essential genes

Summary

Summary: Those genes found in an organism which are necessary for its viability and normal function.

Top Publications

  1. D Elia M, Pereira M, Brown E. Are essential genes really essential?. Trends Microbiol. 2009;17:433-8 pubmed publisher
    ..our understanding of core bacterial physiology, these studies have also uncovered large numbers of essential genes encoding proteins whose functions remain poorly described...
  2. Gerdes S, Edwards R, Kubal M, Fonstein M, Stevens R, Osterman A. Essential genes on metabolic maps. Curr Opin Biotechnol. 2006;17:448-56 pubmed
    ..The analysis of these data, very heterogeneous in nature, is a challenging task. Even the definition of 'essential genes' in various genome-scale studies varies from genes 'absolutely required for survival' to those 'strongly ..
  3. Bijlsma J, Burghout P, Kloosterman T, Bootsma H, De Jong A, Hermans P, et al. Development of genomic array footprinting for identification of conditionally essential genes in Streptococcus pneumoniae. Appl Environ Microbiol. 2007;73:1514-24 pubmed
    ..method on a large mariner transposon library showed that it was highly reproducible and correctly identified essential genes. Comparison of a mariner library to one generated with the in vivo transposition plasmid pGh:ISS1 showed that ..
  4. Martelli C, De Martino A, Marinari E, Marsili M, Pérez Castillo I. Identifying essential genes in Escherichia coli from a metabolic optimization principle. Proc Natl Acad Sci U S A. 2009;106:2607-11 pubmed publisher
    ..Finally, we are able to connect phenomenological gene essentiality with "frozen" fluxes (i.e., fluxes with smaller allowed variability) in E. coli metabolism. ..
  5. Butland G, Peregrín Alvarez J, Li J, Yang W, Yang X, Canadien V, et al. Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature. 2005;433:531-7 pubmed
    ..This study provides insight into the function of previously uncharacterized bacterial proteins and the overall topology of a microbial interaction network, the core components of which are broadly conserved across Prokaryota. ..
  6. Hu W, Sillaots S, Lemieux S, Davison J, Kauffman S, Breton A, et al. Essential gene identification and drug target prioritization in Aspergillus fumigatus. PLoS Pathog. 2007;3:e24 pubmed
    ..fumigatus essential genes for cognate antifungal inhibitors.
  7. Becker D, Selbach M, Rollenhagen C, Ballmaier M, Meyer T, Mann M, et al. Robust Salmonella metabolism limits possibilities for new antimicrobials. Nature. 2006;440:303-7 pubmed
    ..Our comprehensive in vivo analysis thus suggests a shortage of new metabolic targets for broad-spectrum antibiotics, and draws attention to some previously known but unexploited targets. ..
  8. Motter A, Gulbahce N, Almaas E, Barabasi A. Predicting synthetic rescues in metabolic networks. Mol Syst Biol. 2008;4:168 pubmed publisher
    ..The systematic network-based identification of compensatory rescue effects may open new avenues for genetic interventions. ..
  9. McNeil L, Reich C, Aziz R, Bartels D, Cohoon M, Disz T, et al. The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation. Nucleic Acids Res. 2007;35:D347-53 pubmed
    ..Essentiality data collated from genome-wide studies have been curated. Drug target identification and high-throughput, in silico, compound screening are in development. ..

More Information

Publications62

  1. Zhang R, Lin Y. DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes. Nucleic Acids Res. 2009;37:D455-8 pubmed publisher
    b>Essential genes are those indispensable for the survival of an organism, and their functions are therefore considered a foundation of life...
  2. Datta K, Skidmore J, Pu K, Maddock J. The Caulobacter crescentus GTPase CgtAC is required for progression through the cell cycle and for maintaining 50S ribosomal subunit levels. Mol Microbiol. 2004;54:1379-92 pubmed
    ..G80E cells arrest as predivisional cells and stalkless cells. Flow cytometry on synchronized cells reveals a G1-S arrest. Therefore, CgtAC is necessary for DNA replication and progression through the cell cycle. ..
  3. Acencio M, Lemke N. Towards the prediction of essential genes by integration of network topology, cellular localization and biological process information. BMC Bioinformatics. 2009;10:290 pubmed publisher
    The identification of essential genes is important for the understanding of the minimal requirements for cellular life and for practical purposes, such as drug design...
  4. Robertson D, Carroll P, Parish T. Rapid recombination screening to test gene essentiality demonstrates that pyrH is essential in Mycobacterium tuberculosis. Tuberculosis (Edinb). 2007;87:450-8 pubmed
    ..Such vectors would lead to inactivation of the target gene in a single recombination step. For non-essential genes, recombinants can be obtained; for essential genes, no recombinants can be obtained, thus providing a rapid ..
  5. Mnaimneh S, Davierwala A, Haynes J, Moffat J, Peng W, Zhang W, et al. Exploration of essential gene functions via titratable promoter alleles. Cell. 2004;118:31-44 pubmed
    ..We furthermore show that these strains are compatible with automated genetic analysis. This study underscores the importance of analyzing mutant phenotypes and provides a resource to complement the yeast knockout collection. ..
  6. Larsson J, Svensson M, Stenberg P, M kitalo M. Painting of fourth in genus Drosophila suggests autosome-specific gene regulation. Proc Natl Acad Sci U S A. 2004;101:9728-33 pubmed publisher
    ..The chromosome specificity is determined at the species level and not by the amino acid sequence. We argue that POF is involved in a chromosome-specific regulatory function...
  7. Eng K, Kvitek D, Keles S, Gasch A. Transient genotype-by-environment interactions following environmental shock provide a source of expression variation for essential genes. Genetics. 2010;184:587-93 pubmed publisher
    ..for nonessential genes with upstream TATA elements, those displaying transient GEIs were enriched for essential genes regardless of TATA regulation...
  8. Molina Henares M, De La Torre J, García Salamanca A, Molina Henares A, Herrera M, Ramos J, et al. Identification of conditionally essential genes for growth of Pseudomonas putida KT2440 on minimal medium through the screening of a genome-wide mutant library. Environ Microbiol. 2010;12:1468-85 pubmed publisher
    ..to be conditionally essential based on in silico models, whereas another 24 newly implicated conditionally essential genes have been found...
  9. Zotenko E, Mestre J, O Leary D, Przytycka T. Why do hubs in the yeast protein interaction network tend to be essential: reexamining the connection between the network topology and essentiality. PLoS Comput Biol. 2008;4:e1000140 pubmed publisher
  10. Zhang C, Zhang R. Gene essentiality analysis based on DEG, a database of essential genes. Methods Mol Biol. 2008;416:391-400 pubmed publisher
    b>Essential genes are the genes that are indispensable for the survival of an organism...
  11. Kumar S, Chaudhary K, Foster J, Novelli J, Zhang Y, Wang S, et al. Mining predicted essential genes of Brugia malayi for nematode drug targets. PLoS ONE. 2007;2:e1189 pubmed
    ..elegans, we identify potentially essential genes in B. malayi...
  12. Yeh I, Hanekamp T, Tsoka S, Karp P, Altman R. Computational analysis of Plasmodium falciparum metabolism: organizing genomic information to facilitate drug discovery. Genome Res. 2004;14:917-24 pubmed
    ..A total of 87.5% of proposed drug targets with biological evidence in the literature are chokepoint reactions. Therefore, identifying chokepoint enzymes represents one systematic way to identify potential metabolic drug targets. ..
  13. Davierwala A, Haynes J, Li Z, Brost R, Robinson M, Yu L, et al. The synthetic genetic interaction spectrum of essential genes. Nat Genet. 2005;37:1147-52 pubmed
    The nature of synthetic genetic interactions involving essential genes (those required for viability) has not been previously examined in a broad and unbiased manner...
  14. Ohl F, Jung M, Radonic A, Sachs M, Loening S, Jung K. Identification and validation of suitable endogenous reference genes for gene expression studies of human bladder cancer. J Urol. 2006;175:1915-20 pubmed
    ..For normalization purposes in gene profiling studies of bladder cancer the genes SDH and TBP are recommended as single reference genes depending on the expression level of the target gene or more favorably in combination. ..
  15. Meinke D, Muralla R, Sweeney C, Dickerman A. Identifying essential genes in Arabidopsis thaliana. Trends Plant Sci. 2008;13:483-91 pubmed publisher
    ..growth and development? The purpose of this review is to summarize different strategies employed to identify essential genes in Arabidopsis, an important component of the minimal gene set in plants, to present an overview of the ..
  16. Kim J, Youm G, Kwon Y. Essential genes in Salmonella enteritidis as identified by TnAraOut mutagenesis. Curr Microbiol. 2008;57:391-4 pubmed publisher
    ..TnAraOut mutagenesis previously used to identify essential genes in Vibrio cholerae can also be used to identify in vitro essential genes in Salmonella enteritidis...
  17. Robinson K, Meers J, Gravel J, McCarthy F, Mahony T. The essential and non-essential genes of Bovine herpesvirus 1. J Gen Virol. 2008;89:2851-63 pubmed publisher
    ..To further develop BoHV-1 as a vaccine vector, a study was conducted to identify the essential and non-essential genes required for in vitro viability...
  18. Norris M, Kang Y, Lu D, Wilcox B, Hoang T. Glyphosate resistance as a novel select-agent-compliant, non-antibiotic-selectable marker in chromosomal mutagenesis of the essential genes asd and dapB of Burkholderia pseudomallei. Appl Environ Microbiol. 2009;75:6062-75 pubmed publisher
    ..Together with the bar gene, the gat cassette will facilitate various genetic manipulations of Burkholderia select-agent species. ..
  19. Plaimas K, Eils R, König R. Identifying essential genes in bacterial metabolic networks with machine learning methods. BMC Syst Biol. 2010;4:56 pubmed publisher
    Identifying essential genes in bacteria supports to identify potential drug targets and an understanding of minimal requirements for a synthetic cell...
  20. Song J, Ko K. Detection of essential genes in Streptococcus pneumoniae using bioinformatics and allelic replacement mutagenesis. Methods Mol Biol. 2008;416:401-8 pubmed publisher
    ..of comparative genomics and the gene knock-out procedure can provide effective ways to identify the essential genes of bacterial pathogens (3)...
  21. Liao B, Zhang J. Null mutations in human and mouse orthologs frequently result in different phenotypes. Proc Natl Acad Sci U S A. 2008;105:6987-92 pubmed publisher
    ..Comparing documented phenotypes of null mutations in humans and mice, we find that >20% of human essential genes have nonessential mouse orthologs...
  22. Liang H, Li W. Gene essentiality, gene duplicability and protein connectivity in human and mouse. Trends Genet. 2007;23:375-8 pubmed
  23. Hoffmann K, Wollherr A, Larsen M, Rachinger M, Liesegang H, Ehrenreich A, et al. Facilitation of direct conditional knockout of essential genes in Bacillus licheniformis DSM13 by comparative genetic analysis and manipulation of genetic competence. Appl Environ Microbiol. 2010;76:5046-57 pubmed publisher
    ..The obtained increased genetic tractability of this industrial workhorse should improve a wide array of scientific investigations. ..
  24. Glass J, Assad Garcia N, Alperovich N, Yooseph S, Lewis M, Maruf M, et al. Essential genes of a minimal bacterium. Proc Natl Acad Sci U S A. 2006;103:425-30 pubmed
    ..Genes encoding proteins of unknown function constitute 28% of the essential protein-coding genes set. Disruption of some genes accelerated M. genitalium growth. ..
  25. Papp B, Pal C, Hurst L. Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast. Nature. 2004;429:661-4 pubmed
    ..Instead their presence is better explained by selection for high enzymatic flux. ..
  26. Martinez M, Roy S, Archuletta A, Wentzell P, Anna Arriola S, Rodriguez A, et al. Genomic analysis of stationary-phase and exit in Saccharomyces cerevisiae: gene expression and identification of novel essential genes. Mol Biol Cell. 2004;15:5295-305 pubmed
  27. Widlund P, Davis T. A high-efficiency method to replace essential genes with mutant alleles in yeast. Yeast. 2005;22:769-74 pubmed
    ..TS), internally deleted and truncated alleles are important tools to facilitate the characterization of essential genes. We have developed a straightforward method to replace a wild-type gene with a mutant allele at the ..
  28. De Lay N, Cronan J. Gene-specific random mutagenesis of Escherichia coli in vivo: isolation of temperature-sensitive mutations in the acyl carrier protein of fatty acid synthesis. J Bacteriol. 2006;188:287-96 pubmed
    ..Fatty acid synthesis in strains that carried the D38V or A68T/N73D mutations was inhibited upon a shift to the nonpermissive temperature and in the latter case declined to a small percentage of the rate of the wild-type strain. ..
  29. Seringhaus M, Paccanaro A, Borneman A, Snyder M, Gerstein M. Predicting essential genes in fungal genomes. Genome Res. 2006;16:1126-35 pubmed
    b>Essential genes are required for an organism's viability, and the ability to identify these genes in pathogens is crucial to directed drug development...
  30. Lin Y, Gao F, Zhang C. Functionality of essential genes drives gene strand-bias in bacterial genomes. Biochem Biophys Res Commun. 2010;396:472-6 pubmed publisher
    b>Essential genes, indispensable genes for an organism's survival, encode functions that are considered a foundation of life...
  31. Tu Z, Wang L, Xu M, Zhou X, Chen T, Sun F. Further understanding human disease genes by comparing with housekeeping genes and other genes. BMC Genomics. 2006;7:31 pubmed
    ..A potential problem in those studies is that the non-disease genes contained a large number of essential genes--genes which are indispensable for humans to survive and reproduce...
  32. Keller P, Knop M. Evolution of mutational robustness in the yeast genome: a link to essential genes and meiotic recombination hotspots. PLoS Genet. 2009;5:e1000533 pubmed publisher
    ..We hypothesize that purging of deleterious mutations in essential genes constitutes an important factor driving meiotic crossover...
  33. Davydenko S, Juselius J, Munder T, Bogengruber E, Jantti J, Keränen S. Screening for novel essential genes of Saccharomyces cerevisiae involved in protein secretion. Yeast. 2004;21:463-71 pubmed
    ..takes advantage of yeast strains constructed within the EUROFAN project, in which the promoters of the novel essential genes were replaced by the doxycycline-regulated tetO(7)-CYC1 promoter...
  34. Altmann K, Westermann B. Role of essential genes in mitochondrial morphogenesis in Saccharomyces cerevisiae. Mol Biol Cell. 2005;16:5410-7 pubmed
    ..Here we asked which essential genes are required for mitochondrial distribution and morphology...
  35. Hwang Y, Lin C, Chang J, Mori H, Juan H, Huang H. Predicting essential genes based on network and sequence analysis. Mol Biosyst. 2009;5:1672-8 pubmed publisher
    b>Essential genes are indispensable to the viability of an organism. Identification and analysis of essential genes is key to understanding the systems level organization of living cells...
  36. Song J, Ko K, Lee J, Baek J, Oh W, Yoon H, et al. Identification of essential genes in Streptococcus pneumoniae by allelic replacement mutagenesis. Mol Cells. 2005;19:365-74 pubmed
    To find potential targets of novel antimicrobial agents, we identified essential genes of Streptococcus pneumoniae using comparative genomics and allelic replacement mutagenesis. We compared the genome of S...
  37. Matsuo M, Kurokawa K, Lee B, Sekimizu K. Shuttle vectors derived from pN315 for study of essential genes in Staphylococcus aureus. Biol Pharm Bull. 2010;33:198-203 pubmed
    ..In contrast, other two genes were shown to be dispensable by this system. Thus, the pN315-based plasmids appear to be useful for studying genes essential for S. aureus cell growth. ..
  38. Palumbo M, Colosimo A, Giuliani A, Farina L. Essentiality is an emergent property of metabolic network wiring. FEBS Lett. 2007;581:2485-9 pubmed
    ..We demonstrate that the 'missing alternative' paradigm is sufficient to explain the generation of essentiality for double mutations in which each single deleted element is non-essential. ..
  39. Deutscher D, Meilijson I, Kupiec M, Ruppin E. Multiple knockout analysis of genetic robustness in the yeast metabolic network. Nat Genet. 2006;38:993-8 pubmed
    ..The genes' k robustness is shown to be a solid indicator of their biological buffering capacity and is correlated with both the genes' environmental specificity and their evolutionary retention. ..
  40. Hunt A, Rawlins J, Thomaides H, Errington J. Functional analysis of 11 putative essential genes in Bacillus subtilis. Microbiology. 2006;152:2895-907 pubmed publisher
    ..The results suggest that other novel essential proteins may be involved in lipid synthesis and control of cell wall synthesis...
  41. Salama N, Shepherd B, Falkow S. Global transposon mutagenesis and essential gene analysis of Helicobacter pylori. J Bacteriol. 2004;186:7926-35 pubmed
    ..344 genes had no detectable transposon insertions, and this list is predicted to be highly enriched for essential genes. Comparison to the essential gene set of other bacteria revealed a surprisingly limited overlap with all ..
  42. Silva J, Marran K, Parker J, Silva J, Golding M, Schlabach M, et al. Profiling essential genes in human mammary cells by multiplex RNAi screening. Science. 2008;319:617-20 pubmed publisher
    ..These studies establish a practical platform for genome-scale screening of complex phenotypes in mammalian cells and demonstrate that RNAi can be used to expose genotype-specific sensitivities. ..
  43. Yu B, Sung B, Lee J, Son S, Kim M, Kim S. sucAB and sucCD are mutually essential genes in Escherichia coli. FEMS Microbiol Lett. 2006;254:245-50 pubmed
    ..1% arabinose, but not in the absence of arabinose unless the medium was supplemented with succinyl-CoA. Our results indicate that either sucAB or sucCD is enough to produce succinyl-CoA that is essential for cell viability. ..
  44. Joyce A, Palsson B. Predicting gene essentiality using genome-scale in silico models. Methods Mol Biol. 2008;416:433-57 pubmed publisher
    ..This chapter introduces the constraint-based modeling approach and focuses on its application to computationally predicting gene essentiality. ..
  45. Becker S, Palsson B. Three factors underlying incorrect in silico predictions of essential metabolic genes. BMC Syst Biol. 2008;2:14 pubmed publisher
    ..success rate of these predictions is less than desirable, especially with regard to comprehensively locating essential genes. We show that genes that are falsely predicted to be non-essential (for growth) share three characteristics ..
  46. Wong S, Akerley B. Identification and analysis of essential genes in Haemophilus influenzae. Methods Mol Biol. 2008;416:27-44 pubmed publisher
    ..method that exploits the natural transformation feature of this organism for the identification of essential genes. In addition, we describe strategies for conditional expression systems that would facilitate further ..
  47. Fraser H, Hirsh A, Giaever G, Kumm J, Eisen M. Noise minimization in eukaryotic gene expression. PLoS Biol. 2004;2:e137 pubmed
    ..Our results support the hypothesis that noise in gene expression is a biologically important variable, is generally detrimental to organismal fitness, and is subject to natural selection. ..
  48. Herring C, Blattner F. Conditional lethal amber mutations in essential Escherichia coli genes. J Bacteriol. 2004;186:2673-81 pubmed
    The essential genes of microorganisms encode biological functions important for survival and thus tend to be of high scientific interest...
  49. Coulomb S, Bauer M, Bernard D, Marsolier Kergoat M. Gene essentiality and the topology of protein interaction networks. Proc Biol Sci. 2005;272:1721-5 pubmed
    ..e. a propensity for their vertices to associate according to their degrees. Gene essentiality and more generally cell resistance against mutations thus seem largely unrelated to many parameters of protein network topology. ..
  50. Wei J, Rubin E. The many roads to essential genes. Tuberculosis (Edinb). 2008;88 Suppl 1:S19-24 pubmed publisher
    ..Here we review the strategies that have been used to identify and validate essential genes in mycobacteria and look forward to possible future advances.
  51. Reznikoff W, Winterberg K. Transposon-based strategies for the identification of essential bacterial genes. Methods Mol Biol. 2008;416:13-26 pubmed publisher
    ..This latter approach has the potential to experimentally define the minimal required genome for a given organism. ..
  52. Boneca I, Ecobichon C, Chaput C, Mathieu A, Guadagnini S, Prevost M, et al. Development of inducible systems to engineer conditional mutants of essential genes of Helicobacter pylori. Appl Environ Microbiol. 2008;74:2095-102 pubmed publisher
    ..pylori. Finally, we demonstrated that following in vitro methylation of the recombinant plasmids, these could be introduced into a large variety of H. pylori isolates with different genetic backgrounds. ..
  53. Hentges K, Pollock D, Liu B, Justice M. Regional variation in the density of essential genes in mice. PLoS Genet. 2007;3:e72 pubmed
    ..In most species, and particularly in vertebrates, the percentage of genes absolutely required for survival, the essential genes, has not been estimated...