Genome-wide bimolecular fluorescence complementation analysis of SUMO interactome in yeast

The definition of protein–protein interactions (PPIs) in the natural cellular context is essential for properly understanding various biological processes. So far, however, most large-scale PPI analyses have not been performed in the natural cellular context. Here, we describe the construction of a Saccharomyces cerevisiae fusion library in which each endogenous gene is C-terminally tagged with the N-terminal fragment of Venus (VN) for a genome-wide bimolecular fluorescence complementation assay, a powerful technique for identifying PPIs in living cells. We illustrate the utility of the VN fusion library by systematically analyzing the interactome of the small ubiquitin-related modifier (SUMO) and provide previously unavailable information on the subcellular localization, types, and protease dependence of SUMO interactions. Our data set is highly complementary to the existing data sets and represents a useful resource for expanding the understanding of the physiological roles of SUMO. In addition, the VN fusion library provides a useful research tool that makes it feasible to systematically analyze PPIs in the natural cellular context.Most biological processes are mediated by complicated networks of protein–protein interactions (PPIs). Thus, the identification of the occurrence and components of PPIs provides invaluable insights into the cellular functions of proteins. In addition to conventional coimmunoprecipitation techniques, several methods have been developed to study PPIs, including the yeast two-hybrid analysis (Fields and Song 1989), the split ubiquitin system (Johnsson and Varshavsky 1994), fluorescence resonance energy transfer (FRET) assays (Periasamy and Day 1999; Pollok and Heim 1999), tandem affinity purification (TAP) followed by mass spectrometry (MS) analysis (Rigaut et al. 1999), and protein fragment complementation (PFC) assays (Remy and Michnick 1999; Ghosh et al. 2000; Wehrman et al. 2002; Paulmurugan and Gambhir 2003). Recently, the bimolecular fluorescence complementation (BiFC) assay, a specialized form of the PFC assay that uses fluorescent proteins as a reporter, has been developed (Hu et al. 2002). The BiFC assay is based on the formation of a fluorescent complex when two proteins fused to nonfluorescent fragments of a fluorescent protein interact with each other. This approach enables direct visualization of the occurrence and subcellular localization of PPIs with simple equipment.The budding yeast Saccharomyces cerevisiae has been a valuable eukaryotic model system, not only for traditional molecular and cell biology but also for the fields of functional genomics and proteomics. In S. cerevisiae, several large-scale analyses of PPIs have been performed with the yeast two-hybrid method (Uetz et al. 2000; Ito et al. 2001) or TAP-MS analysis (Gavin et al. 2002, 2006; Ho et al. 2002; Krogan et al. 2006). However, these approaches do not measure PPI in the natural cellular context; the yeast two-hybrid method is not appropriate for analyzing the interactions between proteins that cannot be transported to the nucleus or that form interactions only in the presence of other stabilizing interactions, and TAP-MS analysis is not amenable to studying protein complexes that are weakly or transiently formed or that do not survive in vitro purification. Compared with the yeast two-hybrid method and TAP-MS analysis, the FRET, PFC, and BiFC assays have several advantages in that they can detect the interactions between proteins in their natural cellular environment. Recently, a large-scale PPI screen using the PFC assay based on reconstituted dihydrofolate reductase (DHFR) activity has been reported (Tarassov et al. 2008), which is the first example of genome-wide PPI analysis using the PFC assay. However, because positive PPIs are selected by methotrexate resistance in the DHFR PFC assay, it is possible that the addition of methotrexate to the assay medium may perturb cellular physiology and proper PPI networks. In this regard, large-scale PPI screens using the BiFC or FRET assay that do not require any exogenous reagents would provide more accurate information about the structural organization of PPI networks in cells. To date, however, there is no report describing the application of the BiFC or FRET assay to genome-wide PPI analyses, particularly using proteins expressed from their own native promoters.The small ubiquitin-related modifier (SUMO) proteins are ∼10 kDa in size and comprise a family of evolutionarily conserved polypeptides that are post-translationally attached to the lysine residues of target proteins to regulate their subcellular localization, stability, and activity (Kerscher et al. 2006; Geiss-Friedlander and Melchior 2007). SUMO conjugation plays a variety of important roles in diverse eukaryotic cellular processes. SUMO can also mediate the non-covalent interaction of substrate proteins with proteins containing SUMO-interacting motifs and modulate their function (Song et al. 2004). In this regard, the identification of SUMO target proteins is crucial for the elucidation of the function of SUMO. Recent genome-wide PPI screens have identified over 500 putative SUMO conjugates in S. cerevisiae (Panse et al. 2004; Wohlschlegel et al. 2004; Zhou et al. 2004; Denison et al. 2005; Hannich et al. 2005; Wykoff and O''Shea 2005). More recently, an elegant study integrating the information of PPIs and genetic interactions has been conducted and has uncovered novel functional relationships between the SUMO pathway and various biological processes (Makhnevych et al. 2009). These systematic analyses have expanded the pool of SUMO substrates and the understanding of the biological function of sumoylation. However, because SUMO substrates can undergo rapid cycles of modification and demodification, and most target proteins appear to be modified to a small percentage at steady state (Geiss-Friedlander and Melchior 2007), it is likely that many unknown SUMO substrates remain to be discovered. Moreover, previous systematic PPI screens to identify SUMO substrates have primarily been performed with the yeast two-hybrid method and TAP-MS, which do not measure PPIs in the natural cellular context. The low agreement between the data from previous systematic screens demonstrates the limitation of the experimental methods used in those analyses and indicates that no single screen has been comprehensive. For this reason, different systematic approaches, with methods that can detect the interactions between proteins in their natural cellular environment, would greatly contribute to the identification of novel SUMO substrates and thus to the understanding of the function of the SUMO pathway.In the present study, we generated a collection of yeast strains expressing full-length proteins tagged with the N-terminal fragment of Venus (VN), a yellow fluorescent protein variant, from their own native promoters. Through a systematic analysis with the VN fusion library, we identified the interactome of SUMO, comprising 367 proteins, and also obtained previously unavailable information on the subcellular localization, types, and protease dependence of SUMO interactions in living yeast cells. Our data not only highlight a novel relationship between sumoylation and various biological processes but also represent a valuable resource that can be used to study the functional roles of the SUMO pathway. This is the first report that describes the application of the BiFC assay to a genome-wide PPI analysis using proteins expressed from their own native promoters. As demonstrated here, the VN fusion library provides a useful research tool that makes it feasible to systematically analyze PPIs in the natural cellular context.     

Usefulness of 3-Dimensional-Printed Breast Surgical Guides for Undetectable Ductal Carcinoma In Situ on Ultrasonography: A Report of 2 Cases

Tumor localization is challenging in the context of ductal carcinoma in situ (DCIS) treated with breast-conserving surgery. Conventional localization methods are generally performed under the guidance of ultrasonography or mammography and are rarely performed with magnetic resonance imaging (MRI), which is more sensitive than the aforementioned modalities in detecting DCIS. Here, we report the application of MRI-based individualized 3-dimensional (3D)-printed breast surgical guides (BSGs) for patients with breast cancer. We successfully resected indeterminate and suspicious lesions that were only detected using preoperative MRI, and the final histopathologic results confirmed DCIS with clear resection margins. MRI guidance combined with 3D-printed BSGs can be used for DCIS localization, especially for lesions easily detectable using MRI only.     

Digital Workflow for Retrofitting a Surveyed Crown Using a Removable Partial Denture as an Antagonist

Digital workflow expedites the procedure of retrofitting a surveyed crown against an existing removable partial denture (RPD). This article describes a simple and straightforward technique of digital workflow where an existing RPD is scanned as an antagonist to design the rest seat, guide plane, and height of contour of a surveyed crown.     

Accuracy of Diffusion Tensor Imaging for Diagnosing Cervical Spondylotic Myelopathy in Patients Showing Spinal Cord Compression

ObjectiveTo assess the performance of diffusion tensor imaging (DTI) for the diagnosis of cervical spondylotic myelopathy (CSM) in patients with deformed spinal cord but otherwise unremarkable conventional magnetic resonance imaging (MRI) findings.ResultsThe MD, LD, and RD cut-off values were 1.079 × 10^-3, 1.719 × 10^-3, and 0.749 × 10^-3 mm²/sec, respectively, and that of FA was 0.475. Sensitivity, specificity, positive predictive value and negative predictive value were: 100 (4/4), 44.8 (13/29), 20 (4/20), and 100 (13/13) for MD; 100 (4/4), 27.6 (8/29), 16 (4/25), and 100 (8/8) for FA; 100 (4/4), 58.6 (17/29), 25 (4/16), and 100 (17/17) for MD∩FA; 100 (4/4), 68.9 (20/29), 30.8 (4/13), and 100 (20/20) for LD∩FA; and 75 (3/4), 68.9 (20/29), 25 (3/12), and 95.2 (20/21) for RD∩FA in percentage value. Diagnostic performance comparisons revealed significant differences only in specificity between FA and MD∩FA (p = 0.003), FA and LD∩FA (p < 0.001), FA and RD∩FA (p < 0.001), MD and LD∩FA (p = 0.024) and MD and RD∩FA (p = 0.024).ConclusionFractional anisotropy combined with MD, RD, or LD is expected to be more useful than FA and MD for diagnosing CSM in patients who show deformed spinal cords without signal changes on MRI.     

Ultrasound-Guided Percutaneous Removal of Wooden Foreign Bodies in the Extremities with Hydro-Dissection Technique

ObjectiveWe described the technique of ultrasound (US)-guided percutaneous removal of the foreign bodies (FB) with hydro-dissection in the radiologic department and presented video files of several cases.ResultsThe mean time required for the entire procedure was approximately 20 minutes. There were no significant complications during the US-guided removal or long-term complications after the procedure. All 4 FBs were successfully removed from the soft tissue under US guidance.ConclusionUltrasound-guided percutaneous removal of the FBs with hydro-dissection in the radiology department is a less invasive and safe method over surgical removal in the operating room. Additionally, the use of a guide wire and serial dilator may help minimize soft tissue injury and facilitate the introduction of forceps.     

A diaphragmatic retroperitoneal cyst

Diaphragmatic lesions are usually congenital bronchogenic cysts. A patient with a known diaphragmatic cyst presented with new onset right upper quadrant pain. Repeat imaging showed enlargement of the cyst, the CA19–9 cancer marker was raised at 312iu/ml (normal: <27iu/ml) and positron emission tomography combined with computed tomography showed focally increased uptake in the cystic wall. In view of symptoms and risk of neoplasia, the lesion was excised. Histology showed a benign epidermoid cyst. Features falsely suggesting neoplasia have been reported previously with benign splenic cysts but not with a benign diaphragmatic epidermoid cyst.