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.

[1]  Jae-Hoon Song,et al.  Identification of essential genes in Streptococcus pneumoniae by allelic replacement mutagenesis. , 2005, Molecules and cells.

[2]  Adam P. Arkin,et al.  Evidence-Based Annotation of Gene Function in Shewanella oneidensis MR-1 Using Genome-Wide Fitness Profiling across 121 Conditions , 2011, PLoS genetics.

[3]  Christian von Mering,et al.  High Confidence Prediction of Essential Genes in Burkholderia Cenocepacia , 2012, PloS one.

[4]  Sanjay Kumar,et al.  Computational prediction of essential genes in an unculturable endosymbiotic bacterium, Wolbachia of Brugia malayi , 2009, BMC Microbiology.

[5]  Frederick M Ausubel,et al.  Correction for Liberati et al., An ordered, nonredundant library of Pseudomonas aeruginosa strain PA14 transposon insertion mutants , 2006, Proceedings of the National Academy of Sciences.

[6]  J. Shea,et al.  Simultaneous identification of bacterial virulence genes by negative selection. , 1995, Science.

[7]  Steven Salzberg,et al.  Identifying bacterial genes and endosymbiont DNA with Glimmer , 2007, Bioinform..

[8]  H. Mori,et al.  Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection , 2006, Molecular systems biology.

[9]  Yan Lin,et al.  DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes , 2008, Nucleic Acids Res..

[10]  E V Koonin,et al.  How many genes can make a cell: the minimal-gene-set concept. , 2000, Annual review of genomics and human genetics.

[11]  Songyan Liu,et al.  The IKMC web portal: a central point of entry to data and resources from the International Knockout Mouse Consortium , 2010, Nucleic Acids Res..

[12]  C. A. Hutchinson,et al.  Genome transplantation in bacteria: changing one species to another. , 2007, Nature Reviews Microbiology.

[13]  A. Camilli,et al.  Tn-seq; high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms , 2009, Nature Methods.

[14]  Thomas R. Ioerger,et al.  High-Resolution Phenotypic Profiling Defines Genes Essential for Mycobacterial Growth and Cholesterol Catabolism , 2011, PLoS pathogens.

[15]  Roy R Chaudhuri,et al.  Comprehensive identification of essential Staphylococcus aureus genes using Transposon-Mediated Differential Hybridisation (TMDH) , 2009, BMC Genomics.

[16]  Cole Trapnell,et al.  Targeted RNA sequencing reveals the deep complexity of the human transcriptome , 2011, Nature Biotechnology.

[17]  Alex Bateman,et al.  A comparison of dense transposon insertion libraries in the Salmonella serovars Typhi and Typhimurium , 2013, Nucleic acids research.

[18]  Feng Gao,et al.  DoriC 5.0: an updated database of oriC regions in both bacterial and archaeal genomes , 2012, Nucleic Acids Res..

[19]  Y. Dong,et al.  Systematic functional analysis of the Caenorhabditis elegans genome using RNAi , 2003, Nature.

[20]  Eduardo Abeliuk,et al.  The essential genome of a bacterium , 2011, Molecular systems biology.

[21]  Dongsup Kim,et al.  Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe , 2010, Nature Biotechnology.

[22]  Jörg Stülke,et al.  Essential genes in Bacillus subtilis: a re-evaluation after ten years. , 2013, Molecular bioSystems.

[23]  Peer Bork,et al.  OGEE: an online gene essentiality database , 2011, Nucleic Acids Res..

[24]  Steven C. Ricke,et al.  Genome Scanning for Conditionally Essential Genes in Salmonella enterica Serotype Typhimurium , 2012, Applied and Environmental Microbiology.

[25]  Granger Ridout,et al.  Control of Virulence by Small RNAs in Streptococcus pneumoniae , 2012, PLoS pathogens.

[26]  Lee Ji-Young,et al.  Screening of Essential Genes in Staphylococcus aureus N315 Using Comparative Genomics and Allelic Replacement Mutagenesis , 2006 .

[27]  Ren Zhang,et al.  DEG: a database of essential genes. , 2004, Nucleic acids research.

[28]  S. Ehrlich,et al.  Essential Bacillus subtilis genes , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[29]  Vincent Schächter,et al.  A complete collection of single-gene deletion mutants of Acinetobacter baylyi ADP1 , 2008, Molecular systems biology.

[30]  O. White,et al.  Global transposon mutagenesis and a minimal Mycoplasma genome. , 1999, Science.

[31]  Bartek Wilczynski,et al.  Biopython: freely available Python tools for computational molecular biology and bioinformatics , 2009, Bioinform..

[32]  Charles Boone,et al.  Signature-tagged mutagenesis: barcoding mutants for genome-wide screens , 2006, Nature Reviews Genetics.

[33]  Feng-Biao Guo,et al.  ZCURVE: a new system for recognizing protein-coding genes in bacterial and archaeal genomes. , 2003, Nucleic acids research.

[34]  J. Mekalanos,et al.  A genome-scale analysis for identification of genes required for growth or survival of Haemophilus influenzae , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[35]  Gregory A. Buck,et al.  Genome-wide essential gene identification in Streptococcus sanguinis , 2011, Scientific reports.

[36]  W. Reeburgh.  Oceanic methane biogeochemistry. , 2007, Chemical reviews.

[37]  Rick Stevens,et al.  Essential genes on metabolic maps. , 2006, Current opinion in biotechnology.

[38]  Nancy Hopkins,et al.  Identification of 315 genes essential for early zebrafish development. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[39]  Stanley Falkow,et al.  Global Transposon Mutagenesis and Essential Gene Analysis of Helicobacter pylori , 2004, Journal of bacteriology.

[40]  Jozsef Baranyi,et al.  In vivo and in silico determination of essential genes of Campylobacter jejuni , 2011, BMC Genomics.

[41]  Terry Roemer,et al.  Essential Gene Identification and Drug Target Prioritization in Aspergillus fumigatus , 2007, PLoS pathogens.

[42]  Michael Y. Galperin,et al.  Searching for drug targets in microbial genomes. , 1999, Current opinion in biotechnology.

[43]  D Botstein,et al.  Genetic footprinting: a genomic strategy for determining a gene's function given its sequence. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[44]  Rob Knight,et al.  Identifying genetic determinants needed to establish a human gut symbiont in its habitat. , 2009, Cell host & microbe.

[45]  David Meinke,et al.  Identifying essential genes in Arabidopsis thaliana. , 2008, Trends in plant science.

[46]  Lars Barquist,et al.  Approaches to querying bacterial genomes with transposon-insertion sequencing , 2013, RNA biology.

[47]  Elie Dolgin,et al.  Mouse library set to be knockout , 2011, Nature.

[48]  Peer Bork,et al.  Younger Genes Are Less Likely to Be Essential than Older Genes, and Duplicates Are Less Likely to Be Essential than Singletons of the Same Age , 2012, Molecular biology and evolution.

[49]  Howard Xu,et al.  A genome‐wide strategy for the identification of essential genes in Staphylococcus aureus , 2002, Molecular microbiology.

[50]  Thomas R. Ioerger,et al.  Global Assessment of Genomic Regions Required for Growth in Mycobacterium tuberculosis , 2012, PLoS pathogens.

[51]  T. Fuchs,et al.  Large‐scale identification of essential Salmonella genes by trapping lethal insertions , 2004, Molecular microbiology.

[52]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[53]  C. Hutchison,et al.  Essential genes of a minimal bacterium. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[54]  Eugene V. Koonin,et al.  Comparative genomics, minimal gene-sets and the last universal common ancestor , 2003, Nature Reviews Microbiology.

[55]  O. Kandler,et al.  Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[56]  Ben-Yang Liao,et al.  Mouse duplicate genes are as essential as singletons. , 2007, Trends in genetics : TIG.

[57]  Martin Rosenberg,et al.  Identification of Critical Staphylococcal Genes Using Conditional Phenotypes Generated by Antisense RNA , 2001, Science.

[58]  John P. Overington,et al.  Genomic-scale prioritization of drug targets: the TDR Targets database , 2008, Nature Reviews Drug Discovery.

[59]  D. Cameron,et al.  A defined transposon mutant library and its use in identifying motility genes in Vibrio cholerae , 2008, Proceedings of the National Academy of Sciences.

[60]  Gemma C. Langridge,et al.  A Genomewide Mutagenesis Screen Identifies Multiple Genes Contributing to Vi Capsular Expression in Salmonella enterica Serovar Typhi , 2013, Journal of bacteriology.

[61]  G. Hong,et al.  Nucleic Acids Research , 2015, Nucleic Acids Research.

[62]  Robert D. Finn,et al.  Rfam: Wikipedia, clans and the “decimal” release , 2010, Nucleic Acids Res..

[63]  Andrew Camilli,et al.  Identification of essential genes of the periodontal pathogen Porphyromonas gingivalis , 2012, BMC Genomics.

[64]  Clémence Roggo,et al.  Genome-wide transposon insertion scanning of environmental survival functions in the polycyclic aromatic hydrocarbon degrading bacterium Sphingomonas wittichii RW1. , 2013, Environmental microbiology.

[65]  B. Dougherty,et al.  Identification of 113 conserved essential genes using a high-throughput gene disruption system in Streptococcus pneumoniae. , 2002, Nucleic acids research.

[66]  Jianzhi Zhang,et al.  Null mutations in human and mouse orthologs frequently result in different phenotypes , 2008, Proceedings of the National Academy of Sciences.

[67]  Jay Shendure,et al.  Genome-Scale Identification of Resistance Functions in Pseudomonas aeruginosa Using Tn-seq , 2011, mBio.

[68]  R. Kaul,et al.  A comprehensive transposon mutant library of Francisella novicida, a bioweapon surrogate , 2007, Proceedings of the National Academy of Sciences.

[69]  Georgia Giannoukos,et al.  Tracking insertion mutants within libraries by deep sequencing and a genome-wide screen for Haemophilus genes required in the lung , 2009, Proceedings of the National Academy of Sciences.

[70]  Leopold Parts,et al.  Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants. , 2009, Genome research.

[71]  Ann E Loraine,et al.  Large‐scale transposon mutagenesis of Mycoplasma pulmonis , 2008, Molecular microbiology.

[72]  Alberto Napuli,et al.  Combining Functional and Structural Genomics to Sample the Essential Burkholderia Structome , 2013, PloS one.

[73]  Ronald W. Davis,et al.  Functional profiling of the Saccharomyces cerevisiae genome , 2002, Nature.

[74]  A. Camilli,et al.  A fine scale phenotype–genotype virulence map of a bacterial pathogen , 2012, Genome research.

[75]  G. Rubin,et al.  The Berkeley Drosophila Genome Project gene disruption project: Single P-element insertions mutating 25% of vital Drosophila genes. , 1999, Genetics.

[76]  M. Bucan,et al.  From Mouse to Human: Evolutionary Genomics Analysis of Human Orthologs of Essential Genes , 2013, PLoS genetics.

[77]  J. W. Campbell,et al.  Experimental Determination and System Level Analysis of Essential Genes in Escherichia coli MG1655 , 2003, Journal of bacteriology.

[78]  Jan Mrázek,et al.  Genome-scale analysis of gene function in the hydrogenotrophic methanogenic archaeon Methanococcus maripaludis , 2013, Proceedings of the National Academy of Sciences.

[79]  E. Rubin,et al.  Genes required for mycobacterial growth defined by high density mutagenesis , 2003, Molecular microbiology.