scholarly journals Distinct cis-acting elements govern purine-responsive regulation of the Leishmania donovani nucleoside transporters, LdNT1 and LdNT2

2020 ◽  
Author(s):  
M. Haley Licon ◽  
Francesca Goodstein ◽  
Diana Ortiz ◽  
Scott M. Landfear ◽  
Phillip A. Yates
Keyword(s):  
Stress Response ◽  
Protein Interactions ◽  
Leishmania Donovani ◽  
Mrna Abundance ◽  
Polypyrimidine Tract ◽  
Protein Protein Interactions ◽  
Cis Acting ◽  
Rna Granules ◽  
Underlying Mechanisms ◽  
Upregulated Genes

AbstractPurine salvage from the host is an obligatory process for all protozoan parasites. In Leishmania donovani, this is accomplished by four membrane nucleoside and nucleobase transporters, or LdNTs. Previously, we demonstrated that purine starvation invokes a robust stress response in Leishmania and characterized the proteomic changes involved. However, because Leishmania do not control the transcription of individual genes, the underlying mechanisms responsible for these changes were ill-defined. LdNT1 and LdNT2 are among the most rapidly and significantly upregulated genes in purine-starved L. donovani parasites. Thus, to better understand post-transcriptional mechanisms of purine-responsive gene expression, we have examined regulation of these genes in molecular detail. Here we report that LdNT1 and LdNT2 are controlled by distinct cis-acting elements. In the case of LdNT2, mRNA abundance and translational enhancement under purine stress depend on a 76 nt-long polypyrimidine tract encoded in the LdNT2 mRNA 3’-UTR. Transcripts containing the LdNT2 polypyrimidine tract were found to localize to discrete cytoplasmic foci in purine-replete cells, suggesting that the LdNT2 message may be stored in RNA granules at steady-state. In the case of LdNT1, we found that purine-responsiveness is conferred by a 48 nt-long polypyrimidine tract and additional upstream element, termed UE1. Both features are independently required for regulation, with the polypyrimidine tract and UE1 controlling mRNA abundance and translation, respectively. Together, these results highlight a remarkable degree of complexity in the regulation of the Leishmania purine stress response and set the stage for future investigations to identify the larger network of RNA-protein and protein-protein interactions involved.

scholarly journals Issues in performance evaluation for host–pathogen protein interaction prediction

2016 ◽  
Vol 14 (03) ◽  
pp. 1650011 ◽  
Author(s):  
Wajid Arshad Abbasi ◽  
Fayyaz Ul Amir Afsar Minhas
Keyword(s):  
Machine Learning ◽  
Protein Interactions ◽  
Cross Validation ◽  
Protein Protein Interactions ◽  
Evaluation Scheme ◽  
Host Pathogen ◽  
Pathogen Protein ◽  
Protein Interaction Prediction ◽  
Underlying Mechanisms ◽  
Fold Cross Validation

The study of interactions between host and pathogen proteins is important for understanding the underlying mechanisms of infectious diseases and for developing novel therapeutic solutions. Wet-lab techniques for detecting protein–protein interactions (PPIs) can benefit from computational predictions. Machine learning is one of the computational approaches that can assist biologists by predicting promising PPIs. A number of machine learning based methods for predicting host–pathogen interactions (HPI) have been proposed in the literature. The techniques used for assessing the accuracy of such predictors are of critical importance in this domain. In this paper, we question the effectiveness of K-fold cross-validation for estimating the generalization ability of HPI prediction for proteins with no known interactions. K-fold cross-validation does not model this scenario, and we demonstrate a sizable difference between its performance and the performance of an alternative evaluation scheme called leave one pathogen protein out (LOPO) cross-validation. LOPO is more effective in modeling the real world use of HPI predictors, specifically for cases in which no information about the interacting partners of a pathogen protein is available during training. We also point out that currently used metrics such as areas under the precision-recall or receiver operating characteristic curves are not intuitive to biologists and propose simpler and more directly interpretable metrics for this purpose.

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 ADAR1 limits stress granule formation through both translation-dependent and translation-independent mechanisms

2021 ◽  
Author(s):  
Giulia A. Corbet ◽  
James M. Burke ◽  
Roy Parker
Keyword(s):  
Immune Response ◽  
Stress Response ◽  
Protein Interactions ◽  
Binding Activity ◽  
Innate Immune ◽  
Protein Protein Interactions ◽  
Granule Formation ◽  
Translation Inhibition ◽  
Translation Repression ◽  
Dsrna Binding

Stress granules (SGs) are cytoplasmic assemblies of RNA and protein that form when translation is repressed during the integrated stress response (ISR). SGs assemble from the combination of RNA-RNA, RNA-protein, and protein-protein interactions between mRNPs. The protein Adenosine deaminase acting on RNA 1 (ADAR1) recognizes and modifies dsRNAs within cells to prevent an aberrant innate immune response. ADAR1 localizes to SGs, and since RNA-RNA interactions contribute to SG assembly and dsRNA induces SGs, we examined how ADAR1 affects SG formation. First, we demonstrate that ADAR1 depletion triggers SGs by allowing endogenous dsRNA to activate the ISR through PKR activation and translation repression. However, we also show that ADAR1 limits SG formation independently of translation inhibition. ADAR1 repression of SGs is independent of deaminase activity, but dependent on dsRNA-binding activity, suggesting a model where ADAR1 binding limits RNA-RNA and/or RNA-protein interactions necessary for recruitment to SGs. Given that ADAR1 expression is induced during viral infection, these findings have implications for ADAR1's role in the antiviral response.

Towards an Understanding of Plant Gene Regulation: The Action of Nuclear Factors

1991 ◽  
Vol 46 (1-2) ◽  
pp. 1-11 ◽  
Author(s):  
Kurt Weising ◽  
Günter Kahl
Keyword(s):  
Protein Interactions ◽  
Regulation Of Gene Expression ◽  
Regulatory Proteins ◽  
Regulatory Sequences ◽  
Protein Protein Interactions ◽  
Cis Acting ◽  
Plant Gene ◽  
Eukaryotic Genes ◽  
Genes Encoding ◽  
Plant Genes

Abstract Over the last decade an intensive research on the regulation of gene expression in viral and animal systems has led to the discovery of cis-acting regulatory sequences, the identification of sequence-specific DNA -binding proteins (trans-acting factors), the characterization of protein domains involved in DNA -protein recognition and binding as well as in protein -protein interactions, and the cloning and sequencing of genes encoding regulatory proteins. The tre­mendous progress in this field is now being complemented by advances in our understanding of how plant genes are regulated. A wealth of data has accumulated in the past few years witnessing basic similarities in the transcriptional regulation of various eukaryotic genes, but also specific features of plant genes. This article collects presently available data, focusses on DNA -protein interactions in plant genes, particularly in light-regulated and “constitutively expressed” genes, reports on the isolation of plant genes encoding regulatory proteins, an dismeant to induce further activities in plant gene research.

scholarly journals YjbH Requires Its Thioredoxin Active Motif for the Nitrosative Stress Response, Cell-to-Cell Spread, and Protein-Protein Interactions in Listeria monocytogenes

2020 ◽  
Vol 202 (12) ◽  
Author(s):  
Brittany R. Ruhland ◽  
Michelle L. Reniere
Keyword(s):  
Listeria Monocytogenes ◽  
Stress Response ◽  
Protein Interactions ◽  
Nitrosative Stress ◽  
Transcriptional Regulator ◽  
Cysteine Residues ◽  
Posttranslational Regulation ◽  
Protein Protein Interactions ◽  
Content Type ◽  
Cell Spread

ABSTRACT Listeria monocytogenes is a model facultative intracellular pathogen. Tight regulation of virulence proteins is essential for a successful infection, and the gene encoding the annotated thioredoxin YjbH was identified in two forward genetic screens as required for virulence factor production. Accordingly, an L. monocytogenes strain lacking yjbH is attenuated in a murine model of infection. However, the function of YjbH in L. monocytogenes has not been investigated. Here, we provide evidence that L. monocytogenes YjbH is involved in the nitrosative stress response, likely through its interaction with the redox-responsive transcriptional regulator SpxA1. YjbH physically interacted with SpxA1, and our data support a model in which YjbH is a protease adaptor that regulates SpxA1 protein abundance. Whole-cell proteomics identified eight additional proteins whose abundance was altered by YjbH, and we demonstrated that YjbH physically interacted with each in bacterial two-hybrid assays. Thioredoxin proteins canonically require active motif cysteines for function, but thioredoxin activity has not been tested for L. monocytogenes YjbH. We demonstrated that cysteine residues of the YjbH thioredoxin domain active motif are essential for L. monocytogenes sensitivity to nitrosative stress, cell-to-cell spread in a tissue culture model of infection, and several protein-protein interactions. Together, these results demonstrated that the function of YjbH in L. monocytogenes requires its thioredoxin active motif and that YjbH has a role in the posttranslational regulation of several proteins, including SpxA1. IMPORTANCE The annotated thioredoxin YjbH in Listeria monocytogenes has been implicated in virulence, but its function in the cell is unknown. In other bacterial species, YjbH is a protease adaptor that mediates degradation of the transcriptional regulator Spx. Here, we investigated the function of L. monocytogenes YjbH and demonstrated its role in the nitrosative stress response and posttranslational regulation of several proteins with which YjbH physically interacts, including SpxA1. Furthermore, we demonstrated that the cysteine residues of the YjbH thioredoxin active motif are required for the nitrosative stress response, cell-to-cell spread, and some protein-protein interactions. YjbH is widely conserved among Firmicutes, and this work reveals its unique requirement of the thioredoxin-active motif in L. monocytogenes.

scholarly journals Exploring the Antitumor Mechanisms of Zingiberis Rhizoma Combined with Coptidis Rhizoma Using a Network Pharmacology Approach

2020 ◽  
Vol 2020 ◽  
pp. 1-18
Author(s):  
Meng Wang ◽  
Youke Qi ◽  
Yongning Sun
Keyword(s):  
Gene Expression ◽  
Molecular Docking ◽  
Protein Interactions ◽  
Disease Free Survival ◽  
Network Pharmacology ◽  
Protein Protein Interactions ◽  
Active Components ◽  
Antitumor Effects ◽  
Coptidis Rhizoma ◽  
Underlying Mechanisms

Background. Although the combination of Zingiberis rhizoma (ZR) and Coptidis rhizoma (CR) is a classic traditional Chinese medicine-based herbal pair used for its antitumor effect, the material basis and underlying mechanisms are unclear. Here, a network pharmacology approach was used to elucidate the antitumor mechanisms of ZR-CR. Materials and Methods. To predict the targets of ZR-CR in treating tumors, we constructed protein–protein interactions and hub component-target networks and performed pathway and process enrichment and molecular docking analysis. We used a surface plasmon resonance (SPR) assay to validate the predicted component-target affinities. Hub gene expression and survival analysis in patients with tumors were used to predict the clinical significance. Results. The active components of ZR-CR—shogaol, daucosterol, ginkgetin, berberine, quercetin, chlorogenic acid, and vanillic acid—exhibited antitumor activities via the MAPK, PI3K-AKT, TNF, FOXO, HIF-1, and VEGF signaling pathways. Molecular docking and SPR analyses suggested direct binding of berberine with AKT1 and TP53; quercetin with EGFR and VEGF165; and ginkgetin, isoginkgetin, and daucosterol with VEGF165 with weak affinities. Gene expression levels of the hub targets of ZR-CR were associated with overall survival and disease-free survival in patients with various tumor types. Conclusions. The antitumor components of the ZR-CR herbal pair and the mechanisms underlying their antitumor effects were identified. These antitumor components deserve to be explored further in experimental and clinical studies.

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 ZAP-70 constitutively regulates gene expression and protein synthesis in chronic lymphocytic leukemia

Blood ◽  
2021 ◽  
Author(s):  
Jingyu Chen ◽  
Vijitha Sathiaseelan ◽  
Andrew Douglas Moore ◽  
Shengjiang Tan ◽  
Chandra SR Chilamakuri ◽  
...  
Keyword(s):  
Protein Synthesis ◽  
Cell Survival ◽  
Protein Interactions ◽  
Ribosomal Proteins ◽  
Cell Receptor ◽  
Lymphocytic Leukemia ◽  
Protein Protein Interactions ◽  
Global Protein Synthesis ◽  
Bcr Signaling ◽  
Underlying Mechanisms

The expression of ZAP-70 in a subset of CLL patients strongly correlates with a more aggressive clinical course, though the exact underlying mechanisms remain elusive. The ability of ZAP-70 to enhance B cell receptor (BCR) signaling, independently of its kinase function, is considered to contribute. Here we employed RNA-sequencing and proteomic analyses of primary cells differing only in their expression of ZAP-70 to further define how ZAP-70 increases aggressiveness of CLL. We identified that ZAP-70 is directly required for cell survival in the absence of an overt BCR signal, which can compensate for ZAP-70 deficiency as an anti-apoptotic signal. In addition, the expression of ZAP-70 regulates the transcription of factors regulating recruitment and activation of T cells, such as CCL3, CCL4 and IL4I1. Quantitative mass spectrometry of double-cross linked ZAP-70 complexes further demonstrated constitutive and direct protein-protein interactions between ZAP-70 and BCR-signaling components. Unexpectedly, ZAP-70 also binds to ribosomal proteins, which is not dependent on, but further increased by BCR-stimulation. Importantly, decreased expression of ZAP-70 significantly reduced MYC-expression and global protein synthesis, providing evidence that ZAP-70 contributes to translational dysregulation in CLL. In conclusion, ZAP-70 constitutively promotes cell survival, microenvironment-interactions and protein synthesis in CLL cells, likely to improve cellular fitness and to further drive disease progression.

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