Combining Shigella Tn-seq data with gold-standard E. coli gene deletion data suggests rare transitions between essential and non-essential gene functionality

[1]  David Weiss,et al.  Faculty Opinions recommendation of A Comprehensive, CRISPR-based Functional Analysis of Essential Genes in Bacteria. , 2016 .

[2]  John S. Hawkins,et al.  A Comprehensive, CRISPR-based Functional Analysis of Essential Genes in Bacteria , 2016, Cell.

[3]  M. Waldor,et al.  The design and analysis of transposon insertion sequencing experiments , 2016, Nature Reviews Microbiology.

[4]  Hyungwon Choi,et al.  Gene Essentiality Is a Quantitative Property Linked to Cellular Evolvability , 2015, Cell.

[5]  Soyeon I Lippman,et al.  General and condition-specific essential functions of Pseudomonas aeruginosa , 2015, Proceedings of the National Academy of Sciences.

[6]  Bingyao Zhu,et al.  Bacillus subtilis and Escherichia coli essential genes and minimal cell factories after one decade of genome engineering. , 2014, Microbiology.

[7]  Matthew K. Waldor,et al.  ARTIST: High-Resolution Genome-Wide Assessment of Fitness Using Transposon-Insertion Sequencing , 2014, PLoS genetics.

[8]  Y. Brun,et al.  Identification of essential alphaproteobacterial genes reveals operational variability in conserved developmental and cell cycle systems , 2014, Molecular microbiology.

[9]  R. Schlapbach,et al.  Shigella reroutes host cell central metabolism to obtain high-flux nutrient supply for vigorous intracellular growth , 2014, Proceedings of the National Academy of Sciences.

[10]  Bernhard O. Palsson,et al.  Optimizing genome-scale network reconstructions , 2014, Nature Biotechnology.

[11]  M. Ackermann,et al.  The predictability of molecular evolution during functional innovation , 2014, Proceedings of the National Academy of Sciences.

[12]  Andrew Camilli,et al.  Gene Fitness Landscapes of Vibrio cholerae at Important Stages of Its Life Cycle , 2013, PLoS pathogens.

[13]  Joshua A. Lerman,et al.  Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments , 2013, Proceedings of the National Academy of Sciences.

[14]  Anton J. Enright,et al.  Kraken: A set of tools for quality control and analysis of high-throughput sequence data , 2013, Methods.

[15]  Jonathan Livny,et al.  High-resolution definition of the Vibrio cholerae essential gene set with hidden Markov model–based analyses of transposon-insertion sequencing data , 2013, Nucleic acids research.

[16]  A. Camilli,et al.  Transposon insertion sequencing: a new tool for systems-level analysis of microorganisms , 2013, Nature Reviews Microbiology.

[17]  Saso Dzeroski,et al.  Phyletic Profiling with Cliques of Orthologs Is Enhanced by Signatures of Paralogy Relationships , 2013, PLoS Comput. Biol..

[18]  C. Zagaglia,et al.  Outer Membrane Protein A (OmpA): A New Player in Shigella flexneri Protrusion Formation and Inter-Cellular Spreading , 2012, PloS one.

[19]  Peter D. Karp,et al.  EcoCyc: fusing model organism databases with systems biology , 2012, Nucleic Acids Res..

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

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

[22]  M. Ackermann,et al.  Patterns of Evolutionary Conservation of Essential Genes Correlate with Their Compensability , 2012, PLoS genetics.

[23]  S. Clifton,et al.  High-throughput comparison of gene fitness among related bacteria , 2012, BMC Genomics.

[24]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[25]  Heng Li,et al.  A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data , 2011, Bioinform..

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

[27]  Masaru Tomita,et al.  Update on the Keio collection of Escherichia coli single-gene deletion mutants , 2009, Molecular systems biology.

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

[29]  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.

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

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

[32]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[33]  M. Ackermann,et al.  The constancy of gene conservation across divergent bacterial orders , 2009, BMC Research Notes.

[34]  G. Bennett,et al.  Reduction of acetate accumulation in Escherichia coli cultures for increased recombinant protein production. , 2008, Metabolic engineering.

[35]  J. Kato,et al.  Construction of consecutive deletions of the Escherichia coli chromosome , 2007, Molecular systems biology.

[36]  D. Court,et al.  Essentiality of Ribosomal and Transcription Antitermination Proteins Analyzed by Systematic Gene Replacement in Escherichia coli , 2007, Journal of bacteriology.

[37]  H. Mori,et al.  Genome-Wide Screening of Genes Required for Swarming Motility in Escherichia coli K-12 , 2006, Journal of bacteriology.

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

[39]  Stanley Falkow,et al.  Microarray-Based Detection of Salmonella enterica Serovar Typhimurium Transposon Mutants That Cannot Survive in Macrophages and Mice , 2005, Infection and Immunity.

[40]  Eric Haugen,et al.  Comprehensive transposon mutant library of Pseudomonas aeruginosa , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[41]  D. P. Wall,et al.  Detecting putative orthologs , 2003, Bioinform..

[42]  F. Blattner,et al.  Erratum: Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T (Infection and Immunity (2003) 71:5 (2775-2786)) , 2003 .

[43]  Karl W. Broman,et al.  A postgenomic method for predicting essential genes at subsaturation levels of mutagenesis: Application to Mycobacterium tuberculosis , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[44]  Q. Jin,et al.  Comparative genome analysis of deleted genes in Shigella flexneri 2a strain 301 , 2003 .

[45]  S M Payne,et al.  Complete Genome Sequence and Comparative Genomics of Shigella flexneri Serotype 2a Strain 2457T , 2003, Infection and Immunity.

[46]  S. Corvaisier,et al.  Inhibition of Transfer Messenger RNA Aminoacylation and trans-Translation by Aminoglycoside Antibiotics* 210 , 2003, The Journal of Biological Chemistry.

[47]  E. Crooke,et al.  Identification of a Novel Membrane-Associated Gene Product That Suppresses Toxicity of a TrfA Peptide from Plasmid RK2 and Its Relationship to the DnaA Host Initiation Protein , 2003, Journal of bacteriology.

[48]  S. Hooper,et al.  Gene Import or Deletion: A Study of the Different Genes in Escherichia coli Strains K12 and O157:H7 , 2002, Journal of Molecular Evolution.

[49]  J. Shendure,et al.  Selection analyses of insertional mutants using subgenic-resolution arrays , 2001, Nature Biotechnology.

[50]  M. Kothary,et al.  Infective dose of foodborne pathogens in volunteers : A Review , 2001 .

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

[52]  S. Maloy,et al.  A cryptic proline permease in Salmonella typhimurium. , 1997, Microbiology.

[53]  O. Fayet,et al.  Isolation and characterization of a priB mutant of Escherichia coli influencing plasmid copy number of delta rop ColE1-type plasmids , 1997, Journal of bacteriology.

[54]  J. Theriot,et al.  Shigella flexneri surface protein IcsA is sufficient to direct actin-based motility. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[55]  J. Hearst,et al.  Genes acrA and acrB encode a stress‐induced efflux system of Escherichia coli , 1995, Molecular microbiology.

[56]  G. Caetano-Anollés,et al.  Amplifying DNA with arbitrary oligonucleotide primers. , 1993, PCR methods and applications.

[57]  Y. Nakamura,et al.  Differential regulation of two genes encoding lysyl‐tRNA synthetases in Escherichia coli: lysU‐constitutive mutations compensate for a lysS null mutation , 1992, Molecular microbiology.

[58]  C. Kurland,et al.  Effects of miaA on translation and growth rates , 1987, Molecular and General Genetics MGG.

[59]  R. G. Lloyd,et al.  Analysis of the ruv locus of Escherichia coli K-12 and identification of the gene product , 1985, Journal of bacteriology.

[60]  N. Kleckner,et al.  Unusual alleles of recB and recC stimulate excision of inverted repeat transposons Tn10 and Tn5. , 1984, Proceedings of the National Academy of Sciences of the United States of America.

[61]  P. Sansonetti,et al.  Involvement of a plasmid in the invasive ability of Shigella flexneri , 1982, Infection and immunity.

[62]  N. Kleckner,et al.  A symmetrical six-base-pair target site sequence determines Tn10 insertion specificity , 1982, Cell.

[63]  P. Sparling.  Kasugamycin Resistance: 30S Ribosomal Mutation with an Unusual Location on the Escherichia coli Chromosome , 1970, Science.

[64]  Mark Behrens,et al.  The construction of , 2014 .

[65]  Oliver Bembom,et al.  seqLogo: An R package for plotting DNA sequence logos. , 2007 .

[66]  A. Lau,et al.  Effects of recB , recC and recF mutations on Tn 10 Transposition in Escherichia coli , 2006 .

[67]  U. Henning,et al.  Lethal mutations in the structural gene of an outer membrane protein (OmpA) of Escherichia coli K12 , 2004, Molecular and General Genetics MGG.

[68]  Xueying,et al.  Comparative genome analysis of deleted genes in Shigella flexneri 2a strain 301 , 2003 .

[69]  M. Riley,et al.  MultiFun, a multifunctional classification scheme for Escherichia coli K-12 gene products. , 2000, Microbial & comparative genomics.

[70]  N. Kleckner,et al.  Uses of transposons with emphasis on Tn10. , 1991, Methods in enzymology.

[71]  N. Kleckner,et al.  Transposable elements in prokaryotes. , 1981, Annual review of genetics.

[72]  A. Okuyama,et al.  [Kasugamycin resistance]. , 1975, Nihon saikingaku zasshi. Japanese journal of bacteriology.