Class 1 · Oxidoreductases: EC 1
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This is mainly due to the increased ability of genome-wide gene essentiality screens in bacteria. So far, genome-wide or large-scale gene essentiality screens have been performed in 14 genomes . Many studies have been performed to examine the characteristics of bacterial essential genes. For instance, it has been found that, compared to non-essential ones, bacterial essential genes tend to encode functions such as transcription, translation and replication  ,  , tend to reside in the leading strand  , are more evolutionarily conserved  , and have different protein interaction network degrees .
Enzymes are the catalysts of biological systems, and most of them are proteins that catalyze specific chemical reactions. Enzymes have two striking characteristics, catalytic power and specificity. Enzymes can tremendously accelerate the rate of chemical reactions, and are highly selective for the substrates by only catalyzing very specific reactions.
Therefore enzymes are critical for almost all cellular activities. Nevertheless, essential genes have not been examined systematically from the aspect of enzymes. Because of the critical functions of enzymes, we hypothesized that bacterial essential genes are enriched with enzymes, and some chemical reactions are preferentially catalyzed by essential enzymes. To test this hypothesis, we examined enzyme proportions, and enzyme type distribution in essential and non-essential genes, using all the 14 genomes that have large-scale gene essentiality screens performed.
We found that essential genes have higher proportion of enzymes, and that essential enzymes are enriched with ligases especially those forming carbon-oxygen bonds and carbon-nitrogen bonds , nucleotidyltransferases and phosphotransferases, while have underrepresented oxidoreductases. These results provide further insights into the understanding of the functionalities of essential genes, and provide useful parameters that can be incorporated into gene essentiality prediction algorithms.
Because of the critical functions of enzymes, we examined whether enzymes are enriched in bacterial essential genes. Based on the GenBank annotation, each enzyme has at least an Enzyme Commission number EC code  , which specifies the chemical reactions that the enzyme catalyzes. So far, in 14 bacterial genomes, genome-wide or large-scale gene essentiality screens have been performed Table 1. We then calculated the proportions of enzymes between essential and non-essential genes in these 14 genomes.
On average, essential genes had more than 2-fold of enzymes than non-essential genes. The average percentages of enzymes in essential and non-essential genes were For all the 14 genomes, the enzyme proportions in essential genes were higher than those of non-essential genes Fig.
These results suggest that enzymes are enriched in bacterial essential genes. A Averaged percentage of enzymes in essential and non-essential genes. B Percentages of enzymes in the 14 genomes in which large-scale gene essentiality screens have been performed. The EC number is specific to a chemical reaction, but does not specify genes. All enzymes can be classified into 1 of the 6 classes.
We then examined the distribution of the 6 enzyme types among essential and non-essential genes. On average, essential genes had more than 3 fold of ligases than non-essential genes. The percentages of ligases for essential and non-essential genes were The percentages for oxidoreductases for essential and non-essential genes were The difference of proportions for other enzyme types, transferases, lyases and isomerases, was less significant Fig.
Twelve of the 14 genomes had a higher proportion of oxidoreductases in non-essential genes Fig. These results suggest that ligases are overrepresented and oxidoreductases are underrepresented in essential genes. A Enzymes are classified into 1 of the 6 classes, oxidoreductases, transferases, hydrolases, lyases, isomerases and ligases.
The proportion of oxidoreductases is significantly lower, while that of ligases is significantly higher in essential than in non-essential genes. B Percentages of oxidoreductases and C ligases in the 14 genomes studied. Enzymes are broadly classified into 6 classes, and within each class, there are many subclasses. For instance, ligases are further classified into 6 subclasses, which include reactions forming carbon-oxygen bonds, carbon-sulfur bonds, carbon-nitrogen bonds, carbon-carbon bonds, phosphoric ester bonds and nitrogen-metal Bonds.
We then examined the subclass distribution, and found that 4 subclasses were either over or under represented with statistical significance in essential genes. Essential genes had underrepresented enzymes of the following types Fig. Essential genes had overrepresented enzymes of the following types.
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Essential genes also tended to have higher proportion of transferases transferring phosphorus-containing groups EC 2. The overrepresentation and underrepresentation of these enzyme types reveal important characteristics of essential genes from the aspect of chemical reactions. Significantly over- and under-represented second level enzyme types of A EC 1.
EC codes have 4 levels, with progressively finer classification of enzyme types. For instance, EC 2. Therefore it is necessary to examine further detailed enzyme classification for the second level enzymes that showed significant differences. However, with finer classification, the enzyme number becomes lower, and it is more stringent to reach significance with statistical tests. We found that following 3 enzyme types were especially enriched in essential genes. Similarly, in essential genes, the proportions of nucleotidyltransferases EC 2.
Significantly enriched third enzyme types of A EC 6. Gene ontology GO describes gene products with controlled vocabulary in a species-independent manner . To describe functions, GO uses 3 domains structured vocabularies , cellular components, molecular functions and biological processes. A cellular component is the part of a cell or its extracellular environment; the molecular function refers to the elemental activities of a gene product at the molecular level and the biological process refers to operations or sets of molecular events with a defined beginning and end, pertinent to the functioning of integrated cells .
A gene can be associated with 1 or more GO domains. We found that essential enzymes tended to associate with all the 3 GO domains. The percentages of 1 GO domain essential and non-essential enzymes were 1. When combined, the percentages of either 1 or 2 GO domain essential and non-essential enzymes were The percentages of 3 GO domain essential and non-essential enzymes were The observations that compared to non-essential ones, essential enzymes had lower proportion of genes associated with either 1 or 2-GO domains, but higher proportion of 3-GO domains, hold for all the genomes studied Fig.
The observation that essential enzymes tend to be associated with more gene ontology domains seems to reflect the multi-functional features of essential enzymes, consistent with their lethality phenotypes. Based on gene ontology, genes can be assigned 3 GO domains, molecular function, biological process and cellular component, which are independent of each other.
Every organism and the complex cellular activities that support its survival is an end product of evolution of millions of years. Life, to a large degree, can be regarded as a series of chemical reactions. Then enzymes that catalyze these chemical reactions must play a special role in the survival of an organism. By definition, essential genes are those absolutely needed for the survival of an organism. Of note, experimentally determined essential genes rely on specific conditions, such as minimal medium .
In this study, we calculated the enzyme proportions in essential genes comprehensively in 14 bacterial genomes that have large-scale gene essentiality screens performed.
Indeed, essential genes had a higher proportion of enzymes. The common name will be dehydrogenase, wherever this is possible; as an alternative, reductase can be used. Oxidase is only used in cases where O2 is the acceptor. The second figure in the code number of the oxidoreductases, unless it is 11, 13, 14 or 15, indicates the group in the hydrogen or electron donor that undergoes oxidation: 1 denotes a -CHOH- group, 2 a -CHO or -CO-COOH group or carbon monoxide, and so on, as listed in the key.
The third figure, except in subclasses EC 1. In subclasses EC 1. It should be noted that in reactions with a nicotinamide coenzyme this is always regarded as acceptor, even if this direction of the reaction is not readily demonstrated. The only exception is the subclass EC 1.
Although not used as a criterion for classification, the two hydrogen atoms at carbon-4 of the dihydropyridine ring of nicotinamide nucleotides are not equivalent in that the hydrogen is transferred stereospecifically. Class 2. Transferases are enzymes transferring a group, e. Class 2.
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Transferases are enzymes transferring a group, e. The systematic names are formed according to the scheme donor:acceptor grouptransferase. The common names are normally formed according to acceptor grouptransferase or donor grouptransferase. In many cases, the donor is a cofactor coenzyme charged with the group to be transferred. A special case is that of the transaminases see below.
Class 1 Oxidoreductases : EC 1
Some transferase reactions can be viewed in different ways. Where Z represents phosphate or arsenate, the process is often spoken of as 'phosphorolysis' or 'arsenolysis', respectively, and a number of enzyme names based on the pattern of phosphorylase have come into use. These names are not suitable for a systematic nomenclature, because there is no reason to single out these particular enzymes from the other transferases, and it is better to regard them simply as Y-transferases.
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