Molecular Evolution of the Escherichia Coli Chromosome. I. Analysis of Structure and Natural Variation in a Previously Uncharacterized Region Between Trp and TonB

Overview

Journal Genetics

Publisher Oxford University Press

Specialty Genetics

Date 1988 Oct 1

PMID 3058546

Citations 28

Authors

A Stoltzfus

J F Leslie

R Milkman

Affiliations

Soon will be listed here.

Abstract

We present the sequence of a 3500-bp region of the Escherichia coli strain K12 chromosome lying between the tryptophan operon and the tonB gene. Analysis of the sequence yields six open reading frames that have properties characteristic of genes for proteins. The reading frames are closely spaced, and putative transcription units and control sites compose over 95% of the DNA. The sequences of several wild strains of E. coli have been determined for a large segment of the region described. Comparison of these sequences reveals the effects of base substitutions, DNA rearrangements, and recombination. In the regions presumably expressed as polypeptides, most of the natural variation results from synonymous substitutions. However, the DNA rearrangements identified have end points within the open reading frames and disrupt them in a variety of ways. The effects of genetic recombination between strains, recently found to be significant on a large scale in E. coli, are also apparent in the region between trp and tonB.

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References

Milkman R . Electrophoretic variation in Escherichia coli from natural sources. Science. 1973; 182(4116):1024-6. DOI: 10.1126/science.182.4116.1024. View

Calos M, Miller J . Transposable elements. Cell. 1980; 20(3):579-95. DOI: 10.1016/0092-8674(80)90305-0. View

Sommer H, Schumacher B, Saedler H . A new type of IS1-mediated deletion. Mol Gen Genet. 1981; 184(2):300-7. DOI: 10.1007/BF00272921. View

Stormo G, Schneider T, Gold L . Characterization of translational initiation sites in E. coli. Nucleic Acids Res. 1982; 10(9):2971-96. PMC: 320669. DOI: 10.1093/nar/10.9.2971. View

Michaelis S, Beckwith J . Mechanism of incorporation of cell envelope proteins in Escherichia coli. Annu Rev Microbiol. 1982; 36:435-65. DOI: 10.1146/annurev.mi.36.100182.002251. View

Kozak M . Comparison of initiation of protein synthesis in procaryotes, eucaryotes, and organelles. Microbiol Rev. 1983; 47(1):1-45. PMC: 281560. DOI: 10.1128/mr.47.1.1-45.1983. View

Milkman R, Crawford I . Clustered third-base substitutions among wild strains of Escherichia coli. Science. 1983; 221(4608):378-80. DOI: 10.1126/science.6346486. View

Bachmann B . Linkage map of Escherichia coli K-12, edition 7. Microbiol Rev. 1983; 47(2):180-230. PMC: 281571. DOI: 10.1128/mr.47.2.180-230.1983. View

Postle K, Good R . DNA sequence of the Escherichia coli tonB gene. Proc Natl Acad Sci U S A. 1983; 80(17):5235-9. PMC: 384227. DOI: 10.1073/pnas.80.17.5235. View

10.

Ochman H, Selander R . Standard reference strains of Escherichia coli from natural populations. J Bacteriol. 1984; 157(2):690-3. PMC: 215307. DOI: 10.1128/jb.157.2.690-693.1984. View

11.

Lagrimini L, Brentano S, Donelson J . A DNA sequence analysis package for the IBM personal computer. Nucleic Acids Res. 1984; 12(1 Pt 2):605-14. PMC: 321074. DOI: 10.1093/nar/12.1part2.605. View

12.

Mulligan M, HAWLEY D, Entriken R, McClure W . Escherichia coli promoter sequences predict in vitro RNA polymerase selectivity. Nucleic Acids Res. 1984; 12(1 Pt 2):789-800. PMC: 321093. DOI: 10.1093/nar/12.1part2.789. View

13.

Garger S, Griffith O, Grill L . Rapid purification of plasmid DNA by a single centrifugation in a two-step cesium chloride-ethidium bromide gradient. Biochem Biophys Res Commun. 1983; 117(3):835-42. DOI: 10.1016/0006-291x(83)91672-8. View

14.

Postle K, Good R . A bidirectional rho-independent transcription terminator between the E. coli tonB gene and an opposing gene. Cell. 1985; 41(2):577-85. DOI: 10.1016/s0092-8674(85)80030-1. View

15.

Vieira J, Messing J . Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene. 1985; 33(1):103-19. DOI: 10.1016/0378-1119(85)90120-9. View

16.

Wu A, Chapman A, Platt T, Guarente L, Beckwith J . Deletions of distal sequence after termination of transcription at the end of the tryptophan operon in E. coli. Cell. 1980; 19(4):829-36. DOI: 10.1016/0092-8674(80)90073-2. View

17.

Johnsrud L . DNA sequence of the transposable element IS1. Mol Gen Genet. 1979; 169(2):213-8. DOI: 10.1007/BF00271673. View