Is EC class predictable from reaction mechanism?

We thank the Scottish Universities Life Sciences Alliance (SULSA) and the Scottish Overseas Research Student Awards Scheme of the Scottish Funding Council (SFC) for financial support.Background: We investigate the relationships between the EC (Enzyme Commission) class, the associated chemical reaction, and the reaction mechanism by building predictive models using Support Vector Machine (SVM), Random Forest (RF) and k-Nearest Neighbours (kNN). We consider two ways of encoding the reaction mechanism in descriptors, and also three approaches that encode only the overall chemical reaction. Both cross-validation and also an external test set are used. Results: The three descriptor sets encoding overall chemical transformation perform better than the two descriptions of mechanism. SVM and RF models perform comparably well; kNN is less successful. Oxidoreductases and hydrolases are relatively well predicted by all types of descriptor; isomerases are well predicted by overall reaction descriptors but not by mechanistic ones. Conclusions: Our results suggest that pairs of similar enzyme reactions tend to proceed by different mechanisms. Oxidoreductases, hydrolases, and to some extent isomerases and ligases, have clear chemical signatures, making them easier to predict than transferases and lyases. We find evidence that isomerases as a class are notably mechanistically diverse and that their one shared property, of substrate and product being isomers, can arise in various unrelated ways. The performance of the different machine learning algorithms is in line with many cheminformatics applications, with SVM and RF being roughly equally effective. kNN is less successful, given the role that non-local information plays in successful classification. We note also that, despite a lack of clarity in the literature, EC number prediction is not a single problem; the challenge of predicting protein function from available sequence data is quite different from assigning an EC classification from a cheminformatics representation of a reaction.Publisher PDFPeer reviewe

Dimethyl Sulfoxide Promotes the Multiple Functions of the Tumor Suppressor HLJ1 through Activator Protein-1 Activation in NSCLC Cells

Background: Dimethyl sulfoxide (DMSO) is an amphipathic molecule that displays a diversity of antitumor activities. Previous studies have demonstrated that DMSO can modulate AP-1 activity and lead to cell cycle arrest at the G1 phase. HLJ1 is a newly identified tumor and invasion suppressor that inhibits tumorigenesis and cancer metastasis. Its transcriptional activity is regulated by the transcription factor AP-1. However, the effects of DMSO on HLJ1 are still unknown. In the present study, we investigate the antitumor effects of DMSO through HLJ1 induction and demonstrate the mechanisms involved. Methods and Findings: Low-HLJ1-expressing highly invasive CL1–5 lung adenocarcinoma cells were treated with various concentrations of DMSO. We found that DMSO can significantly inhibit cancer cell invasion, migration, proliferation, and colony formation capabilities through upregulation of HLJ1 in a concentration-dependent manner, whereas ethanol has no effect. In addition, the HLJ1 promoter and enhancer reporter assay revealed that DMSO transcriptionally upregulates HLJ1 expression through an AP-1 site within the HLJ1 enhancer. The AP-1 subfamily members JunD and JunB were significantly upregulated by DMSO in a concentration-dependent manner. Furthermore, pretreatment with DMSO led to a significant increase in the percentage of UV-induced apoptotic cells. Conclusions: Our results suggest that DMSO may be an important stimulator of the tumor suppressor protein HLJ1 throug

Selective inhibition of RNA polymerase I transcription as a potential approach to treat African trypanosomiasis.

Trypanosoma brucei relies on an essential Variant Surface Glycoprotein (VSG) coat for survival in the mammalian bloodstream. High VSG expression within an expression site body (ESB) is mediated by RNA polymerase I (Pol I), which in other eukaryotes exclusively transcribes ribosomal RNA genes (rDNA). As T. brucei is reliant on Pol I for VSG transcription, we investigated Pol I transcription inhibitors for selective anti-trypanosomal activity. The Pol I inhibitors quarfloxin (CX-3543), CX-5461, and BMH-21 are currently under investigation for treating cancer, as rapidly dividing cancer cells are particularly dependent on high levels of Pol I transcription compared with nontransformed cells. In T. brucei all three Pol I inhibitors have IC50 concentrations for cell proliferation in the nanomolar range: quarfloxin (155 nM), CX-5461 (279 nM) or BMH-21 (134 nM) compared with IC50 concentrations in the MCF10A human breast epithelial cell line (4.44 μM, 6.89 μM or 460 nM, respectively). T. brucei was therefore 29-fold more sensitive to quarfloxin, 25-fold more sensitive to CX-5461 and 3.4-fold more sensitive to BMH-21. Cell death in T. brucei was due to rapid inhibition of Pol I transcription, as within 15 minutes treatment with the inhibitors rRNA precursor transcript was reduced 97-98% and VSG precursor transcript 91-94%. Incubation with Pol I transcription inhibitors also resulted in disintegration of the ESB as well as the nucleolus subnuclear structures, within one hour. Rapid ESB loss following the block in Pol I transcription argues that the ESB is a Pol I transcription nucleated structure, similar to the nucleolus. In addition to providing insight into Pol I transcription and ES control, Pol I transcription inhibitors potentially also provide new approaches to treat trypanosomiasis

Prognostic value of coronary revascularisation-related myocardial injury: a cardiac magnetic resonance imaging study.

AIMS: Myocardial revascularisation improves outcomes in patients with coronary artery disease. However, these procedures may themselves cause irreversible myocardial injury. The prognostic value of procedural myocardial injury is uncertain. METHODS AND RESULTS: We quantified procedural myocardial necrosis using delayed enhancement cardiovascular magnetic resonance imaging (DE-CMR) in 152 consecutive patients before and shortly after percutaneous coronary intervention (PCI) or coronary artery bypass graft (CABG). The primary endpoint was defined as death, non-fatal myocardial infarction, sustained ventricular arrhythmia, unstable angina or heart failure requiring hospitalisation. During a median follow-up of 2.9 years, 27 patients (18%) reached the primary endpoint. 49 patients (32%) had evidence of new procedure-related myocardial hyperenhancement with a median mass of 5.0 g (interquartile range 2.7-9.8). After adjustment for age and sex, these patients had a 3.1-fold (95% confidence interval 1.4 to 6.8; p = 0.004) higher risk of adverse outcome than patients without new hyperenhancement. Cardiac troponin levels and quantitative measures of left ventricular function after procedure did not show any significant independent association with the primary endpoint and they did not alter the independent association of new hyperenhancement. CONCLUSIONS: Myocardial injury during PCI or CABG, identified by DE-CMR, adversely affects clinical outcome. This suggests the benefits from revascularisation could partially be offset by new myocardial injury caused by the intervention itself

Variable resistance to Quambalaria pitereka in spotted gum reveal opportunities for disease screening

Quambalaria shoot blight, caused by the fungus Quambalaria pitereka, is a serious disease affecting the development of spotted gum (Corymbia citriodora subsp. citriodora, C. citriodora subsp. variegata, C. henryi and C. maculata) plantations in subtropical and tropical Australia. Incorporation of screening for resistance to Q. pitereka into current breeding programs is essential for the future development of plantations using spotted gum and Corymbia hybrids. The aim of this study was to determine whether there is variability in resistance among and within different species provenances and families of spotted gum to infection by Q. pitereka. A secondary aim was to consider whether the origin of seed source is a significant indicator of resistance to Q. pitereka. Assessments were conducted in trials consisting of spotted gum provenances, families and clones, all at the same site with high levels of disease pressure and with optimum climatic conditions for disease development. While all species and provenances of spotted gum could be infected by Q. pitereka, results showed that there are high levels of variability in resistance between and within species, provenances and families, indicating the potential to select for disease resistance. Provenance was shown to be an unreliable indicator of resistance to Q. pitereka