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      Selection of key sequence-based features for prediction of essential genes in 31 diverse bacterial species

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          Abstract

          Genes that are indispensable for survival are essential genes. Many features have been proposed for computational prediction of essential genes. In this paper, the least absolute shrinkage and selection operator method was used to screen key sequence-based features related to gene essentiality. To assess the effects, the selected features were used to predict the essential genes from 31 bacterial species based on a support vector machine classifier. For all 31 bacterial objects (21 Gram-negative objects and ten Gram-positive objects), the features in the three datasets were reduced from 57, 59, and 58, to 40, 37, and 38, respectively, without loss of prediction accuracy. Results showed that some features were redundant for gene essentiality, so could be eliminated from future analyses. The selected features contained more complex (or key) biological information for gene essentiality, and could be of use in related research projects, such as gene prediction, synthetic biology, and drug design.

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          Most cited references26

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          DEG 10, an update of the database of essential genes that includes both protein-coding genes and noncoding genomic elements

          The combination of high-density transposon-mediated mutagenesis and high-throughput sequencing has led to significant advancements in research on essential genes, resulting in a dramatic increase in the number of identified prokaryotic essential genes under diverse conditions and a revised essential-gene concept that includes all essential genomic elements, rather than focusing on protein-coding genes only. DEG 10, a new release of the Database of Essential Genes (available at http://www.essentialgene.org), has been developed to accommodate these quantitative and qualitative advancements. In addition to increasing the number of bacterial and archaeal essential genes determined by genome-wide gene essentiality screens, DEG 10 also harbors essential noncoding RNAs, promoters, regulatory sequences and replication origins. These essential genomic elements are determined not only in vitro, but also in vivo, under diverse conditions including those for survival, pathogenesis and antibiotic resistance. We have developed customizable BLAST tools that allow users to perform species- and experiment-specific BLAST searches for a single gene, a list of genes, annotated or unannotated genomes. Therefore, DEG 10 includes essential genomic elements under different conditions in three domains of life, with customizable BLAST tools.
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            Experimental Determination and System Level Analysis of Essential Genes in <i>Escherichia coli</i> MG1655

            Journal of Bacteriology, 185(19), 5673-5684 Defining the gene products that play an essential role in an organism's functional repertoire is vital to understanding the system level organization of living cells. We used a genetic footprinting technique for a genome-wide assessment of genes required for robust aerobic growth of in rich media. We identified 620 genes as essential and 3,126 genes as dispensable for growth under these conditions. Functional context analysis of these data allows individual functional assignments to be refined. Evolutionary context analysis demonstrates a significant tendency of essential genes to be preserved throughout the bacterial kingdom. Projection of these data over metabolic subsystems reveals topologic modules with essential and evolutionarily preserved enzymes with reduced capacity for error tolerance.
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              Essential genes are more evolutionarily conserved than are nonessential genes in bacteria.

              The "knockout-rate" prediction holds that essential genes should be more evolutionarily conserved than are nonessential genes. This is because negative (purifying) selection acting on essential genes is expected to be more stringent than that for nonessential genes, which are more functionally dispensable and/or redundant. However, a recent survey of evolutionary distances between Saccharomyces cerevisiae and Caenorhabditis elegans proteins did not reveal any difference between the rates of evolution for essential and nonessential genes. An analysis of mouse and rat orthologous genes also found that essential and nonessential genes evolved at similar rates when genes thought to evolve under directional selection were excluded from the analysis. In the present study, we combine genomic sequence data with experimental knockout data to compare the rates of evolution and the levels of selection for essential versus nonessential bacterial genes. In contrast to the results obtained for eukaryotic genes, essential bacterial genes appear to be more conserved than are nonessential genes over both relatively short (microevolutionary) and longer (macroevolutionary) time scales.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                30 March 2017
                2017
                : 12
                : 3
                : e0174638
                Affiliations
                [1 ]College of Communication Engineering, Chongqing University, Chongqing, China
                [2 ]Key Laboratory of Chongqing for Bio-perception and Intelligent Information Processing, Chongqing, China
                [3 ]Chongqing City Management College, Chongqing, China
                Instituto Nacional de Medicina Genomica, MEXICO
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                • Conceptualization: XL BJW.

                • Data curation: XL BJW.

                • Formal analysis: XL BJW HLT GQX.

                • Funding acquisition: XL.

                • Investigation: XL BJW LX.

                • Methodology: XL BJW.

                • Project administration: XL.

                • Resources: XL BJW.

                • Software: BJW LX.

                • Supervision: XL.

                • Validation: XL BJW LX HLT.

                • Visualization: BJW.

                • Writing – original draft: XL BJW LX HLT.

                • Writing – review & editing: XL BJW HLT GQX.

                Article
                PONE-D-16-33362
                10.1371/journal.pone.0174638
                5373589
                28358836
                0b056c62-6488-402b-9ca2-4890ca25ea3b
                © 2017 Liu et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 20 August 2016
                : 12 March 2017
                Page count
                Figures: 2, Tables: 4, Pages: 13
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/501100001809, National Natural Science Foundation of China;
                Award ID: 61001157
                Award Recipient :
                Funded by: Fundamental Research Funds for the Central Universities
                Award ID: 106112014CDJZR165503
                Award Recipient :
                This work was supported by the National Natural Science Foundation of China (Grant No. 61001157), the China Postdoctoral Science Foundation funded project (Grant No. 2012M521673), and the Fundamental Research Funds for the Central Universities (Project No. 106112014CDJZR165503, CDJRC10160011, CDJZR12160007).
                Categories
                Research Article
                Biology and Life Sciences
                Computational Biology
                Genome Analysis
                Gene Prediction
                Biology and Life Sciences
                Genetics
                Genomics
                Genome Analysis
                Gene Prediction
                Computer and Information Sciences
                Artificial Intelligence
                Machine Learning
                Biology and Life Sciences
                Microbiology
                Bacteriology
                Gram Negative Bacteria
                Biology and Life Sciences
                Microbiology
                Bacteriology
                Gram Positive Bacteria
                Research and Analysis Methods
                Mathematical and Statistical Techniques
                Statistical Methods
                Forecasting
                Physical Sciences
                Mathematics
                Statistics (Mathematics)
                Statistical Methods
                Forecasting
                Computer and Information Sciences
                Artificial Intelligence
                Machine Learning
                Support Vector Machines
                Research and Analysis Methods
                Experimental Organism Systems
                Model Organisms
                Saccharomyces Cerevisiae
                Research and Analysis Methods
                Model Organisms
                Saccharomyces Cerevisiae
                Biology and Life Sciences
                Organisms
                Fungi
                Yeast
                Saccharomyces
                Saccharomyces Cerevisiae
                Research and Analysis Methods
                Experimental Organism Systems
                Yeast and Fungal Models
                Saccharomyces Cerevisiae
                Biology and Life Sciences
                Ecology
                Ecological Metrics
                Species Diversity
                Ecology and Environmental Sciences
                Ecology
                Ecological Metrics
                Species Diversity
                Custom metadata
                All relevant data are within the paper and its Supporting Information files.

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                Uncategorized

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