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1
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32944464059
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Bacterial genomics and pathogen evolution
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This review provides a broad overview of current trends in bacterial genomics, including methods for computational sequence analysis to identify novel virulence factors, strategies for identifying essential genes in vitro and in vivo, and techniques for microarray-based comparative genomics.
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Raskin D.M., Seshadri R., Pukatzki S.U., and Mekalanos J.J. Bacterial genomics and pathogen evolution. Cell 124 (2006) 703-714. This review provides a broad overview of current trends in bacterial genomics, including methods for computational sequence analysis to identify novel virulence factors, strategies for identifying essential genes in vitro and in vivo, and techniques for microarray-based comparative genomics.
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Cell
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Modeling the function of bacterial virulence factors in Saccharomyces cerevisiae
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Valdivia R.H. Modeling the function of bacterial virulence factors in Saccharomyces cerevisiae. Eukaryot Cell 3 (2004) 827-834
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Genomic dissection of microbial pathogenesis in cultured Drosophila cells
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Ayres J.S., and Schneider D.S. Genomic dissection of microbial pathogenesis in cultured Drosophila cells. Trends Microbiol 14 (2006) 101-104
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Trends Microbiol
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Genomic characterization of non-O1, non-O139 Vibrio cholerae reveals genes for a type III secretion system
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Dziejman M., Serruto D., Tam V.C., Sturtevant D., Diraphat P., Faruque S.M., Rahman M.H., Heidelberg J.F., Decker J., Li L., et al. Genomic characterization of non-O1, non-O139 Vibrio cholerae reveals genes for a type III secretion system. Proc Natl Acad Sci USA 102 (2005) 3465-3470
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Heidelberg, J.F.8
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Li, L.10
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The opportunistic pathogen Pseudomonas aeruginosa carries a secretable arachidonate 15-lipoxygenase
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Vance R.E., Hong S., Gronert K., Serhan C.N., and Mekalanos J.J. The opportunistic pathogen Pseudomonas aeruginosa carries a secretable arachidonate 15-lipoxygenase. Proc Natl Acad Sci USA 101 (2004) 2135-2139
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Vance, R.E.1
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Seeking completeness in bacterial mutant hunts
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Salama N.R., and Manoil C. Seeking completeness in bacterial mutant hunts. Curr Opin Microbiol 9 (2006) 307-311
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Comprehensive transposon mutant library of Pseudomonas aeruginosa
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Jacobs M.A., Alwood A., Thaipisuttikul I., Spencer D., Haugen E., Ernst S., Will O., Kaul R., Raymond C., Levy R., et al. Comprehensive transposon mutant library of Pseudomonas aeruginosa. Proc Natl Acad Sci USA 100 (2003) 14339-14344
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Haugen, E.5
Ernst, S.6
Will, O.7
Kaul, R.8
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8
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33644504829
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An ordered, nonredundant library of Pseudomonas aeruginosa strain PA14 transposon insertion mutants
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Liberati N.T., Urbach J.M., Miyata S., Lee D.G., Drenkard E., Wu G., Villanueva J., Wei T., and Ausubel F.M. An ordered, nonredundant library of Pseudomonas aeruginosa strain PA14 transposon insertion mutants. Proc Natl Acad Sci USA 103 (2006) 2833-2838
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Wu, G.6
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9
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31544450286
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Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection
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2006.0008
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Baba T., Ara T., Hasegawa M., Takai Y., Okumura Y., Baba M., Datsenko K.A., Tomita M., Wanner B.L., and Mori H. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2 (2006) 2006.0008
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Wanner, B.L.9
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Genetic requirements for mycobacterial survival during infection
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Sassetti C.M., and Rubin E.J. Genetic requirements for mycobacterial survival during infection. Proc Natl Acad Sci USA 100 (2003) 12989-12994
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Sassetti, C.M.1
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Genome-wide requirements for Mycobacterium tuberculosis adaptation and survival in macrophages
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Rengarajan J., Bloom B.R., and Rubin E.J. Genome-wide requirements for Mycobacterium tuberculosis adaptation and survival in macrophages. Proc Natl Acad Sci USA 102 (2005) 8327-8332
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Rengarajan, J.1
Bloom, B.R.2
Rubin, E.J.3
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Designer arrays for defined mutant analysis to detect genes essential for survival of Mycobacterium tuberculosis in mouse lungs
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Lamichhane G., Tyagi S., and Bishai W.R. Designer arrays for defined mutant analysis to detect genes essential for survival of Mycobacterium tuberculosis in mouse lungs. Infect Immun 73 (2005) 2533-2540
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Lamichhane, G.1
Tyagi, S.2
Bishai, W.R.3
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13
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23944491257
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Microarray-based detection of Salmonella enterica serovar Typhimurium transposon mutants that cannot survive in macrophages and mice
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Chan K., Kim C.C., and Falkow S. Microarray-based detection of Salmonella enterica serovar Typhimurium transposon mutants that cannot survive in macrophages and mice. Infect Immun 73 (2005) 5438-5449
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Chan, K.1
Kim, C.C.2
Falkow, S.3
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14
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33645777008
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Genome-wide screen for Salmonella genes required for long-term systemic infection of the mouse
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The authors use a microarray-based negative selection screen to identify S. enterica serovar Typhimurium transposon mutants that fail to establish a persistent infection in 129X1/SvJ mice over a period of 28 days. They observed a progressive selection against serovar Typhimurium mutants over time, indicating that different classes of genes might be required at different stages of infection.
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Lawley T.D., Chan K., Thompson L.J., Kim C.C., Govoni G.R., and Monack D.M. Genome-wide screen for Salmonella genes required for long-term systemic infection of the mouse. PLoS Pathog 2 (2006) e11. The authors use a microarray-based negative selection screen to identify S. enterica serovar Typhimurium transposon mutants that fail to establish a persistent infection in 129X1/SvJ mice over a period of 28 days. They observed a progressive selection against serovar Typhimurium mutants over time, indicating that different classes of genes might be required at different stages of infection.
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PLoS Pathog
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Lawley, T.D.1
Chan, K.2
Thompson, L.J.3
Kim, C.C.4
Govoni, G.R.5
Monack, D.M.6
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15
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Genes directly controlled by CtrA, a master regulator of the Caulobacter cell cycle
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Laub M.T., Chen S.L., Shapiro L., and McAdams H.H. Genes directly controlled by CtrA, a master regulator of the Caulobacter cell cycle. Proc Natl Acad Sci USA 99 (2002) 4632-4637
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Laub, M.T.1
Chen, S.L.2
Shapiro, L.3
McAdams, H.H.4
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16
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The Spo0A regulon of Bacillus subtilis
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Molle V., Fujita M., Jensen S.T., Eichenberger P., Gonzalez-Pastor J.E., Liu J.S., and Losick R. The Spo0A regulon of Bacillus subtilis. Mol Microbiol 50 (2003) 1683-1701
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Molle, V.1
Fujita, M.2
Jensen, S.T.3
Eichenberger, P.4
Gonzalez-Pastor, J.E.5
Liu, J.S.6
Losick, R.7
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17
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4944225301
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Genomic studies with Escherichia coli MelR protein: applications of chromatin immunoprecipitation and microarrays
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Grainger D.C., Overton T.W., Reppas N., Wade J.T., Tamai E., Hobman J.L., Constantinidou C., Struhl K., Church G., and Busby S.J. Genomic studies with Escherichia coli MelR protein: applications of chromatin immunoprecipitation and microarrays. J Bacteriol 186 (2004) 6938-6943
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Hobman, J.L.6
Constantinidou, C.7
Struhl, K.8
Church, G.9
Busby, S.J.10
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18
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33745460953
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In vivo dissection of the Helicobacter pylori Fur regulatory circuit by genome-wide location analysis
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Danielli A., Roncarati D., Delany I., Chiarini V., Rappuoli R., and Scarlato V. In vivo dissection of the Helicobacter pylori Fur regulatory circuit by genome-wide location analysis. J Bacteriol 188 (2006) 4654-4662
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J Bacteriol
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Danielli, A.1
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Delany, I.3
Chiarini, V.4
Rappuoli, R.5
Scarlato, V.6
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19
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29644439241
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Iron and pH homeostasis intersect at the level of Fur regulation in the gastric pathogen Helicobacter pylori
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Gancz H., Censini S., and Merrell D.S. Iron and pH homeostasis intersect at the level of Fur regulation in the gastric pathogen Helicobacter pylori. Infect Immun 74 (2006) 602-614
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Censini, S.2
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Expression of microbial virulence proteins in Saccharomyces cerevisiae models mammalian infection
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Lesser C.F., and Miller S.I. Expression of microbial virulence proteins in Saccharomyces cerevisiae models mammalian infection. EMBO J 20 (2001) 1840-1849
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A yeast genetic system for the identification and characterization of substrate proteins transferred into host cells by the Legionella pneumophila Dot/Icm system
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Campodonico E.M., Chesnel L., and Roy C.R. A yeast genetic system for the identification and characterization of substrate proteins transferred into host cells by the Legionella pneumophila Dot/Icm system. Mol Microbiol 56 (2005) 918-933
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Mol Microbiol
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Pathogen effector protein screening in yeast identifies Legionella factors that interfere with membrane trafficking
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Shohdy N., Efe J.A., Emr S.D., and Shuman H.A. Pathogen effector protein screening in yeast identifies Legionella factors that interfere with membrane trafficking. Proc Natl Acad Sci USA 102 (2005) 4866-4871
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Shohdy, N.1
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Shuman, H.A.4
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23
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33644838378
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Multifunctional analysis of Chlamydia-specific genes in a yeast expression system
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A defined library of Chlamydia trachomatis ORFs was cloned and expressed in S. cerevisiae. Yeast strains expressing chlamydial proteins were then screened for growth defects and subcellular localization of the bacterial protein. Analysis of these phenotypes, combined with antibody-based screening to identify chlamydial proteins secreted during infection of mammalian cells, identified several new putative virulence factors.
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Sisko J.L., Spaeth K., Kumar Y., and Valdivia R.H. Multifunctional analysis of Chlamydia-specific genes in a yeast expression system. Mol Microbiol 60 (2006) 51-66. A defined library of Chlamydia trachomatis ORFs was cloned and expressed in S. cerevisiae. Yeast strains expressing chlamydial proteins were then screened for growth defects and subcellular localization of the bacterial protein. Analysis of these phenotypes, combined with antibody-based screening to identify chlamydial proteins secreted during infection of mammalian cells, identified several new putative virulence factors.
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Mol Microbiol
, vol.60
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Sisko, J.L.1
Spaeth, K.2
Kumar, Y.3
Valdivia, R.H.4
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Human macrophage activation programs induced by bacterial pathogens
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Nau G.J., Richmond J.F., Schlesinger A., Jennings E.G., Lander E.S., and Young R.A. Human macrophage activation programs induced by bacterial pathogens. Proc Natl Acad Sci USA 99 (2002) 1503-1508
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Young, R.A.6
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25
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27244454772
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Genome-wide analysis of host responses to the Pseudomonas aeruginosa type III secretion system yields synergistic effects
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Ichikawa J.K., English S.B., Wolfgang M.C., Jackson R., Butte A.J., and Lory S. Genome-wide analysis of host responses to the Pseudomonas aeruginosa type III secretion system yields synergistic effects. Cell Microbiol 7 (2005) 1635-1646
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Cell Microbiol
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26
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EST-based genome-wide gene inactivation identifies ARAP3 as a host protein affecting cellular susceptibility to anthrax toxin
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Lu Q., Wei W., Kowalski P.E., Chang A.C., and Cohen S.N. EST-based genome-wide gene inactivation identifies ARAP3 as a host protein affecting cellular susceptibility to anthrax toxin. Proc Natl Acad Sci USA 101 (2004) 17246-17251
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Lu, Q.1
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Cohen, S.N.5
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27
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33646033137
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A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen
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Moffat J., Grueneberg D.A., Yang X., Kim S.Y., Kloepfer A.M., Hinkle G., Piqani B., Eisenhaure T.M., Luo B., Grenier J.K., et al. A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen. Cell 124 (2006) 1283-1298
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Moffat, J.1
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Piqani, B.7
Eisenhaure, T.M.8
Luo, B.9
Grenier, J.K.10
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28
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27644436787
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Second-generation shRNA libraries covering the mouse and human genomes
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Silva J.M., Li M.Z., Chang K., Ge W., Golding M.C., Rickles R.J., Siolas D., Hu G., Paddison P.J., Schlabach M.R., et al. Second-generation shRNA libraries covering the mouse and human genomes. Nat Genet 37 (2005) 1281-1288
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Siolas, D.7
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Drosophila melanogaster S2 cells: a model system to study Chlamydia interaction with host cells
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Elwell C., and Engel J.N. Drosophila melanogaster S2 cells: a model system to study Chlamydia interaction with host cells. Cell Microbiol 7 (2005) 725-739
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Cheng L.W., and Portnoy D.A. Drosophila S2 cells: an alternative infection model for Listeria monocytogenes. Cell Microbiol 5 (2003) 875-885
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Exploration of host-pathogen interactions using Listeria monocytogenes and Drosophila melanogaster
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Mansfield B.E., Dionne M.S., Schneider D.S., and Freitag N.E. Exploration of host-pathogen interactions using Listeria monocytogenes and Drosophila melanogaster. Cell Microbiol 5 (2003) 901-911
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23844531867
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Drosophila RNAi screen reveals CD36 family member required for mycobacterial infection
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••], this work describes the first genome-wide screen for host cell proteins required for infection by an intracellular bacterial pathogen. This study also identified the CD36 host receptor as important for uptake of mycobacterial species.
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••], this work describes the first genome-wide screen for host cell proteins required for infection by an intracellular bacterial pathogen. This study also identified the CD36 host receptor as important for uptake of mycobacterial species.
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Science
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Philips, J.A.1
Rubin, E.J.2
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33646234683
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RNA interference analysis of Legionella in Drosophila cells: exploitation of early secretory apparatus dynamics
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This study conducted a sub-genomic RNAi screen in Drosophila cells to identify gene products with roles in the secretory pathway, endocytic functions and ER-related processes that are important for Legionella pneumophila intracellular replication. Results showed that, in many cases, although treatment with individual dsRNAs did not alter L. pneumophila replication, RNAi targeting of multiple factors in the secretory pathway had profound effects on L. pneumophila growth.
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Dorer M.S., Kirton D., Bader J.S., and Isberg R.R. RNA interference analysis of Legionella in Drosophila cells: exploitation of early secretory apparatus dynamics. PLoS Pathog 2 (2006) e34. This study conducted a sub-genomic RNAi screen in Drosophila cells to identify gene products with roles in the secretory pathway, endocytic functions and ER-related processes that are important for Legionella pneumophila intracellular replication. Results showed that, in many cases, although treatment with individual dsRNAs did not alter L. pneumophila replication, RNAi targeting of multiple factors in the secretory pathway had profound effects on L. pneumophila growth.
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PLoS Pathog
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Dorer, M.S.1
Kirton, D.2
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23844442475
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Genome-wide RNAi screen for host factors required for intracellular bacterial infection
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••] this work describes the first genome-wide screen for host cell proteins required for infection by an intracellular bacterial pathogen. This work also compares and contrasts the requirements of host factors for a cytosolic pathogen, L. monocytogenes, with those of a vacuolar pathogen, M. fortuitum.
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••] this work describes the first genome-wide screen for host cell proteins required for infection by an intracellular bacterial pathogen. This work also compares and contrasts the requirements of host factors for a cytosolic pathogen, L. monocytogenes, with those of a vacuolar pathogen, M. fortuitum.
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Science
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Agaisse, H.1
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Higgins, D.E.6
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35
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26444472477
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Use of RNA interference in Drosophila S2 cells to identify host pathways controlling compartmentalization of an intracellular pathogen
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The authors completed three genome-scale RNAi screens in Drosophila cells using wild type L. monocytogenes and two mutant strains to identify host factors important for intracellular growth of bacteria.
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Cheng L.W., Viala J.P., Stuurman N., Wiedemann U., Vale R.D., and Portnoy D.A. Use of RNA interference in Drosophila S2 cells to identify host pathways controlling compartmentalization of an intracellular pathogen. Proc Natl Acad Sci USA 102 (2005) 13646-13651. The authors completed three genome-scale RNAi screens in Drosophila cells using wild type L. monocytogenes and two mutant strains to identify host factors important for intracellular growth of bacteria.
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Proc Natl Acad Sci USA
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Cheng, L.W.1
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Wiedemann, U.4
Vale, R.D.5
Portnoy, D.A.6
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