scholarly journals microProtein Prediction Program (miP3): A Software for Predicting microProteins and Their Target Transcription Factors

2015 ◽  
Vol 2015 ◽  
pp. 1-4 ◽  
Author(s):  
Niek de Klein ◽  
Enrico Magnani ◽  
Michael Banf ◽  
Seung Yon Rhee
Keyword(s):  
Transcriptional Regulation ◽  
Transcription Factors ◽  
Protein Interactions ◽  
Protein Protein Interactions ◽  
Feedback Controls ◽  
Prediction Program ◽  
Functional Classes ◽  
Shed Light

An emerging concept in transcriptional regulation is that a class of truncated transcription factors (TFs), called microProteins (miPs), engages in protein-protein interactions with TF complexes and provides feedback controls. A handful of miP examples have been described in the literature but the extent of their prevalence is unclear. Here we present an algorithm that predicts miPs and their target TFs from a sequenced genome. The algorithm is called miP prediction program (miP3), which is implemented in Python. The software will help shed light on the prevalence, biological roles, and evolution of miPs. Moreover, miP3 can be used to predict other types of miP-like proteins that may have evolved from other functional classes such as kinases and receptors. The program is freely available and can be applied to any sequenced genome.

scholarly journals TRI_tool: a web-tool for prediction of protein–protein interactions in human transcriptional regulation

2016 ◽  
Vol 33 (2) ◽  
pp. 289-291 ◽  
Author(s):  
Vladimir Perovic ◽  
Neven Sumonja ◽  
Branislava Gemovic ◽  
Eneda Toska ◽  
Stefan G. Roberts ◽  
...  
Keyword(s):  
Transcriptional Regulation ◽  
Protein Interactions ◽  
Protein Protein Interactions ◽  
Web Tool

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.

scholarly journals The transcription factors Elk-1 and serum response factor interact by direct protein-protein contacts mediated by a short region of Elk-1.

1994 ◽  
Vol 14 (5) ◽  
pp. 3283-3291 ◽  
Author(s):  
P Shore ◽  
A D Sharrocks
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Protein Interactions ◽  
Serum Response Factor ◽  
Specific Protein ◽  
Response Factor ◽  
Protein Protein Interactions ◽  
Amino Acid Peptide ◽  
Necessary And Sufficient ◽  
Serum Response

Transcriptional induction of the c-fos gene in response to epidermal growth factor stimulation is mediated in part by a ternary nucleoprotein complex within the promoter consisting of serum response factor (SRF), p62TCF/Elk-1 and the serum response element (SRE). Both SRF and p62TCF/Elk-1 contact the DNA and bind in a cooperative manner to the SRE. In this study, we demonstrate that SRF and Elk-1 interact directly in the absence of the SRE. A 30-amino-acid peptide from Elk-1 (B-box) is both necessary and sufficient to mediate protein-protein contacts with SRF. Moreover, the Elk-1 B-box is necessary to enable SRF-dependent binding of an alternative ETS domain (from the transcription factor PU.1) to the c-fos SRE. Mutations in either the Elk-1 B-box or the C-terminal half of the SRF DNA-binding domain (coreSRF) which show reduced ability to form ternary complexes also show greatly reduced protein-protein interactions in the absence of the SRE. Our results clearly demonstrate that direct protein-protein interactions between the transcription factors Elk-1 and SRF, in addition to DNA contacts, contribute to the formation of a ternary complex on the c-fos SRE. We discuss the wider applicability of our results in describing specific protein-protein interactions between short well-defined transcription factor domains.

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