Assignment of EC Numbers to Enzymatic Reactions with Reaction Difference Fingerprints

The EC numbers represent enzymes and enzyme genes (genomic information), but they are also utilized as identifiers of enzymatic reactions (chemical information). In the present work (ECAssigner), our newly proposed reaction difference fingerprints (RDF) are applied to assign EC numbers to enzymatic reactions. The fingerprints of reactant molecules minus the fingerprints of product molecules will generate reaction difference fingerprints, which are then used to calculate reaction Euclidean distance, a reaction similarity measurement, of two reactions. The EC number of the most similar training reaction will be assigned to an input reaction. For 5120 balanced enzymatic reactions, the RDF with a fingerprint length at 3 obtained at the sub-subclass, subclass, and main class level with cross-validation accuracies of 83.1%, 86.7%, and 92.6% respectively. Compared with three published methods, ECAssigner is the first fully automatic server for EC number assignment. The EC assignment system (ECAssigner) is freely available via: http://cadd.whu.edu.cn/ecassigner/.     

Automatic Assignment of Prokaryotic Genes to Functional Categories Using Literature Profiling

In the last years, there was an exponential increase in the number of publicly available genomes. Once finished, most genome projects lack financial support to review annotations. A few of these gene annotations are based on a combination of bioinformatics evidence, however, in most cases, annotations are based solely on sequence similarity to a previously known gene, which was most probably annotated in the same way. As a result, a large number of predicted genes remain unassigned to any functional category despite the fact that there is enough evidence in the literature to predict their function. We developed a classifier trained with term-frequency vectors automatically disclosed from text corpora of an ensemble of genes representative of each functional category of the J. Craig Venter Institute Comprehensive Microbial Resource (JCVI-CMR) ontology. The classifier achieved up to 84% precision with 68% recall (for confidence≥0.4), F-measure 0.76 (recall and precision equally weighted) in an independent set of 2,220 genes, from 13 bacterial species, previously classified by JCVI-CMR into unambiguous categories of its ontology. Finally, the classifier assigned (confidence≥0.7) to functional categories a total of 5,235 out of the ∼24 thousand genes previously in categories “Unknown function” or “Unclassified” for which there is literature in MEDLINE. Two biologists reviewed the literature of 100 of these genes, randomly picket, and assigned them to the same functional categories predicted by the automatic classifier. Our results confirmed the hypothesis that it is possible to confidently assign genes of a real world repository to functional categories, based exclusively on the automatic profiling of its associated literature. The LitProf - Gene Classifier web server is accessible at: www.cebio.org/litprofGC.     

Assignment of a gene for human quinoid-dihydropteridine reductase (QDPR,EC 1.6.5.1) to chromosome 4

Summary An acrylamide gel electrophoretic procedure is described which allows the separation of human quinoid-dihydropteridine reductase (QDPR), EC 1.6.5.1) from the homologous enzyme expressed in established rodent cell lines. The human enzyme marker segregates exclusively with chromosome 4 in a series of well characterized man-mouse somatic cell hybrid clones from our clone bank. This observation supports the assignment of a structural gene for QDPR to human chromosome 4.     

病毒衣壳结构亚单位的种类数与三角形剖分数关系的研究和探讨

本文报道了在正廿面体病毒衣壳中,当蛋白结构亚单位以“三聚体”的形式聚集在单位三角形(?)时,其亚单位的种类数应等于该病毒的三角形剖分数值。     

Assignment of a gene for human mitochondrial isocitrate dehydrogenase (ICD-M,EC 1. 1. 1. 41) to chromosome 15

Summary Segregation analysis of human biochemical markers and chromosomes in human-mouse somatic cell hybrids allowed to demonstrate synteny of ICD _M with the genes for phosphomannose isomerase and pyruvate kinase and to assign the linkage group to human chromosome 15.     

Metalloendopeptidases EC 3.4.24.15 and EC 3.4.24.16: potential roles in vascular physiology

The zinc metalloendopeptidases EC 3.4.24.15 (EP24.15) and EC 3.4.24.16 (EP 24.16) are closely relatedubiquitous enzymes, which have well-defined in vitroactivities in generation and degradation of a range ofspecific peptide targets. Despite this, little is knownregarding their roles in whole animal physiology. One of thepeptides degraded by these enzymes in vitro isbradykinin, a mediator with potent effects on the vasculatureat both systemic and local levels. This review summarises thework that has examined the role of EP 24.15/24.16 inregulation of the vascular effects of bradykinin invivo. This work was made possible by the development of aspecific stable inhibitor of these enzymes, JA-2. Use of thisinhibitor has shown that EP 24.15/24.16 are capable ofregulating responses induced by exogenous bradykinin. Thiseffect was observed at a systemic level with an increase inthe hypotensive effect of intravenous bradykinin. Further workis required to determine whether these enzymes also regulatebradykinin produced endogenously.     

The New Shape of EC

The journal Eukaryotic Cell has served the eukaryotic microbiology community since 2002. It will continue to do so as it merges into the new broad-scope open-access journal mSphere in 2016.     

Metalloendopeptidases EC 3.4.24.15 and EC 3.4.24.16: potential roles in vascular physiology

Summary The zinc metalloendopeptidases EC 3.4.24.15 (EP 24.15) and EC 3.4.24.16 (EP 24.16) are closely related ubiquitous enzymes, which have well-defined in vitro activities in generation and degradation of a range of specific peptide targets. Despite this, little is known regarding their roles in whole animal physiology. One of the peptides degraded by these enzymes in vitro is bradykinin, a mediator with potent effects on the vasculature at both systemic and local levels. This review summarises the work that has examined the role of EP 24.15/24.16 in regulation of the vascular effects of bradykinin in vivo. This work was made possible by the development of a specific stable inhibitor of these enzymes, JA-2. Use of this inhibitor has shown that EP 24.15/24.16 are capable of regulating responses induced by exogenous bradykinin. This effect was observed at a systemic level with an increase in the hypotensive effect of intravenous bradykinin. Further work is required to determine whether these enzymes also regulate bradykinin produced endogenously.     

A Comparison of Different Estimation Methods for Fungicide EC50 and EC95 Values

EC₅₀ and EC₉₅ (the effective concentrations to cause inhibitions by 50 and 95%, respectively) are commonly used to express fungicide potency. Different methods are currently employed to calculate EC₅₀ and EC₉₅ values. In this study, EC₅₀ and EC₉₅ values for fungicide epoxiconazole against 34 isolates of Sclerotinia sclerotiorum were calculated with seven different methods. Results showed that for both EC₅₀ and EC₉₅ calculations, there was no significant difference among three statistical programs IBM spss ^®, GraphPad Prism^® and dps ^® (P ≥ 0.066). Methods linear log (linear regression of mycelial growth inhibition vs. logarithmic concentration) and interpolation log (linear interpolation from inhibition and logarithmic concentration data) were not significantly different (P ≥ 0.058) from IBM spss in EC₅₀ calculations. These results indicate that among the seven methods, the three statistical programs IBM spss , GraphPad Prism, dps and linear log method are appropriate for EC₅₀ calculations. But for EC₉₅ calculations, only the three statistical programs are recommended, and GraphPad Prism is likely to give a little higher values than spss and dps .     

Role of calcium in the release of EC 3.4.24.15 and EC 3.4.24.16 from endothelial cells

Summary The two closely related soluble zinc metalloendopeptidases EC 3.4.24.15 (EP24.15) and EC 3.4.24.16 (EP24.16) readily hydrolyze the vasocative peptide bradykinin in vitro, and therefore may play a role in cardiovascular regulation. Although primarily soluble cytosolic enzymes, both secreted and membrane-associated forms of both peptidases have been reported. However, these enzymes have neither a transmembrane domain nor a signal sequence; thus, the mechanisms of membrane anchoring and secretion are unknown. In the present study, secreted/released EP24.15 and EP24.16 activity from aortic endothelial cells in culture was assessed by the cleavage of a specific quenched fluorescent substrate. An increase in enzyme activity released from endothelial cells, which express both peptidases, was seen following incubation with calcium-free media. In the AtT-20 endocrine cell (mouse pituitary corticotrope), which predominantly expresses EP24.15, the release of activity into media was unaffected by calcium removal. The release of enzyme activity from endothelial cells was inversely proportional to calcium concentrations ranging between 0.01 mM (activity equivalent to calcium-free media) and 0.5 mM (activity equivalent to normal media). Cleavage of the EP24.16-specific substrate AcNT_8–13 indicated that the increase in enzyme activity released upon incubation with calcium-free medium was due at least in part to the release of EP24.16. These results suggest that EP24.15 and EP24.16 are secreted from endothelial cells, and that removal of calcium selectively enhances the release of EP24.16 by an as yet unknown mechanism.     

Role of calcium in the release of EC 3.4.24.15 and EC 3.4.24.16 from endothelial cells

The two closely related soluble zinc metalloendopeptidases EC 3.4.24.15 (EP24.15) and EC 3.4.24.16 (EP24.16) readily hydrolyze the vasoactive peptide bradykinin in vitro, and therefore may play a role in cardiovascular regulation. Although primarily soluble cytosolic enzymes, both secreted and membrane-associated forms of both peptidases have been reported. However, these enzymes have neither a transmembrane domain nor a signal sequence; thus, the mechanisms of membrane anchoring and secretion are unknown. In the present study, secreted/released EP24.15 and EP24.16 activity from aortic endothelial cells in culture was assessed by the cleavage of a specific quenched fluorescent substrate. An increase in enzyme activity released from endothelial cells, which express both peptidases, was seen following incubation with calcium-free media. In the AtT-20 endocrine cell (mouse pituitary corticotrope), which predominantly expresses EP24.15, the release of activity into media was unaffected by calcium removal. The release of enzyme activity from endothelial cells was inversely proportional to calcium concentrations ranging between 0.01 mM (activity equivalent to calcium-free media) and 0.5 mM (activity equivalent to normal media). Cleavage of the EP24.16-specific substrate AcNT_8-13 indicated that the increase in enzyme activity released upon incubation with calcium-free medium was due at least in part to the release of EP24.16. These results suggest that EP24.15 and EP24.16 are secreted from endothelial cells, and that removal of calcium selectively enhances the release of EP24.16 by an as yet unknown mechanism.     

Computation of Most Probable Numbers

A rapid computational method for maximum likelihood estimation of most-probable-number values, incorporating a modified Newton-Raphson method, is presented. The method offers a much greater reliability for the most-probable-number estimate of total viable bacteria, i.e., those capable of growth in laboratory media.