Strategies for isolation of in vivo expressed genes from bacteria

FEMS Microbiology Reviews

Volumn 23, Issue 1, 1999, Pages 69-91

  Handfield, Martin ^a,c   Levesque, Roger C ^b  

^a Hlth and Life Sci Research Center   (Canada)

^b UNIVERSITÉ LAVAL   (Canada)

^c UNIVERSITY OF FLORIDA COLLEGE OF DENTISTRY   (United States)

Author keywords

Arbitrarily primed polymerase chain reaction; Differential display; Differential hybridization; Gene expression; Gene fusion; Genomics; In vivo expression technology; In vivo induced; Oligonucleotide array; Proteome; Signature tagged mutagenesis; Subtractive hybridization; Transposon

Indexed keywords

OLIGONUCLEOTIDE;

ANTIMICROBIAL THERAPY; BACTERIAL GENE; BACTERIAL VIRULENCE; FLUORESCENCE; GENE EXPRESSION; GENE FUSION; GENE ISOLATION; HYBRIDIZATION; MUTAGENESIS; NONHUMAN; PATHOGENICITY; POLYMERASE CHAIN REACTION; REVIEW; SURVIVAL; TRANSPOSON;

EID: 0032966773     PISSN: 01686445     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0168-6445(98)00033-3     Document Type: Article

References (98)

1. Mekalanos, J.J. (1992) Environmental signals controlling expression of virulence determinants in bacteria. J. Bacteriol. 174, 1-7.
2. Finlay, B.B. and Falkow, S. (1997) Common themes in microbial pathogenicity. Microbiol. Rev. 53, 210-230.
3. Solotorovsky, M. (1963) Cell Culture in the Story of Bacterial Disease, pp. 1-121. Rutgers University Press, New Brunswick, NJ.
4. Salyers, A.A. and Whitt, D.D. (1994) Bacterial Pathogenesis, A Molecular Approach, pp. 1-418. American Society for Microbiology Press, Washington, DC.
5. Silhavy, T.J. and Beckwith, J.R. (1985) Uses of lac fusions for the study of biological problems. Microbiol. Rev. 49, 398-418.
6. Casadaban, M.J. (1976) Transposition and fusion of the lac genes to selected promoters in Escherichia coli using bacteriophage λ and Mu. J. Mol. Biol. 104, 541-555.
7. Hedges, R.W. and Jacob, A.E. (1974) Transposition of ampicillin resistance from RP4 to other replicons. Mol. Gen. Genet. 132, 31-40.
8. Kleckner, N., Roth, J. and Botstein, D. (1977) Genetic engineering in vivo using translocatable drug-resistance elements. New methods in bacterial genetics. J. Mol. Biol. 116, 125-159.
9. de Lorenzo, V., Herrero, M., Jakubzik, U. and Timmis, K.E. (1990) Mini-Tn5 transposons derivatives for insertion mutagenesis, promoter probing, and chromosomal insertion of cloned DNA in Gram-negative eubacteria. J. Bacteriol. 172, 6568-6572.
10. Casadaban, M.J. and Cohen, S.N. (1979) Lactose genes fused to exogenous promoters in one step using a Mu-lac bacteriophage: in vivo probe for transcriptional control sequences. Proc. Natl. Acad. Sci. USA 76, 4530-4533.
11. Kenyon, C.J. and Walker, G.C. (1980) DNA-damaging agents stimulate gene expression at specific loci in Escherichia coli. Proc. Natl. Acad. Sci. USA 77, 2819-2823.
12. Wanner, B.L. and McSharry, R. (1982) Phosphate-controlled gene expression in Escherichia coli K12 using Mud1-directed lacZ fusions. J. Mol. Biol. 158, 347-363.
13. Metcalf, W.W., Steed, P.M. and Wanner, B.L. (1990) Identification of phosphate starvation-inducible genes in Escherichia coli K-12 by DNA sequences analysis of psi::lacZ(Mud1) transcriptional fusions. J. Bacteriol. 172, 3191-3200.
14. Spector, M.P., Park, Y.K., Tirgari, S., Gonzalez, T. and Foster, J.W. (1988) Identification and characterization of starvation-regulated genetic loci in Salmonella typhimurium by using Mud-directed lacZ operon fusions. J. Bacteriol. 170, 345-351.
15. Manoil, C. and Beckwith, J. (1985) TnphoA: a transposon probe for protein export signals. Proc. Natl. Acad. Sci. USA 82, 8129-8133.
16. Miller, I., Maskell, D., Hormaeche, C., Johnson, K., Pickard, D. and Dougan, G. (1989) Isolation of orally attenuated Salmonella typhimurium following TnphoA mutagenesis. Infect. Immun. 57, 2758-2763.
17. Gutierrez, C., Barondess, J., Manoil, C. and Beckwith, J. (1987) The use of transposon TnphoA to detect genes for cell envelope proteins subject to a common regulatory stimulus. J. Mol. Biol. 195, 289-297.
18. Smith, V., Botstein, D. and Brown, P. (1995). Genetic footprinting: a genomic strategy for determining a gene's function given its sequence. Proc. Natl. Acad. Sci. USA 92, 6479-6483.
19. Akerley, B.J., Rubin, E.J., Camilli, A., Lampe, D.J., Robertson, H.M. and Mekalanos, J. J. (1998) Systematic identification of essential genes by in vitro mariner mutagenesis. Proc. Natl. Acad. Sci. USA 95, 8927-8932.
20. O'Farrell, P.H. (1975) High resolution two-dimensional electrophoresis of proteins. J. Biol. Chem. 250, 4007-4021.
21. Buchmeier, N.A. and Heffron, F. (1990) Induction of Salmonella stress proteins upon infection of macrophages. Science 248, 730-732.
22. Chuang, S.-E., Daniels, D.L. and Blattner, F.R. (1993) Global regulation of gene expression in Escherichia coli. J. Bacteriol. 175, 2026-2036.
23. Humphrey-Smith, I. and Blackstock, W. (1997) Proteome analysis: genomic via the output rather than the input code. J. Protein Chem. 16, 537-544.
24. Humphrey-Smith, I., Cordwell, S.J. and Blackstock, W. (1997) Proteome research: complementarity and limitations with respect to the RNA and DNA worlds. Electrophoresis 18, 1217-1242.
25. Roepstorff, P. (1997) Mass spectrometry in protein studies from genome to function. Curr. Opin. Biotechnol. 8, 6-13.
26. Ito, T. and Sakaki, Y. (1996) Toward genome-wide scanning of gene expression: a functional aspect of the genome project. Essays Biochem. 31, 11-21.
27. VanBogelen, R.A., Abshire, K.Z., Moldover, B., Olson, E.R. and Neidhardt, F. (1997) Escherichia coli proteome analysis using the gene-protein database. Electrophoresis 18,1243-1251.
28. Link, A.J., Robison, K. and Church, G.M. (1997) Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12. Electrophoresis 18,1259-1313.
29. Karp, P., Riley, M., Paley, S. and Pellegrini-Toole, A. (1997) EcoCyc: electronic encyclopedia of E. coli genes and metabolism. Nucleic Acids Res. 25, 43-50.
30. Karp, P. (1998) Metabolic databases. Trends Biochem. Sci. 23, 114-116.
31. Blattner, F.R., Plunkett, G.I., Bloch, C.A., Perna, N.T., Burland, V., Riley, M. et al. (1997) The complete sequence of Escherichia coli K-12. Science 277, 1453-1474.
32. Elliott, S.M., Wainwright, L.A., McDaniel, T.K., Jarvis, K.J., Deng, Y.K., Lai, L.C., McNamara, B.P., Donnenberg, M.S. and Kaper, J.B. (1998) The complete sequence of the locus of enterocyte effacement (LEE) from enteropathogenic Escherichia coli E2348/69. Mol. Microbiol. 28, 1-4.
33. O'Connor, D.C., Farris, M., Fowler, R. and Qi, S.Y. (1997) The proteome of Salmonella enterica serovar typhimurium: current progress on its determination and some applications. Electrophoresis 18, 1483-1490.
34. Fleishman, R.D., Adams, M.D., White, O., Clayton, R.A., Kirkness, E.F., Kerlavage, A.R., Bult, C.J., Tomb, J.-F., Dougherty, B.A. et al. (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269, 496-512.
35. Link, A.J., Hays, L.G., Carmack, E.B. and Yates, J.R. (1997) Identifying the major proteome components of Haemophilus influenzae type-strain TCTC 8143. Electrophoresis 18, 1314-1334.
36. Fountoulakis, M., Takacs, B. and Langen, H. (1997) Two-dimensional map of basic proteins in Haemophilus influenzae. Electrophoresis 19, 761-766.
37. Cash, P., Argo, E., Langford, P.R. and Kroll, J.S. (1997) Development of a Haemophilus two-dimensional protein database. Electrophoresis 18, 1472-1482.
38. Cordwell, S.J., Basseal, D.J. and Humphrey-Smith, I. (1997) Proteome analysis of Spiroplasma melliferum (A56) and protein characterisation across species boundaries. Electrophoresis 18, 1335-1346.
39. Cordwell, S.J., Basseal, D.J., Bjellqvist, B., Shaw, D.C. and Humphrey-Smith, I. (1997) Characterisation of basic proteins from Spiroplasma melliferum using novel immobilised pH gradients. Electrophoresis 18, 1393-1398.
40. Phan-Thanh, L. and Gormon, T. (1997) Stress proteins in Listeria monocytogenes. Electrophoresis 18, 1464-1471.
41. Urquhart, B.L., Atsalos, T.E., Roach, D., Basseal, D.J., Bjellqvist, B., Britton, W.L. and Humphrey-Smith, I. (1997) Proteomic contigs of Mycobacterium tuberculosis and Mycobacterium bovis (BCG) using novel immobilised pH gradients. Electrophoresis 18, 1384-1392.
42. Sturgill-Koszycki, S., Haddix, P.L. and Russell, D.G. (1997) The interaction between Mycobacterium and the macrophage analyzed by two dimensional polyacrylamide gel electrophoresis. Electrophoresis 18, 2558-2565.
43. Pelicic, V., Reyrat, J.-M. and Gicquel, B. (1998) Genetic advances for studying Mycobacterium tuberculosis pathogenicity. Mol. Microbiol. 28, 413-420.
44. Vohradsky, J., Li, X.M. and Thompson, C.J. (1997) Identification of prokaryotic developmental stages by statistical analyses of two-dimensional gel patterns. Electrophoresis 18, 1418-1428.
45. Rudd, K.E., Humphrey-Smith, I., Wasinger, V.C. and Bairoch, A. (1998) Low molecular weight proteins: a challenge for post genomic research. Electrophoresis 19, 536-544.
46. Lönnenborg, A., Sharma, P. and Stougaard, P. (1995) Construction of a subtractive cDNA library using magnetic beads and PCR. In: PCR Primer. A Laboratory Manual (Dieffenbach, C.W. and Dveksler, G.S., Eds.), pp. 439-452. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
47. Sargent, T.D. (1987) Isolation of differentially expressed genes. Methods Enzymol. 152, 423-432.
48. Sambrook, J., Fritsch, E.F. and Maniatis, T. (1989) Construction and analysis of cDNA libraries. In : Molecular Cloning: A Laboratory Manual, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
49. Plum, G. and Clarck-Curtiss, J.E. (1994) Induction of Mycobacterium avium gene expression following phagocytosis by human macrophages. Infect. Immun. 62, 476-483.
50. Schmidt, K.D., Schmidt-Rose, T., Romlig, U. and Tummler, B. (1998) Differential genome analysis of bacteria by genomic subtractive hybridization and pulsed field gel electrophoresis. Electrophoresis 19, 509-514.
51. Schena, M., Shalon, D. and Davis, R.W. (1995) Quantitative monitoring of gene expression patterns with a complimentary DNA microarray. Science 270, 467-470.
52. Lashkari, D.A., DeRisi, J.L., McCusker, J.H., Namath, A.F., Gentile, C., Hwang, S.Y., Brown, P.O. and Davis, R.W. (1997) Yeast microarrays for genome wide parallel genetic and gene expression analysis. Proc. Natl. Acad. Sci. USA 94, 13057-13062.
53. de Saizieu, A., Certa, U., Warrington, J., Gray, C., Keck, W. and Mous, J. (1998) Bacterial transcript imaging by hybridization of total RNA to oligonucleotide arrays. Nature Biotechnol. 16, 45-48.
54. Sharma, P., Lonnenborg, A. and Stougaard, P. (1993) PCR-based construction of subtractive cDNA library using magnetic beads. BioTechniques 15, 610-611.
55. Mahan, M.J., Slauch, J.M. and Mekalanos, J.J. (1993) Selection of bacterial virulence genes that are specifically induced in host tissues. Science 259, 686-688.
56. Slauch, J.M., Mahan, M.J. and Mekalanos, J.J. (1994) Assay of β-galactosidase using a fluorescent substrate. BioTechniques 16, 642-644.
57. Handfield, M., Sanschagrin, F., Cardinal, G., Mahan, M.J. and Levesque, R.C. (1997) Selection of Pseudomonas aeruginosa genes expressed in vivo. 97th General Meeting of the American Society for Microbiology, Miami Beach, FL, Abstract B-359.
58. Handfield, M., Schweizer, H.P., Mahan, M.J., Sanschagrin, F., Hoang, T. and Levesque, R.C. (1998) Asd-GFP vectors for in vivo expression technology in Pseudomonas aeruginosa and other Gram-negative bacteria. BioTechniques 24, 261-264.
59. Heithoff, D.M., Conner, C.P., Hanna, P.C., Julio, S.M., Hentschel, U. and Mahan, M.J. (1997) Bacterial infection as assessed by in vivo gene expression. Proc. Natl. Acad. Sci. USA 94, 934-939.
60. Wang, J., Mushegian, A., Lory, S. and Jin, S. (1996) Large scale isolation of candidate virulence genes of Pseudomonas aeruginosa by in vivo selection. Proc. Natl. Acad. Sci. USA 93, 10434-10439.
61. Wang, J., Lory, S., Ramphal, R. and Jin, S. (1996) Isolation and characterization of Pseudomonas aeruginosa genes inducible by respiratory mucus derived from cystic fibrosis patients. Mol. Microbiol. 22, 1005-1012.
62. Mion, P., Teyssier, J., Liautard, J.P. and Koehler, S. (1997) Identification of Brucella suis genes specifically induced during intracellular growth in human macrophages-like cells. 97th General Meeting of the American Society for Microbiology, Miami Beach, FL, Abstract B-150.
63. Steyn, A.J.C., Brown, A.M., Bloom, B.R. and Jacobs, W.R. (1997) Construction of vectors (IVET) for selection of Mycobacterium tuberculosis genes specifically induced in host tissues. 97th General Meeting of the American Society for Microbiology, Miami Beach, FL, Abstract U-105.
64. Mahan, M.J., Tobias, J.W., Slauch, J.M., Hanna, P.C., Collier, R.J. and Mekalanos, J.J. (1995) Antibiotic-based IVET selection for bacterial virulence genes that are specifically induced during infection of a host. Proc. Natl. Acad. Sci. USA 92, 669-673.
65. Mahan, M.J., Slauch, J.M. and Mekalanos, J.J. (1996) Environmental regulation of virulence gene expression in Escherichia, Salmonella, and Shigella spp. In: Escherichia coli and Salmonella, Cellular and Molecular Biology (Neidhardt, F.C., Curtiss, R., III, Ingraham, J.L., Lin, E.C.C., Low, K.B., Magasanik, B., Reznikoff, W.S., Riley, M., Schaechter, M. and Umbarger, H.E., Eds.), pp. 2803-2815. American Society for Microbiology Press, Washington, DC.
66. Young, G.M. and Miller, V.L. (1997) Identification of novel chromosomal loci affecting Yersinia enterolitica pathogenesis. Mol. Microbiol. 25, 319-328.
67. Staender, L.H., Rohde, M., Timmis, K.N. and Guzmán, C.A. (1995) Identification of Salmonella typhi promoters activated by invasion of eukaryotic cells. Mol. Microbiol. 18, 891-902.
68. Lee, S.-W., Hillman, J.D. and Progulske-Fox, A. (1996) The hemagglutinin genes hagB and hagC of Porphyromonas gingivalis are transcribed in vivo as shown by use of a new expression vector. Infect. Immun. 64, 4802-4810.
69. Camilli, A. and Mekalanos, J.J. (1995) Use of recombinase gene fusions to identify Vibrio cholerae genes induced during infection. Mol. Microbiol. 18, 671-683.
70. Camilli, A. (1996) Noninvasive techniques for studying pathogenic bacteria in the whole animal. Trends Microbiol. 4, 295-296.
71. Lee, S.H. and Camilli, A. (1998) Modified recombinase reporter system to identify differentially expressed infection induced genes. 98th General Meeting of the American Society for Microbiology, Atlanta, GA, Abstract B-330.
72. Conner, C.P., Heithoff, D.M., Julio, S.M., Sinsheimer, R.L. and Mahan, M.J. (1998) Differential patterns of acquired virulence genes distinguish Salmonella strains. Proc. Natl. Acad. Sci. USA 95, 4641-4645.
73. Lowe, A.M., Beattie, D.T. and Deresiewicz, R.L. (1998) Identification of novel staphylococcal virulence genes by in vivo expression technology. Mol. Microbiol. 27, 967-976.
74. Hensel, M., Shea, J.E., Gleeson, C., Jones, M.D., Dalton, E. and Holden, D. (1995) Simultaneous identification of bacterial virulence genes by negative selection. Science 269, 400-403.
75. Hensel, M. (1998) Whole genome scan of habitat genes by signature-tagged mutagenesis. Electrophoresis 19, 608-612.
76. Hensel, M., Shea, J.E., Raupach, B., Monack, D., Falkow, S., Gleeson, C., Kubo, T., Holden, D.W. (1997) Functional analysis of ssaJ and the ssaK/U operon, 13 genes encoding components of the type III secretion apparatus of Salmonella pathogenicity island 1 and 2. Mol. Microbiol. 24, 155-167.
77. Zhao, H., Li, X., Taylor, B., Johnson, D.E. and Mobley, H.L.T. (1997) Identification of virulence genes in uropathogenic Proteus mirabilis by signature-tagged mutagenesis. 97th General Meeting of the American Society for Microbiology, Miami Beach, FL, Abstract B-429.
78. Chiang, S.L. and Mekalanos, J.J. (1998) Use of signature-tagged transposon mutagenesis to identify Vibrio cholerae genes critical for colonization. Mol. Microbiol. 27, 797-805.
79. Mei, J.-M., Nourbakhsh, F., Ford, C.W. and Holden, D.W. (1998) Identification of Staphylococcus aureus virulence genes in a murine model of bacteraemia using signature-tagged mutagenesis. Mol. Microbiol. 26, 399-407.
80. Lehoux, D., Sanschagrin, F. and Levesque, R.C. (1998) New signature-tagged mutagenesis approach for negative selection of in vivo essential genes from Pseudomonas aeruginosa. 98th Annual General Meeting of the American Society for Microbiology, Atlanta, GA, Abstract B-327.
81. Schwan, W.R., Coulter, S.N., Ng, E.Y., Langhorne, M.H., Ritchie, H.D., Brody, L.L., Westbrock-Wadman, S., Bayer, A.S., Folger, K.R. and Stover, K.C. (1998) Identification and characterization of the PutP proline permease that contributes to in vivo survival of Staphylococcus aureus in animal models. Infect. Immun. 66, 567-572.
82. Huang, J., Jiang, X., Satterfield, J., Berry, V., Woodnutt, G. and Vitt, D.N. (1998) Isolation of Pseudomonas aeruginosa mutants with attenuated virulence by signature-tagged mutagenesis (STM). 98th Annual General Meeting of the American Society for Microbiology, Atlanta, GA, Abstract B-328.
83. Lehoux, D., Sanschagrin, F. and Levesque, R.C. (1998) Construction of defined oligonucleotide tag pools and PCR screening for signature-tagged mutagenesis in bacterial genome scanning. BioTechniques (submitted for publication).
84. Valdivia, R.H. and Falkow, S. (1996) Bacterial genetics by flow cytometry: rapid isolation of Salmonella typhimurium acid-inducible promoters by differential fluorescence induction. Mol. Microbiol. 22, 367-378.
85. Valdivia, R.H. and Falkow, S. (1997) Fluorescence-based isolation of bacterial genes expressed within host cells. Science 277, 2007-2011.
86. Valdivia, R.H. and Falkow, S. (1997) Probing bacterial gene expression within host cells. Trends Microbiol. 5, 360-363.
87. Valdivia, R.H., Hromockyj, A.E., Monack, D., Ramakrishnan, L. and Falkow, S. (1996) Application of green fluorescent protein (GFP) in the study of host-pathogen interactions. Gene 173, 47-52.
88. Fislage, R. (1998) Differential display approach to quantitation of environmental stimuli on bacterial gene expression. Electrophoresis 19, 613-616.
89. Warthoe, P., Bauer, D., Rhode, M. and Strauss, M. (1995) Detection and identification of expressed genes by differential display. In: PCR Primer. A Laboratory Manual (Dieffenbach, C.W. and Dveksler, G.S., Eds.), pp. 421-438. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
90. McClelland, M., Mathieu-Daude, F. and Welsh, J. (1995) RNA fingerprinting and differential display using arbitrarily primed PCR. Trends Genet. 11, 242-246.
91. Liang, P. and Pardee, A.B. (1992) Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction. Science 257, 967-971.
92. Welsh, J., Chada, K., Dalal, S.S., Cheng, R., Ralph, D. and McClelland, M. (1992) Arbitrarily primed PCR fingerprinting of RNA. Nucleic Acids Res. 20, 4965-4970.
93. McClelland, M. and Welsh, J. (1995) RNA fingerprinting using arbitrarily primed PCR. In: PCR Primer. A Laboratory Manual (Dieffenbach, C.W. and Dveksler, G.S., Eds.), pp. 213-234. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
94. Welsh, J. and McClelland, M. (1990) Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res. 18, 7213-7218.
95. Bauer, D., Müller, H., Reich, J., Riedel, H., Ahrenkiel, V., Warthoe, P. and Strauss, M. (1993) Identification of differentially expressed mRNA species by an improved display technique (DDRT-PCR). Nucleic Acids Res. 21, 4272-4280.
96. Ralph, D., McClelland, M. and Welsh, J. (1993) RNA fingerprinting using arbitrarily primed PCR identifies differentially regulated RNAs in mink lung (My1Lu) cells growth arrested by transforming growth factor β1. Proc. Natl. Acad. Sci. USA 90, 10710-10714.
97. Carson, A.R. and Storey, D.G. (1997) A novel approach to the identification of antibiotic regulated genes in vivo. 97th General Meeting of the American Society for Microbiology, Miami Beach, FL, Abstract B-360.
98. Shepard, B.D. and Gilmore, M.S. (1997) Identification of virulence genes in Enterococcus faecalis by differential display polymerase chain reaction. Adv. Exp. Med. Biol. 418, 777-779.