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Protocol 1.6: Analysis of Auxotrophs Using a Literature Search

Protocol 1.6: Analysis of Auxotrophs Using a Literature Search

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34



TRANSPOSON MUTAGENESIS OF Escherichia coli



experimental plans, but proceed with the experiments only to the extent

that time and materials are available.

Suggestions for getting started on an auxotroph literature study:

See references for the Auxotroph Library Report, pages 42-44.

2. Check the loci in E. coli known to be involved in the auxotroph. See

Bachmann (1983, 1990) and Bachmann and Low (1980) for information

on the E. coli linkage map. Note the loci on the E. coli map.

Check a biochemistry textbook for information about the biochemical

pathway involved.

Use any of the following methods to localize the Tn5:

a. Nutritional data, such as the feeding of intermediates in a pathway

b. Biochemical assays for enzyme activities

c. Genetic mapping strategies (for a review of methods, see Low (1973)

and Wollmen et al. (1956), as well as genetic texts)

d. Physical mapping, using the Tn5 as a probe

e. Inverse PCR from the transposon ends; use as probe in Koharao

ordered )~ clones of E. coli (Kohara, 1987).

'



e



0



Be sure to include a reasonable amount of detail of how each type

of experiment would be done. For example, in a particular enzyme assay,

do not report the exact millimolar salt concentrations needed in the enzyme assay, but indicate the substrate for the assay, the wavelength for

monitoring the substrate if it is a colorimetric assay, etc. Likewise, in

genetic mapping experiments, indicate specific genetic markers to be used.

In physical mapping, indicate (and reference) appropriate restriction enzymes and plasmids to be used.



Genetic Mapping Strategies

Use of Transduction to Localize the Transposon

Consider several genes involved in the production of cysteine. For

the purposes of this example, assume that the transposon is in either the

cysB or the cysG gene. The modified Tn5' is tet ~.

Gene



Map location



Nearby selectable marker



cysB



28 min

74 min



trp 27.7 min

argD 73.8 min



cysG



For cysB, the donor strain is trp§

trp-cys §



'. The recipient strain is



REFERENCES



35



1. Make a P1 phage lysate on donor strain,

2. Select for recipient strain transduced to

cys; score how many trp § cells are also

plate) or tet ~ (can grow on a mintet5 plus

For cysG, the donor strain is argD§



infect recipient strain.

trp § by plating on min plus

cys ~ (cannot grow on a min

cys plate or a n Ltetl 5 plate).



'. The recipient strain is



argD-cys §

1. Make a P1 phage lysate on donor strain,

2. Select for recipient strain transduced to

cys; score how many arg § cells are also

plate) or tet ~ (can grow on a mintet5 plus



infect recipient strain.

arg § by plating on min plus

cys- (cannot grow on a min

cys plate or a n Ltetl 5 plate).



The results of the transduction experiments will be that the cotransduction of tet ~ or cys- with arg will be high and that with trp will

be zero, indicating the transposon is closely linked to a r g D ~ t h a t is, the

transposon inserted into cysG, or the co-transduction of tet R or cys- with

trp will be high and with arg will be zero, indicating the transposon

inserted into cysB.



NOTE

Auxotrophic markers can be used readily in such co-transduction

experiments. Vinopal (1987) lists many (10.5 pages worth!) selectable

markers. See Miller (1992, pp. 263-274) for details of using bacteriophage

P1 for transduction.



References

Bachman, B. J. (1983). Linkage map of Escherichia coli K-12, ed. 7. Microbiol. Rev. 47,

180-230.

Bachman, B. J. (1990). Linkage map of Escherichia coli K-12, ed. 8. Microbiol. Rev. 54,

130-197.

Bachman, B. J., and Low, K. B. (1980). Linkage map of Escherichia coli K-12, ed. 6. Microbiol.

Rev. 44, 1-56.

Berg, C. M., Berg, D. E., and Groisman, E. A. (1989). Transposable elements and the genetic

engineering of bacteria. In "Mobile DNA" (D. E. Berg and M. M. Howe, eds.), pp.

881-888. American Society for Microbiology, Washington, DC.

Berg, D. E. (1989). Transposon Tn5. In "Mobile DNA" (D. E. Berg and M. M. Howe, eds.),

pp. 185-210. American Society for Microbiology, Washington, DC.

Berg, D. E., and Berg, C. M. (1983). The prokaryotic transposable element T n 5 ~ A review

article. Biotechnology 1, 417-435.

Clowes, R. C., and Hayes, W., eds. (1968). "Experiments in Microbial Genetics." Wiley, New

York.

Davis, B. D. (1948). Isolation of biochemically deficient mutants by penicillin. J. Am. Chem.

Soc. 70, 4267.



36



TRANSPOSON MUTAGENESIS OF Escherichia coil



Davis, B. D. (1993). The penicillin method of mutant selection. BioEssays 15, 837-839.

Davis, R. W., Botstein, D., and Roth, J. R. (1980). "A Manual for Genetic Engineering: Advanced Bacterial Genetics." Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.

Eisenstadt, E., Carlton, B. C., and Brown, B. J. (1994). Gene mutation. In "Methods for General

and Molecular Bacteriology" (P. Gerhardt, R. G. E. Murray, W. A. Wood, and N. R.

Krieg, eds.), pp. 297-316, American Society for Microbiology, Washington, DC.

Finnegan, D. J. (1985). Transposable elements in eukaryotes. Int. Rev. Cytol. 93, 281-326.

Galas, D. J., and Chandler, M. (1989). Bacterial insertion sequences. In "Mobile DNA"

(D. E. Berg and M. M. Howe, eds.), pp. 112-113. American Society for Microbiology,

Washington, DC.

Gutierrez, C., Barondess, J., Mannoil, 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.

Hoffman, C. S., and Wright, A. (1985). Fusions of secreted proteins to alkaline phophatase: An

approach for studying protein secretion. Proc. Natl. Acad. Sci. U.S.A. 82, 5107-5111.

Kleckner, N. (1977). Genetic engineering in vivo using translocatable drug-resistance elements. J. Mol. Biol. 116, 125-159.

Kleckner, N. (1981). Transposable elements in prokaryotes. Annu. Rev. Genet. 15, 341-404.

Kleckner, N. (1990). Regulation of transposition in bacteria. Annu. Rev. Cell Biol. 6, 297-327.

Lederberg, J. (1950). In Isolation and characterization of biochemical mutants of bacteria.

"Methods in Medical Research," 3, (R. W. Gerard, ed.), pp. 5-22. The Year Book

Publishers, Inc.

Lederberg, J., and Zinder, N. (1948). Concentration of biochemical mutants of bacteria with

penicillin. J. Am. Chem. Soc. 70, 4267-4268.

Low, K. B. (1973). Rapid mapping of conditional and auxotrophic mutations in E. coli K12. J. Bacteriol. 113, 798-812.

Manoil, C., and Beckwith, J. (1986). A genetic approach to analyzing membrane protein

topology. Science 233, 1403-1408.

Price, C. A. (1990). Laboratory notebooks: Sacred works. Plant Mol. Biol. Report. 8, 220-221.

Scott, J. R. (1992). Sex and the single circle: Conjugative transposition. J. Bacteriol. 174,

6005-6010.

Stachel, S., An, G., Flores, C., and Nester, E. W. (1985). A Tn3 lacZ transposon for the

random generation of ~-galactosidase gene fusions: Application to the analysis of gene

expression in Agrobacterium. EMBO J. 4, 891-898.

Vinopal, R. T. (1987). Selectable phenotypes. In "Escherichia coli and Salmonella typhimurium Cellular and Molecular Biology." (F. C. Neidhardt, ed.), pp. 990-1015. American

Society for Microbiology, Washington, D.C.

Wilmes-Riesenberg, M. R., and Wanner, B. L. (1992). TnphoA and TnphoA' elements for

making and switching fusions for study of transcription, translation, and cell surface

localization. J. Bacteriol. 174, 4558-4575.

Wollman, E. L., Jacob, F., and Hayes, W. (1956). Conjugation and genetic recombination in

E. call K-12. Cold Spring Harbor Symp. Quant. Biol. 21, 141-162.



5uggested Reading

Phage A

Friedman, D. I., Olson, E. R., Georgopoulos, C., Tilly, K., Herskowitz, I., and Banuett, F.

(1984). Interactions of bacteriophage and host macromolecules in the growth of bacteriophage k. Microbiol. Rev. 48, 299-325.



REFERENCES



37



Hendrix, R. W., ed. (1983). "Lambda II." Cold Spring Harbor Laboratory Press, Cold Spring

Harbor, NY.

Lewin, B. (1994). Phage strategies: Lytic cascades and lysogenic repression. In "Genes V,"

Chap. 17, pp. 491-523. Oxford University Press, New York.



Phage A Receptor

Hall, M. N., Gabay, J., and Schwartz, M. (1983). Evidence for a coupling of synthesis and

export of an outer membrane protein in E. coJi. EMBO J. 2, 15-19.

Ludwig, R. A. (1987). Gene tandem-mediated selection of coliphage ),-receptive Agrobacterium, Pseudomonas, and Rhizobium strains. Proc. Natl. Acad. Sci. U.S.A. 84,

3334-3338.

Roessner, C. A., and Ihler, G. M. (1984). Proteinase sensitivity of bacteriophage lambda tail

proteins gpJ and pH in complexes with the lambda receptor. J. Bacteriol. 157,165-170.

Schwartz, M. (1983). Phage )t receptor (Lamb protein) in E. coll. In "Methods in Enzymology" ( S. Fleischer and B. Fleischer, eds.), Vol. 97, pp. 100-112. Academic Press, San

Diego.

Prokaryotic



Transposons



Adzuma, K., and Mizuuchi, K. (1988). Target immunity of Mu transposition reflects a differential distribution of MuB protein. Cell (Cambridge, Mass.) 53, 257-266.

Calos, M. P., and Miller, J. H. (1980). Transposable elements. Cell 20, 579-595.

Grindley, N. D. F. (1983). Transposition of Tn3 and related transposons. Cell 32, 3-5.

Kleckner, N. (1977). Genetic engineering in vivo using translocatable drug-resistance elements. J. Mol. Biol. 116, 125-159.

Kleckner, N. (1981). Transposable elements in prokaryotes. Annu. Rev. Genet. 15, 341-404.

Kleckner, N. (1990). Regulation of transcription in bacteria. Annu. Rev. Cell Biol. 6, 297-327.

Lewin, B. (1994). Transposons that mobilize via DNA. In "Genes V," Chap. 34, pp. 999-1031.

Oxford University Press, New York.

Reyes, O., Beyon, A., Mignotte-Vieux, C., and Richaud, F. (1987). Mini-Mu transduction:

Cis-inhibition of the insertion of Mud transposon. Plasmid 18, 183-192.

Details of Tn5

Berg, D. E. (1989). Transposon Tn5. In "Mobile DNA" (D. E. Berg and M. M. Howe, eds.),

pp. 185-210. American Society for Microbiology, Washington, DC.

Berg, D. E., and Berg, C. M. (1983). The prokaryotic transposable element Tn5--a review

article. Biotechnology 1, 417-435.

Reznikoff, W. S. (1993). The Tn5 transposon. Annu. Rev. Microbiol. 47, 945-963.



How



Tn5 Works



Biek, D., and Roth, J. R. (1980). Regulation of Tn5 transposition in Salmonella typhimurium.

Proc. Natl. Acad. Sci. U.S.A. 77, 6047-6051.

de la Cruz, N. B., Weinreich, M. D., and Wiegand, R. W. (1993). Characterization of the Tn5

transposase and inhibitor proteins: A model for the inhibition of transposition.

J. Bacteriol. 175, 6932-6938.

Jorgensen, R. A., Rothstein, S. J., and Reznikoff, W. S. (1979). A restriction enzyme cleavage

map of Tn5 and location of a region encoding neomycin resistance. Mol. Gen. Genet.

177, 65-72.

Kendrick, K. E., and Reznikoff, W. S. (1988). Transposition of IS50 L activates downstream

genes. J. Bacteriol. 170, 1965-1968.



38



TRANSPOSON MUTAGENESIS OF Escherichia coli



Kuan, C.-T., and Tessman, I. (1991). LexA protein of Escherichia coli represses expression

of the Tn5 transposase gene. J. Bacteriol. 173, 6406-6410.

Kuan, C.oT., and Tessman, I. (1992). Further evidence that transposition of Tn5 in Escherichia

coli is strongly enhanced by constitutively activated RecA proteins. J. Bacteriol. 174,

6872-6877.

Kuan, C.-T., Liu, S.-K., and Tessman, I. (1991). Excision and transposition of Tn5 as an SOS

activity in Escherichia coll. Genetics 128, 45-57.

Lodge, J. K., and Berg, D. E. (1988). Transposon Tn5 target specificity: Preference for insertion

at G/C pairs. Genetics 120, 645-650.

Lodge, J. K., and Berg, D. E. (1990). Mutations that affect Tn5 insertion into pBR322: Importance of local DNA supercoiling. J. Bacteriol. 172, 5956-5960.

Makris, J. C., Nordmann, P. L., and Reznikoff, W. S. (1988). Mutational analysis of insertion

sequence 50 (IS50) and transposon 5 (Tn5) ends. Proc. Natl. Acad. Sci. U.S.A. 85,

2224-2228.

Makris, J. C., Nordmann, P. L., and Reznikoff, W. S. (1990). Integration host factor plays a

role in IS50 and Tn5 transposition. J. Bacteriol. 172, 1368-1373.

Merrick, M., Filser, M., Kennedy, C., and Dixon, R. (1978). Polarity of mutations induced

by insertion of transposons Tn5, Tn7 and Tnl 0 into the nif gene cluster of Klebsiella

pneumoniae. Mol. Gen. Genet. 165, 103-111.

Rothstein, S. J., and Reznikoff, W. S. (1981). Functional differences in the inverted repeats

of Tn5 are caused by a single base pair nonhomology. Cell 23, 191-199.

Rothstein, S. J., Jorgensen, R. A., Postle, K., and Reznikoff, W. S. (1980). The inverted repeats

of Tn5 are functionally different. Cell (Cambridge, Mass.) 19, 795-805.

Weinreich, M. D., and Reznikoff, W. S. (1992). Fis plays a role in Tn5 and IS50 transposition.

J. Bacteriol. 174, 4530-4537.

Weinreich, M. D., Makris, J. C., and Reznikoff, W. S. (1991). Induction of the SOS response

in Escherichia coli inhibits Tn5 and IS50 transpostion. J. Bacteriol. 173, 6910-6918.

Wiegand, T. W., and Reznikoff, W. S. (1992). Characteristion of two hypertransposing Tn5

mutants. J. Bacteriol. 174, 1229-1239.

Yin, J. C. P., and Reznikoff, W. S. (1987). dnaA, an essential host gene, and Tn5 transposition.

J. Bacteriol. 169, 4637-4645.

Yin, J. C. P., and Reznikoff, W. S. (1988). P2 and inhibition of Tn5 transposition. J. Bacteriol.

170, 3008-3015.

Applications



of Tn5



de Bruijn, F. J., and Lupski, J. R. (1984). The use of transposon Tn5 mutagenesis in the rapid

generation of correlated physical and genetic maps of DNA segments cloned into

multicopy plasmids--a review. Gene 27, 131-149.

Manoil, C., and Beckwith, J. (1985). TnphoA: A transposon probe for protein export signals.

Proc. Natl. Acad. Sci. U.S.A. 82, 8129-8133.

Nag, D. K., Huand, H. V., and Berg, D. E. (1988). Bidirectional chain-termination nucleoo

tide sequencing: Transposon Tn5seql as a mobile source of primer sites. Gene 64,

135-145.

Phadnis, S. H., Huang, H. V., and Berg, D. E. (1989). Tn5supF, a 264obase-pair transposon

derived from Tn5 for insertion mutagenesis and sequencing DNAs cloned in phage

)~. Proc. Natl. Acad. Sci. U.S.A. 86, 5908-5912.

Saskawa, C., and Yoshikawa, M. (1987). A series of Tn5 variants with various drug-resistance

markers and suicide vector for transposon mutagenesis. Gene 56, 283-288.

Sharma, S. B., and Signer, E. R. (1990). Temporal and spatial regulation of the symbiotic

genes of Rhizobium meliloti in planta revealed by transposon Tn5ogusA. Genes Dev.

4, 344-356.



REFERENCES



39



Wang, G., Blakesley, R. W., Berg, D. E., and Berg, C. M. (1993). pDUAL: A transposon-based

cosmid cloning vector for generating nested deletion and DNA sequencing templates

in vivo. Proc. Natl. Acad. Sci. U.S.A. 90, 7874-7878.



Details of TnlO

Bender, J., and Kleckner, N. (1986). Genetic evidence that Tnl0 transposes by a nonreplicative

mechanism. Cell 45, 801-815.

Bender, J., and Kleckner, N. (1992). IS/0 transposase mutations that specifically alter target

site recognition. EMBO I. 11, 741-750.

Bender, J., Kuo, J., and Kleckner, N. (1991). Genetic evidence against intramolecular rejoining

of the donor DNA molecule following IS10 transposition. Genetics 128, 687-694.

Benjamin, H. W., and Kleckner, N. (1989). Intramo|ecular transposition by Tnl0. Cell 59,

373-383.

Benjamin, H. W., and Kleckner, N. (1992). Excision of TnlO from the donor site during

transposition occurs by flush double-strand cleavages at the transposon termini. Proc.

Natl. Acad. Sci. U.S.A. 89, 4648-4652.

Bender, J., and Kleckner, N. (1992). TnlO insertion specificity is strongly dependent upon

sequences immediately adjacent to the target-site consensus sequence. Proc. Natl.

Acad. Sci. U.S.A. 89, 7996-8000.

Ciampi, M. S., Schmid, M. B., and Roth, J. R. (1982). Transposon TnlO provides a promoter

for transcription of adjacent sequences. Proc. Natl. Acad. Sci. U.S.A. 79, 5016-5020.

Davis, M. A., Simons, R. W., and Kleckner, N. (1985). TnlO protects itself at two levels from

fortuitous activation by external promoter. Cell 43, 379-387.

Hailing, S. M., and Kleckner, N. (1982). Symmetrical six-base-pair target site sequence determines Tnl0 insertion specificity. Cell 28, 155-163.

Hailing, S. M., Simons, R. W., Way, J. C., Walsh, R. B., and Kleckner, N. (1982). DNA

sequence organization of IS10-right of Tnl 0 and comparison with IS10-1eft. Proc. Natl.

Acad. Sci. U.S.A. 79, 2608-2612.

Haniford, D. B., Chelouche, A. R., and Kleckner, N. (1989). A specific class of IS10 transposase

mutants are blocked for target site interactions and promote formation of an excised

transposon fragment. Cell (Cambridge, Mass.) 59, 385-394.

Haniford, D. B., Benjamin, H. W., and Kleckner, N. (1991). Kinetic and structural analysis

of a cleaved donor intermediate and a strand transfer intermediate in Tnl 0 transposition. Cell (Cambridge, Mass.) 64, 171-179.

Harayama, S., Oguchi, T., and Iino, T. (1984). Does TnlO transpose via the cointegrate

molecule? Mol. Gen. Genet. 194, 444-450.

Jorgensen, B. A., Berg, D. E., Allet, B., and Reznikoff, W. S. (1979). Restriction enzyme

cleavage map of Tnl 0, a transposon which encodes tetracycline resistance. J. Bacteriol.

137, 681-685.

Kleckner, N. (1979). DNA sequence analysis of TnlO insertions: Origin and role of 9 bp

flanking repetitions during TnlO translation. Cell 16, 711-720.

Kleckner, N. (1989). Transposon TnlO. In "Mobile DNA" (D. E. Berg and M. M. Howe, eds.),

Chap. 8, pp. 227-268. Americal Society for Microbiology, Washington, DC.

Kleckner, N. (1990). Regulating TnlO and ISIO transposition. Genetics 124, 449-454.

Kleckner, N., Bender, J., and Gottesman, S. (1991). Uses of transposons with emphasis on

TnlO. In "Methods in Enzymology" ( J. H. Miller, ed.), Vol. 204, pp. 139-180. Academic

Press, San Diego, CA.

Morisato, D., and Kleckner, N. (1984). Transposase promotes double strand breaks and single

strand joints at TnlO termini in vivo. Cell 39, 181-190.

Morisato, D., Way, J. C., Kim, H-J., and Kleckner, N. (1983). TnlO transposase acts preferentially on nearby transposon ends in vivo. Cell 32, 799-807.



40



TRANSPOSON MUTAGENESIS OF Escherichia coli



Roberts, D., Hooper, B. C., McClure, W. R., and K|eckner, N. (1985). ISIO transposition is

regulated by DNA adenine methylation. Cell 43, 117-130.

Roberts, D. E., Ascherman, D., and Kleckner, N. (1991). ISIO promotes adjacent deletions at

low frequency. Genetics 128, 37-43.

Ross, D. G., Swan, J., and Kleckner, N. (1979). Physical structures of Tnl0--promoted

deletions and inversions: Role of 1400 bp inverted repetitions. Cell 16, 721-731.

Shen, M. M., Raleigh, E. A., and Kleckner, N. (1987). Physical analysis of TnlO- and IS10promoted transpositions and rearrangements. Genetics 116, 359-369.

Simons, R. W., and Kleckner, N. (1988). Biological regulation by antisense RNA in prokaryotes. Annu. Rev. Genet. 22, 567-600 (especially p. 571,589, 590 about IS10).

Way, J. C., and Kleckner, N. (1984). Essential sites at transposon TnlO termini. Proc. Natl.

Acad. Sci. U.S.A. 81, 3452-3456.



TnlO and Anti-Sense RNA in Prokaryotes

Case, C. C., Roels, S. M., Gonzalez, J. E., Simons, E. L., and Simons, R. W. (1988). Analysis

of the promoters and transcripts involved in IS IO anti-sense RNA control. Gene 72,

219-236.

Simons, R. W. (1988). Naturally occurring antisense RNA control--a brief review. Gene 72,

35-44.

Simons, R. W., and Kleckner, N. (1988). Biological regulation by antisense RNA in prokaryotes. Annu. Rev. Genet. 22, 567-600. See pp. 571,589, 590 about ISIO.



Tet R Gene of TnlO

Bertrand, K. P., Postle, K., Wray, L. V., Jr., and Reznikoff, W. S. (1983). Overlapping divergent

promoters control expression of TnlO tetracycline resistance. Gene 23, 149-156.

Bertrand, K. P., Postle, K., Wray, L. V., Jr., and Reznikoff, W. S. (1984). Construction of a

single-copy promoter vector and its use in analysis of regulation of the transposon

Tnl0 tetracycline resistance determinant. J. Bacteriol. 158, 910-919.

Braus, G., Argast, M., and Beck, C. F. (1984). Identification of additional genes on transposon

TnlO:tetC and tetD. J. Bacteriol. 160, 504-509.

Hillen, W., Gatz, C., Altschmied, L., Schollmeir, K., and Meier, I. (1983). Control of expression

of TnlOoencoded tetracycline resistance genes. J. Mol. Biol. 169, 707-721.

Hillen, W., Schollmeier, K., and Gatz, C. (1984). Control of expression of the TnlO-encoded

tetracycline resistance operon II interaction of RNA polymerase and TET repressor

with the tet operon regulatory region. J. Mol. Biol. 172, 185-201.

Isackson, P. J., and Bertrand, K. P. (1985). Dominant negative mutations in the Tnl0 tet

repressor: Evidence for use of the conserved helix-turn-helix motif in DNA binding.

Proc. Natl. Acad. Sci. U.S.A. 82, 6226-6230.

Moyed, H. S., Nguyen, T. T., and Bertrand, K. P. (1983). Multicopy TnlO tet plasmids confer

sensitivity to induction of tet gene expression. J. Bacteriol. 155, 549-556.

Tovar, K., and Hillen, W. (1989). Tet repressor binding induced curvature of tet operator

DNA. Nucleic Acids Res. 17, 6515-6522.



Models of Mechanism of Transposition in Prokaryotes

Bennett, P. M., de la Cruz, F., and Grinsted, J. (1983). Cointegrates are not obligatory intermediates in transposition of Tn3 and Tn21. Nature (London) 305, 743-744.

Chaconas, G., and Surette, M. G. (1988). Mechanism of Mu DNA transposition. BioEssays

9, 205-208.

Galas, D. J., and Chandler, M. (1981). On the molecular mechanisms of transposition. Proc.

Natl. Acad. Sci. U.S.A. 78, 4858-4862.



REFERENCES



41



Harshey, R. M., and Bukhari, A. I. (1981). A mechanism of DNA transposition. Proc. Natl.

Acad. Sci. U.S.A. 78, 1090-1094.

Shapiro, J. A. (1979). Molecular model for the transposition and replication of bacteriphage

Mu and other transposable elements. Proc. Natl. Acad. Sci. U.S.A. 76, 1933-1937.



Other Transposon Mutagenesis Systems

Olson, E. R., Sadowsky, M. J., and Verma, D. P. S. (1985). Identification of genes involved

in Rhizobium-legume symbiosis by Mu-DI (Kan, lac)-generated transcription fusion.

Biotechnology, 3, 143-148.

Stachel, S. E., An, G., Flores, C., and Nester, E. W. (1985). A Tn3 lacZ transposon for

random generation of/3-galactosidase gene fusions: Application to the analysis of gene

expression in Agrobacterium. EMBO J. 4, 891-898.

Way, J. C., Davis, M. A., Morisato, D., Roberts, D., and Kleckner, N. (1984. New TnlO

derivatives for transposon mutagenesis and for construction of lacZ operon fusions

by transposition. Gene 32, 369-379.



Eukaryotic Transposable Elements

Berg, D. E., and Howe, M. M., (eds.) (1989)"Mobile DNA." American Society of Microbiology,

Washington, DC.

Boehe, J. D., Garfinkel, D. J., Styles, C. A., and, Fink, G. R. (1985). Ty elements transpose

through an RNA intermediate. Cell 40, 491-500.

Dujon, B. (1989). Group I introns as mobile genetic elements: Facts and mechanistic speculations--a review. Gene 82, 91-114.

D6ring, H.-P., and Starlinger, P. (1984). Barbara McClintock's controlling elements: Now at

the DNA level. Cell 39, 253-259.

D6ring, H.-P., and Starlinger, P. (1986). Molecular genetics of transposable elements in plants.

Annu. Rev. Genet. 20, 175-200.

Eichinger, D. J., and Boehe, J. D. (1988). The DNA intermediate in yeast Tyl element transposition copurifies with virus-like particles: Cell-free Tyl transposition. Cell 54, 955-966.

Fedoroff, N., Masson, P., and Banks, J. A. (1989). Mutations, epimutations, and the developmental programming of the maize suppressor-mutator transposable element. BioEssays

10, 139-144.

Fink, G. R., Boeke, J. D., and Garfinkel, D. J. (1986). The mechanism and consequences of

retrotransposition. Trends Genet. 2, 118-123.

Finnegan, D. J. (1985). Transposable elements in eukaryotes. Int. Rev. Cytol. 93, 281-326.

Finnegan, D. J. (1989). Eukaryotic transposable elements and genome evolution. Trends

Genet. 5, 103-107.

Finnegan, D. J., and Fawcett, D. H. (1986). Transposable elements in Drosophila melanogaster.

In "Oxford Surveys on Eukaryotic Genes" (N. Maclean, ed.), Vol. 3, pp. 1-62. Oxford

University Press, Oxford.

Georgiev, G. P. (1984). Mobile genetic elements in animal cells and their biological significance. Eur. ]. Biochem. 145, 203-220.

Hastie, N. (1985). Middle repetitive DNA: Amplication, homogeneity, and mobility. Trends

Genet. 1, 37.

Lewin, B. (1994). Retroviruses and retroposons. In "Genes V," Chap. 35, pp. 1053-1056.

Oxford University Press, New York.

Rubin, G. M., and Spradling, A. C. (1982). Genetic transformation of Drosophila with transposable element vectors. Science 218, 348-353.

Shapiro, J. A. (ed.). (1983). "Mobile Genetic Elements." Academic Press, New York.



42



TRANSPOSON MUTAGENESIS OF Escherichia coli



Spradling, A. C., and Rubin, G. M. (1982). Transposition of cloned P elements into Drosophila

germ line chromosomes. Science 218, 314-347.

Wessler, S. R., (1989). The splicing of maize transposable elements from pre-mRNAma

minireview. Gene 82, 127-133.



Mammalian Mobile D N A

Deininger, P. L., and Daniels, G. R. (1986). Recent evolution of mammalian repetitive DNA

elements. Trends Genet. 2, 76-80.

Paulson, K. E., Deka, N., Schmid, C., Mistra, R., Schindler, C., Rush, M., Kadyk, L., and

Leinwand, L. (1985). A transposonolike element in human DNA. Nature (London) 316,

359-363.

Rogers, J. (1983). Retroposons defined. Nature (London) 301, 460.

Rogers, J. (1985). The origin and evolution of retroposons. Int. Rev. Cytol. 93, 187-279.

Sakaki, Y. M., Hattori, M., Fujita, A., Yoshioka, K., Kuhara, S., and Takenaka, O. (1986).

The LINEol family of primates may encode a reverse transcriptase-like protein. Cold

Spring Harbor Symp. Quant. Biol. 51,456-469.

Singer, M. (1982). Sine's and line's: Highly repeated short and long interspersed sequences

in mammalian genomes. Cell (Cambridge, Mass.) 28, 433-434.

Spence, S. E., Young, R. M., Garner, K. J., and Lingrel, J. B. (1985). Localization and characterization of members of a family of repetitive sequences in the goat/3-globin locus.

Nucleic Acids Res. 13, 2171-2186.

Trabuchet, G., Chebloune, Y., Savatier, P., Lachuer, J., Faure, C., Verdier, G., and Nigon,

V. M. (1987). Recent insertion of an Alu sequence in the ~-globin gene cluster of the

gorilla. J. Mol. Evol. 25, 288-291.

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pseudogenes, and transposable elements generated by reverse flow of genetic information. Annu. Rev. Biochem. 55, 631-661.



The Auxotroph Library Report

General Reading

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Mandelstam, J., McQuillen, K., and Dawes, I. W. (1982). "Biochemistry of Bacterial Growth"

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Miller, J. H. (1992). "A Short Course in Bacterial Genetics: A Laboratory Manual and Handbook for Escherichia coli and Related Bacteria." Cold Spring Harbor Laboratory Press,

Cold Spring Harbor, NY. (Especially see the section on P1 transduction, pp. 263-274,

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Neidhardt, F. C., Ingraham, J. L., Low, K. B., Magasanik, B., Schaechter, M., and Umbarger, H.

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Escherichia coli Linkage Map

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130-197.

Bachman, B. J. (1983). Linkage map of E. coli Ko12, ed. 7. Microbiol. Rev. 47, 180-230.



REFERENCES



43



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Other Escherichia coli Information

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Hfr Mapping and Bacterial Conjugation

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Physical Mapping

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44



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Transduction

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Selection of tet Revertants

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Mapping Strategy

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