Interactome under construction

Bonetta, Laura

doi:10.1038/468851a

Cited by 212 publications

(105 citation statements)

References 12 publications

(7 reference statements)

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“…Protein-protein interactions (PPIs) play a central role in biology[1], yet fundamental information such as their subcellular location is lacking for many of them. Among current techniques for analyzing PPIs, bimolecular fluorescence complementation (BiFC) has been commonly used for its ability to directly visualize PPIs within a cell[2], [3], [4].…”

Section: Introductionmentioning

confidence: 99%

Photoactivated Localization Microscopy with Bimolecular Fluorescence Complementation (BiFC-PALM) for Nanoscale Imaging of Protein-Protein Interactions in Cells

et al. 2014

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Bimolecular fluorescence complementation (BiFC) has been widely used to visualize protein-protein interactions (PPIs) in cells. Until now, however, the resolution of BiFC has been limited by the diffraction of light to ∼250 nm, much larger than the nanometer scale at which PPIs occur or are regulated. Cellular imaging at the nanometer scale has recently been realized with single molecule superresolution imaging techniques such as photoactivated localization microscopy (PALM). Here we have combined BiFC with PALM to visualize PPIs inside cells with nanometer spatial resolution and single molecule sensitivity. We demonstrated that PAmCherry1, a photoactivatable fluorescent protein commonly used for PALM, can be used as a BiFC probe when split between residues 159 and 160 into two fragments. PAmCherry1 BiFC exhibits high specificity and high efficiency even at 37°C in detecting PPIs with virtually no background from spontaneous reconstitution. Moreover, the reconstituted protein maintains the fast photoconversion, high contrast ratio, and single molecule brightness of the parent PAmCherry1, which enables selective PALM localization of PPIs with ∼18 nm spatial precision. With BiFC-PALM, we studied the interactions between the small GTPase Ras and its downstream effector Raf, and clearly observed nanoscale clustering and diffusion of individual KRas G12D/CRaf RBD (Ras-binding domain) complexes on the cell membrane. These observations provided novel insights into the regulation of Ras/Raf interaction at the molecular scale, which would be difficult with other techniques such as conventional BiFC, fluorescence co-localization or FRET.

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Section: Introductionmentioning

confidence: 99%

Photoactivated Localization Microscopy with Bimolecular Fluorescence Complementation (BiFC-PALM) for Nanoscale Imaging of Protein-Protein Interactions in Cells

et al. 2014

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“…DE genes were analyzed using STRING for predicting network of proteins encoded by DE genes [16], [17]. Predictions of functional association networks for all DE genes encoded proteins at 6 hpi are presented in Figure 2.…”

Section: Resultsmentioning

confidence: 99%

Transcription Analysis of the Porcine Alveolar Macrophage Response to Mycoplasma hyopneumoniae

Sun

et al. 2014

PLoS ONE

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Mycoplasma hyopneumoniae is considered the major causative agent of porcine respiratory disease complex, occurs worldwide and causes major economic losses to the pig industry. To gain more insights into the pathogenesis of this organism, the high throughput cDNA microarray assays were employed to evaluate host responses of porcine alveolar macrophages to M. hyopneumoniae infection. A total of 1033 and 1235 differentially expressed genes were identified in porcine alveolar macrophages in responses to exposure to M. hyopneumoniae at 6 and 15 hours post infection, respectively. The differentially expressed genes were involved in many vital functional classes, including inflammatory response, immune response, apoptosis, cell adhesion, defense response, signal transduction, protein folding, protein ubiquitination and so on. The pathway analysis demonstrated that the most significant pathways were the chemokine signaling pathway, Toll-like receptor signaling pathway, RIG-I-like receptor signaling pathway, nucleotide-binding oligomerization domains (Nod)-like receptor signaling pathway and apoptosis signaling pathway. The reliability of the data obtained from the microarray was verified by performing quantitative real-time PCR. The expression kinetics of chemokines was further analyzed. The present study is the first to document the response of porcine alveolar macrophages to M. hyopneumoniae infection. The data further developed our understanding of the molecular pathogenesis of M. hyopneumoniae.

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“…Additionally, proteins can interact with different partners within different pathways based on their function: they can interact on a physical level or within a protein complex (66), through regulation (67), or PTMs (62), which makes it challenging to understand the underlying biology and its molecular mechanistic. For accomplishing this, researchers suggest to systematically map gene and protein interactions (68, 69), and there have already been the effort of linking the interactome to human diseases (65, 70). …”

Section: Methodology – Omics Approachesmentioning

confidence: 99%

Systems Medicine as an Emerging Tool for Cardiovascular Genetics

Haase

Börnigen

Müller

et al. 2016

Front. Cardiovasc. Med.

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Cardiovascular disease (CVD) is a major contributor to morbidity and mortality worldwide. However, the pathogenesis of CVD is complex and remains elusive. Within the last years, systems medicine has emerged as a novel tool to study the complex genetic, molecular, and physiological interactions leading to diseases. In this review, we provide an overview about the current approaches for systems medicine in CVD. They include bioinformatical and experimental tools such as cell and animal models, omics technologies, network, and pathway analyses. Additionally, we discuss challenges and current literature examples where systems medicine has been successfully applied for the study of CVD.

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Interactome under construction

Cited by 212 publications

References 12 publications

Photoactivated Localization Microscopy with Bimolecular Fluorescence Complementation (BiFC-PALM) for Nanoscale Imaging of Protein-Protein Interactions in Cells

Photoactivated Localization Microscopy with Bimolecular Fluorescence Complementation (BiFC-PALM) for Nanoscale Imaging of Protein-Protein Interactions in Cells

Transcription Analysis of the Porcine Alveolar Macrophage Response to Mycoplasma hyopneumoniae

Systems Medicine as an Emerging Tool for Cardiovascular Genetics

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