scholarly journals An interaction map of transcription factors controlling gynoecium development in Arabidopsis

2018 ◽  
Author(s):  
Humberto Herrera-Ubaldo ◽  
Sergio E. Campos ◽  
Valentin Luna Garcia ◽  
Victor M. Zuniga-Mayo ◽  
Gerardo Armas-Caballero ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Protein Interactions ◽  
Specific Interaction ◽  
Protein Protein Interactions ◽  
Cytokinin Signaling ◽  
Reproductive Unit ◽  
Reproductive Part ◽  
Spatio Temporal ◽  
Interaction Map ◽  
Gynoecium Development

Flowers are composed of different organs, whose identity is defined at the molecular by the combinatorial activity of transcription factors (TFs). MADS-box TFs interact forming complexes that have been schematized in the quartet model. The gynoecium is the female reproductive part in the flower, crucial for plant reproduction, and fruit and seed production. Once carpel identity is established, a gynoecium containing many tissues arises. Several TFs have been identified as regulators of gynoecium development, and some of these TFs form complexes. However, broad knowledge about the interactions among these TFs is still scarce. In this work, we used a systems biology approach to understand the formation of a complex reproductive unit as the gynoecium by mapping binary interactions between well-characterized TFs. We analyzed over 3500 combinations and detected more than 200 protein-protein interactions (PPIs), resulting in a process specific interaction map. Topological analyses suggest hidden functions and novel roles for many TFs. Furthermore, a relationship between TFs involved in auxin and cytokinin signaling pathways and other TFs was observed. We analyzed the network by combining PPI data, expression and genetic data, allowing us to dissect it into several dynamic spatio-temporal sub-networks related to gynoecium development subprocesses.

scholarly journals The Effect of Proline cis-trans Isomerization on the Folding of the C-Terminal SH2 Domain from p85

2019 ◽  
Vol 21 (1) ◽  
pp. 125
Author(s):  
Francesca Troilo ◽  
Francesca Malagrinò ◽  
Lorenzo Visconti ◽  
Angelo Toto ◽  
Stefano Gianni
Keyword(s):  
Protein Interactions ◽  
Specific Interaction ◽  
Sh2 Domain ◽  
Regulatory Subunit ◽  
Wild Type ◽  
Protein Protein Interactions ◽  
Sh2 Domains ◽  
Trans Isomerization ◽  
A Site ◽  
Kinetics Of

SH2 domains are protein domains that modulate protein–protein interactions through a specific interaction with sequences containing phosphorylated tyrosines. In this work, we analyze the folding pathway of the C-terminal SH2 domain of the p85 regulatory subunit of the protein PI3K, which presents a proline residue in a cis configuration in the loop between the βE and βF strands. By employing single and double jump folding and unfolding experiments, we demonstrate the presence of an on-pathway intermediate that transiently accumulates during (un)folding. By comparing the kinetics of folding of the wild-type protein to that of a site-directed variant of C-SH2 in which the proline was replaced with an alanine, we demonstrate that this intermediate is dictated by the peptidyl prolyl cis-trans isomerization. The results are discussed in the light of previous work on the effect of peptidyl prolyl cis-trans isomerization on folding events.

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 Identification of Protein Complex Associated with LYT1 ofTrypanosoma cruzi

2013 ◽  
Vol 2013 ◽  
pp. 1-11 ◽  
Author(s):  
C. Lugo-Caballero ◽  
G. Ballesteros-Rodea ◽  
S. Martínez-Calvillo ◽  
Rebeca Manning-Cela
Keyword(s):  
Protein Interactions ◽  
Molecular Mechanisms ◽  
Single Gene ◽  
Protein Protein Interactions ◽  
Protein Traffic ◽  
Parasite Stage ◽  
Transgenic Parasites ◽  
Stage Development ◽  
Acidic Conditions ◽  
Interaction Map

To carry out the intracellular phase of its life cycle,Trypanosoma cruzimust infect a host cell. Although a few molecules have been reported to participate in this process, one known protein is LYT1, which promotes lysis under acidic conditions and is involved in parasite infection and development. Alternative transcripts from a singleLYT1gene generate two proteins with differential functions and compartmentalization. Single-gene products targeted to more than one location can interact with disparate proteins that might affect their function and targeting properties. The aim of this work was to study the LYT1 interaction map using coimmunoprecipitation assays with transgenic parasites expressing LYT1 products fused to GFP. We detected several proteins of sizes from 8 to 150 kDa that bind to LYT1 with different binding strengths. By MS-MS analysis, we identified proteins involved in parasite infectivity (trans-sialidase), development (kDSPs and histones H2A and H2B), and motility and protein traffic (dynein andα- andβ-tubulin), as well as protein-protein interactions (TPR-protein and kDSPs) and several hypothetical proteins. Our approach led us to identify the LYT1 interaction profile, thereby providing insights into the molecular mechanisms that contribute to parasite stage development and pathogenesis ofT. cruziinfection.

scholarly journals Probing the Unknowns in Cytokinin-Mediated Immune Defense in Arabidopsis with Systems Biology Approaches

2014 ◽  
Vol 8 ◽  
pp. BBI.S13462 ◽  
Author(s):  
Muhammad Naseem ◽  
Meik Kunz ◽  
Thomas Dandekar
Keyword(s):  
Systems Biology ◽  
Immune Responses ◽  
Protein Interactions ◽  
Immune Defense ◽  
Immune Functions ◽  
Protein Protein Interactions ◽  
Cytokinin Signaling ◽  
Host Immune Responses ◽  
Arabidopsis Protein ◽  
Underlying Mechanisms

Plant hormones involving salicylic acid (SA), jasmonic acid (JA), ethylene (Et), and auxin, gibberellins, and abscisic acid (ABA) are known to regulate host immune responses. However, plant hormone cytokinin has the potential to modulate defense signaling including SA and JA. It promotes plant pathogen and herbivore resistance; underlying mechanisms are still unknown. Using systems biology approaches, we unravel hub points of immune interaction mediated by cytokinin signaling in Arabidopsis. High-confidence Arabidopsis protein—protein interactions (PPI) are coupled to changes in cytokinin-mediated gene expression. Nodes of the cellular interactome that are enriched in immune functions also reconstitute sub-networks. Topological analyses and their specific immunological relevance lead to the identification of functional hubs in cellular interactome. We discuss our identified immune hubs in light of an emerging model of cytokinin-mediated immune defense against pathogen infection in plants.

scholarly journals Mechanism of Mediator Recruitment by Tandem Gcn4 Activation Domains and Three Gal11 Activator-Binding Domains

2010 ◽  
Vol 30 (10) ◽  
pp. 2376-2390 ◽  
Author(s):  
Eric Herbig ◽  
Linda Warfield ◽  
Lisa Fish ◽  
James Fishburn ◽  
Bruce A. Knutson ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Specific Interaction ◽  
Protein Protein Interactions ◽  
Activation Domain ◽  
Activation Domains ◽  
Binding Domains ◽  
Cross Links ◽  
Kix Domain ◽  
The Individual ◽  
Was Gene

ABSTRACT Targets of the tandem Gcn4 acidic activation domains in transcription preinitiation complexes were identified by site-specific cross-linking. The individual Gcn4 activation domains cross-link to three common targets, Gal11/Med15, Taf12, and Tra1, which are subunits of four conserved coactivator complexes, Mediator, SAGA, TFIID, and NuA4. The Gcn4 N-terminal activation domain also cross-links to the Mediator subunit Sin4/Med16. The contribution of the two Gcn4 activation domains to transcription was gene specific and varied from synergistic to less than additive. Gcn4-dependent genes had a requirement for Gal11 ranging from 10-fold dependence to complete Gal11 independence, while the Gcn4-Taf12 interaction did not significantly contribute to the expression of any gene studied. Complementary methods identified three conserved Gal11 activator-binding domains that bind each Gcn4 activation domain with micromolar affinity. These Gal11 activator-binding domains contribute additively to transcription activation and Mediator recruitment at Gcn4- and Gal11-dependent genes. Although we found that the conserved Gal11 KIX domain contributes to Gal11 function, we found no evidence of specific Gcn4-KIX interaction and conclude that the Gal11 KIX domain does not function by specific interaction with Gcn4. Our combined results show gene-specific coactivator requirements, a surprising redundancy in activator-target interactions, and an activator-coactivator interaction mediated by multiple low-affinity protein-protein interactions.

scholarly journals Inferring interaction partners from protein sequences

2016 ◽  
Author(s):  
Anne-Florence Bitbol ◽  
Robert S. Dwyer ◽  
Lucy J. Colwell ◽  
Ned S. Wingreen
Keyword(s):  
Protein Interactions ◽  
Sequence Data ◽  
Protein Complexes ◽  
A Priori ◽  
Specific Interaction ◽  
Three Dimensional ◽  
Specific Protein ◽  
Protein Protein Interactions ◽  
Entropy Model ◽  
Interaction Partners

Specific protein-protein interactions are crucial in the cell, both to ensure the formation and stability of multi-protein complexes, and to enable signal transduction in various pathways. Functional interactions between proteins result in coevolution between the interaction partners. Hence, the sequences of interacting partners are correlated. Here we exploit these correlations to accurately identify which proteins are specific interaction partners from sequence data alone. Our general approach, which employs a pairwise maximum entropy model to infer direct couplings between residues, has been successfully used to predict the three-dimensional structures of proteins from sequences. Building on this approach, we introduce an iterative algorithm to predict specific interaction partners from among the members of two protein families. We assess the algorithm's performance on histidine kinases and response regulators from bacterial two-component signaling systems. The algorithm proves successful without any a priori knowledge of interaction partners, yielding a striking 0.93 true positive fraction on our complete dataset, and we uncover the origin of this surprising success. Finally, we discuss how our method could be used to predict novel protein-protein interactions.

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