (8) ◽  
pp. 2196
Author(s):  
Yue Song ◽  
Meng Jiang ◽  
Huali Zhang ◽  
Ruiqing Li
Keyword(s):  
Zinc Oxide ◽  
Transcription Factors ◽  
Abiotic Stresses ◽  
Foliar Application ◽  
Negative Impact ◽  
Chilling Stress ◽  
Antioxidative System ◽  
Rice Seedlings ◽  
Zno Nps ◽  
Chilling Response

As one of the common abiotic stresses, chilling stress has negative effects on rice growth and development. Minimization of these adverse effects through various ways is vital for the productivity of rice. Nanoparticles (NPs) serve as one of the effective alleviation methods against abiotic stresses. In our research, zinc oxide (ZnO) NPs were utilized as foliar sprays on rice leaves to explore the mechanism underlying the effect of NPs against the negative impact of chilling stress on rice seedlings. We revealed that foliar application of ZnO NPs significantly alleviated chilling stress in hydroponically grown rice seedlings, including improved plant height, root length, and dry biomass. Besides, ZnO NPs also restored chlorophyll accumulation and significantly ameliorated chilling-induced oxidative stress with reduced levels of H2O2, MDA, proline, and increased activities of major antioxidative enzymes, superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD). We further found that foliar application of ZnO NPs induced the chilling-induced gene expression of the antioxidative system (OsCu/ZnSOD1, OsCu/ZnSOD2, OsCu/ZnSOD3, OsPRX11, OsPRX65, OsPRX89, OsCATA, and OsCATB) and chilling response transcription factors (OsbZIP52, OsMYB4, OsMYB30, OsNAC5, OsWRKY76, and OsWRKY94) in leaves of chilling-treated seedlings. Taken together, our results suggest that foliar application of ZnO NPs could alleviate chilling stress in rice via the mediation of the antioxidative system and chilling response transcription factors.

scholarly journals In Vivo Quantitative Estimation of DNA-Dependent Interaction of Sox2 and Oct4 Using BirA-Catalyzed Site-Specific Biotinylation

Biomolecules ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 142 ◽  
Author(s):  
Arman Kulyyassov ◽  
Vasily Ogryzko
Keyword(s):  
Transcription Factors ◽  
Protein Interactions ◽  
Fluorescent Protein ◽  
Quantitative Estimation ◽  
Multiple Reaction Monitoring ◽  
Negative Control ◽  
Protein Protein Interactions ◽  
Close Proximity ◽  
Green Fluorescent

Protein–protein interactions of core pluripotency transcription factors play an important role during cell reprogramming. Cell identity is controlled by a trio of transcription factors: Sox2, Oct4, and Nanog. Thus, methods that help to quantify protein–protein interactions may be useful for understanding the mechanisms of pluripotency at the molecular level. Here, a detailed protocol for the detection and quantitative analysis of in vivo protein–protein proximity of Sox2 and Oct4 using the proximity-utilizing biotinylation (PUB) method is described. The method is based on the coexpression of two proteins of interest fused to a biotin acceptor peptide (BAP)in one case and a biotin ligase enzyme (BirA) in the other. The proximity between the two proteins leads to more efficient biotinylation of the BAP, which can be either detected by Western blotting or quantified using proteomics approaches, such as a multiple reaction monitoring (MRM) analysis. Coexpression of the fusion proteins BAP-X and BirA-Y revealed strong biotinylation of the target proteins when X and Y were, alternatively, the pluripotency transcription factors Sox2 and Oct4, compared with the negative control where X or Y was green fluorescent protein (GFP), which strongly suggests that Sox2 and Oct4 come in close proximity to each other and interact.

scholarly journals Targeting of the Visna Virus Tat Protein to AP-1 Sites: Interactions with the bZIP Domains of Fos and Jun In Vitro and In Vivo

1999 ◽  
Vol 73 (1) ◽  
pp. 37-45 ◽  
Author(s):  
B. A. Morse ◽  
L. M. Carruth ◽  
J. E. Clements
Keyword(s):  
Transcription Factors ◽  
Protein Interactions ◽  
Tat Protein ◽  
Protein Protein Interactions ◽  
Viral Promoter ◽  
Visna Virus ◽  
Cellular Transcription ◽  
Virus Promoter

ABSTRACT The visna virus Tat protein is required for efficient viral transcription from the visna virus long terminal repeat (LTR). AP-1 sites within the visna virus LTR, which can be bound by the cellular transcription factors Fos and Jun, are also necessary for Tat-mediated transcriptional activation. A potential mechanism by which the visna virus Tat protein could target the viral promoter is by protein-protein interactions with Fos and/or Jun bound to AP-1 sites in the visna virus LTR. Once targeted to the visna virus promoter, the Tat protein could then interact with basal transcription factors to activate transcription. To examine protein-protein interactions with cellular proteins at the visna virus promoter, we used an in vitro protein affinity chromatography assay and electrophoretic mobility shift assay, in addition to an in vivo two-hybrid assay, to show that the visna virus Tat protein specifically interacts with the cellular transcription factors Fos and Jun and the basal transcription factor TBP (TATA binding protein). The Tat domain responsible for interactions with Fos and Jun was localized to an alpha-helical domain within amino acids 34 to 69 of the protein. The TBP binding domain was localized to amino acids 1 to 38 of Tat, a region previously described by our laboratory as the visna virus Tat activation domain. The bZIP domains of Fos and Jun were found to be important for the interactions with Tat. Mutations within the basic domains of Fos and Jun abrogated binding to Tat in the in vitro assays. The visna virus Tat protein was also able to interact with covalently cross-linked Fos and Jun dimers. Thus, the visna virus Tat protein appears to target AP-1 sites in the viral promoter in a mechanism similar to the interaction of human T-cell leukemia virus type 1 Tax with the cellular transcription factor CREB, by binding the basic domains of an intact bZIP dimer. The association between Tat, Fos, and Jun would position Tat proximal to the viral TATA box, where the visna virus Tat activation domain could contact TBP to activate viral transcription.

scholarly journals ApicoTFdb: the comprehensive web repository of apicomplexan transcription factors and transcription-associated co-factors

Database ◽  
2019 ◽  
Vol 2019 ◽  
Author(s):  
Rahila Sardar ◽  
Abhinav Kaushik ◽  
Rajan Pandey ◽  
Asif Mohmmed ◽  
Shakir Ali ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Protein Interactions ◽  
Drug Targets ◽  
Complex Life Cycle ◽  
Protein Protein Interactions ◽  
Apicomplexan Parasites ◽  
Reference Protein ◽  
Ap2 Family ◽  
Novel Drug ◽  
Novel Drug Targets

Abstract Despite significant progress in apicomplexan genome sequencing and genomics, the current list of experimentally validated transcription factors (TFs) in these genomes is incomplete and mainly consists of AP2 family of proteins, with only a limited number of non-AP2 family TFs and transcription-associated co-factors (TcoFs). We have performed a systematic bioinformatics-aided prediction of TFs and TcoFs in apicomplexan genomes and developed the ApicoTFdb database which consists of experimentally validated as well as computationally predicted TFs and TcoFs in 14 apicomplexan species. The predicted TFs are manually curated to complement the existing annotations. The current version of the database includes 1292 TFs which includes experimentally validated and computationally predicted TFs, representing 20 distinct families across 14 apicomplexan species. The predictions include TFs of TUB, NAC, BSD, HTH, Cupin/Jumonji, winged helix and FHA family proteins, not reported earlier as TFs in the genomes. Apart from TFs, ApicoTFdb also classifies TcoFs into three main subclasses: TRs, CRRs and RNARs, representing 2491 TcoFs in 14 apicomplexan species, are analyzed in this study. The database is designed to integrate different tools for comparative analysis. All entries in the database are dynamically linked with other databases, literature reference, protein–protein interactions, pathways and annotations associated with each protein. ApicoTFdb will be useful to the researchers interested in less-studied gene regulatory mechanisms mediating the complex life cycle of the apicomplexan parasites. The database will aid in the discovery of novel drug targets to much needed combat the growing drug resistance in the parasites.

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