Functional Diversity and Structural Disorder in the Human Ubiquitination Pathway

The ubiquitin-proteasome system plays a central role in cellular regulation and protein quality control (PQC). The system is built as a pyramid of increasing complexity, with two E1 (ubiquitin activating), few dozen E2 (ubiquitin conjugating) and several hundred E3 (ubiquitin ligase) enzymes. By collecting and analyzing E3 sequences from the KEGG BRITE database and literature, we assembled a coherent dataset of 563 human E3s and analyzed their various physical features. We found an increase in structural disorder of the system with multiple disorder predictors (IUPred - E1: 5.97%, E2: 17.74%, E3: 20.03%). E3s that can bind E2 and substrate simultaneously (single subunit E3, ssE3) have significantly higher disorder (22.98%) than E3s in which E2 binding (multi RING-finger, mRF, 0.62%), scaffolding (6.01%) and substrate binding (adaptor/substrate recognition subunits, 17.33%) functions are separated. In ssE3s, the disorder was localized in the substrate/adaptor binding domains, whereas the E2-binding RING/HECT-domains were structured. To demonstrate the involvement of disorder in E3 function, we applied normal modes and molecular dynamics analyses to show how a disordered and highly flexible linker in human CBL (an E3 that acts as a regulator of several tyrosine kinase-mediated signalling pathways) facilitates long-range conformational changes bringing substrate and E2-binding domains towards each other and thus assisting in ubiquitin transfer. E3s with multiple interaction partners (as evidenced by data in STRING) also possess elevated levels of disorder (hubs, 22.90% vs. non-hubs, 18.36%). Furthermore, a search in PDB uncovered 21 distinct human E3 interactions, in 7 of which the disordered region of E3s undergoes induced folding (or mutual induced folding) in the presence of the partner. In conclusion, our data highlights the primary role of structural disorder in the functions of E3 ligases that manifests itself in the substrate/adaptor binding functions as well as the mechanism of ubiquitin transfer by long-range conformational transitions. © 2013 Bhowmick et al

Capillary electrophoresis mass spectrometry-based saliva metabolomics identified oral, breast and pancreatic cancer-specific profiles

Saliva is a readily accessible and informative biofluid, making it ideal for the early detection of a wide range of diseases including cardiovascular, renal, and autoimmune diseases, viral and bacterial infections and, importantly, cancers. Saliva-based diagnostics, particularly those based on metabolomics technology, are emerging and offer a promising clinical strategy, characterizing the association between salivary analytes and a particular disease. Here, we conducted a comprehensive metabolite analysis of saliva samples obtained from 215 individuals (69 oral, 18 pancreatic and 30 breast cancer patients, 11 periodontal disease patients and 87 healthy controls) using capillary electrophoresis time-of-flight mass spectrometry (CE-TOF-MS). We identified 57 principal metabolites that can be used to accurately predict the probability of being affected by each individual disease. Although small but significant correlations were found between the known patient characteristics and the quantified metabolites, the profiles manifested relatively higher concentrations of most of the metabolites detected in all three cancers in comparison with those in people with periodontal disease and control subjects. This suggests that cancer-specific signatures are embedded in saliva metabolites. Multiple logistic regression models yielded high area under the receiver-operating characteristic curves (AUCs) to discriminate healthy controls from each disease. The AUCs were 0.865 for oral cancer, 0.973 for breast cancer, 0.993 for pancreatic cancer, and 0.969 for periodontal diseases. The accuracy of the models was also high, with cross-validation AUCs of 0.810, 0.881, 0.994, and 0.954, respectively. Quantitative information for these 57 metabolites and their combinations enable us to predict disease susceptibility. These metabolites are promising biomarkers for medical screening

Impact of experimental hyperlipidemia on histology of major salivary glands

Objectives: To examine the histologic structure of major salivary glands in high-fat diet induced hyperlipidemic rat

The use of the ipsilateral versus contralateral pedicle and vertical versus horizontal flap inset models in TRAM flap breast reconstruction: The aesthetic outcome

The use of an ipsilateral or a contralateral rectus abdominis muscle as a pedicle and comparison of their advantages and disadvantages in TRAM flap breast reconstruction have been reported in the literature. In our clinical experience with 22 pedicled TRAM flap breast reconstructions, the use of either an ipsilateral or contralateral pedicle was found to be equivocal regarding the flap viability and the aesthetic outcome. Thus, it seems better to decide their use according to the needs of an individual patient

Identification of nitrate leaching hot spots in a large area with contrasting soil texture and management

Identification of nitrate (NO3) leaching hot spots is important in mitigating environmental effect of NO3. Once identified, the hot spots can be further analyzed in detail for evaluating appropriate alternative management techniques to reduce impact of nitrate on groundwater. This study was conducted to identify NO3 leaching hot spots in an approximately 36,000 ha area in Serik plain, which is used intensively for agriculture in the Antalya region of Southern Turkey. Geo-referenced water samples were taken from 161 wells and from the representative soils around the wells during the period from late May to early June of 2009. The data were analyzed by classical statistics and geostatistics. Both soil and groundwater NO3-N concentrations demonstrated a considerably high variation, with a mean of 10.2 mg kg-1 and 2.1 mg L-1 NO3-N for soil and groundwater, respectively. The NO3-N concentrations ranged from 0.01 to 102.5 mg L-1 in well waters and from 1.89 to 106.4 mg kg-1 in soils. Nitrate leaching was spatially dependent in the study area. Six hot spots were identified in the plain, and in general, the hot spots coincided with high water table, high sand content, and irrigated wheat and cotton. The adverse effects of NO3 can be mitigated by switching the surface and furrow irrigation methods to sprinkler irrigation, which results in a more efficient N and water use. Computer models such as NLEAP can be used to analyze alternative management practices together with soil, aquifer, and climate characteristics to determine a set of management alternatives to mitigate NO3 effect in these hot spot areas.Geostatistics Groundwater nitrate Soil nitrate Spatial variation Irrigation