Chapter 12 : Local Genetic Context, Supercoiling, and Gene Expression

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This chapter discusses the influence a gene's neighbors can have on that gene's expression and looks at the mechanisms by which this can occur. Both the packaging of DNA and its metabolic functioning are greatly facilitated by supercoiling. Supercoiling imparts torsional stress to DNA, which influences its interaction with RNA polymerase and other DNA-binding proteins as well as contributing to its compaction. The importance of supercoiling to cellular functioning is illustrated by the tight control prokaryotes maintain over this property of their genomes. The greatest difference between small plasmids and larger molecules may be that plasmids can rotate the entire molecule around its long axis during transcription, relieving local changes in supercoding levels. One additional finding that further supports the twin-supercoil domain model is that the length of the transcript located upstream from the -500 promoter affects the level of supercoiling changes. The large difference in transcription rates between mutant and wild-type strains may here be obscuring the fact that doubling the output of a gene can have significant consequences for a cell, either good or bad, depending on the situation. 4,5',8-trimethylpsoralen (TMP) is a sensitive indicator of supercoiling, and it is claimed to be able to detect changes in supercoil levels of 15% and 12%. Changes of this magnitude are regularly experienced by the genome of .

Citation: St. Jean A. 1999. Local Genetic Context, Supercoiling, and Gene Expression, p 203-215. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch12

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Gene Expression and Regulation
Chromosomal DNA
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Image of FIGURE 1

Two alternate conformations that may be adopted by supercoiled DNA. (A) DNA wrapped around itself in plectonemic supercoils with a terminal loop to the left. The radius of the plectoneme—indicated by the letter —varies greatly with even modest changes in the linking number of the DNA, decreasing as the number of supercoils increases ( ). The length of the plectoneme—indicated by the letter —remains relatively constant over the range of linking numbers normally experienced in vivo and is 41% of the length of the linear DNA strand ( ). Bacterial plasmids and at least portions of chromosomal DNA regularly adopt this conformation. (B) DNA wound in solenoidal supercoils, forming a toroidal shape. The best known example of this conformation is the eukaryotic nucleosome, with its DNA wrapped around the core histone proteins.

Citation: St. Jean A. 1999. Local Genetic Context, Supercoiling, and Gene Expression, p 203-215. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch12
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Image of FIGURE 2

Transcription on a plectonemically supercoiled DNA molecule. The RNA polymerase (black oval) positions itself at the terminal loop of the plectoneme and maintains this position throughout the transcription process. The polymerase enzyme remains on one side of the loop to prevent the nascent RNA strand from becoming entangled in the DNA molecule. This necessitates the rotation of the DNA around its long axis. The maintenance of the polymerase enzyme at the terminal loop also means that the interwound strands of the plectoneme slither past one another, allowing distantly positioned sequences to come into close apposition. Both movements of the DNA molecule are indicated by arrows.

Citation: St. Jean A. 1999. Local Genetic Context, Supercoiling, and Gene Expression, p 203-215. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch12
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1. Balke, V.,, and J. Graila. 1987. Changes in the linking number of supercoiled DNA accompany growth transitions in Escherichia coli . J. Bacteriol. 169:44994506.
2. Bates, A. D.,, and A. Maxwell,. 1993. DNA supercoiling, p. 1745. In D. Rickwood, (ed.), DNA Topology (In Focus series). IRL Press, Oxford, England.
3. Bertin, P.,, P. Lejeune,, C. Laurent-Winter,, and A. Danchin. 1990. Mutations in bglY, the structural gene for the DNA-binding protein HI, affect expression of several Escherichia coli genes. Biochimie 72:889891.
4. Bliska, J. B.,, H. W. Benjamin,, and N. R. Cozzarelli. 1991. Mechanism of Tn3 resolvase recombination in vivo. J. Biol. Chem. 266: 20412047.
5. Bliska, J. B.,, and N. R. Cozzarelli. 1987. Use of site-specific recombination as a probe of DNA structure and metabolism in vivo. J. Mol. Biol. 194:205218.
6. Boles, T. C.,, J. H. White,, and N. R. Cozzarelli. 1990. Structure of plectonemically supercoiled DNA. J. Mol. Biol. 213:931951.
7. Charlebois, R. L.,, and A. St. Jean. 1995. Supercoiling and map stability in the bacterial chromosome. J. Mol. Evol. 41:1523.
8. Chen, D.,, R. P. Bowater,, C. J. Dorman,, and D. M. J. Lilley. 1992. Activity of a plasmid-borne leu-500 promoter depends on the transcription and translation of an adjacent gene. Proc. Natl. Acad. Sci. USA 89:87848788.
9. Chen, D.,, R. P. Bowater,, and D. M. J. Lilley. 1993. Activation of the leu-500 promoter: a topological domain generated by divergent transcription in a plasmid. Biochemistry 32:1316213170.
10. Cook, D. N.,, G. A. Armstrong,, and J. E. Hearst. 1989. Induction of anaerobic gene expression in Rhodobacter capsulatus is not accompanied by a local change in chromosomal supercoiling as measured by a novel assay. J. Bacteriol. 171:48364843.
11. Drlica, K. 1992. Control of bacterial DNA supercoiling. Mol. Microbiol. 6:425433.
12. Dubnau, E.,, and P. Margolin. 1972. Suppression of promoter mutations by the pleiotropic supX mutations. Mol. Gen. Genet. 117:91112.
13. Dürrenberger, M.,, M.-A. Bjornsti,, T. Uetz,, J. A. Hobot,, and E. Kellenberger. 1988. Intracellular location of the histonelike protein HU in Escherichia coli. J. Bacteriol. 170:47574768.
14. Fang, M.,, and H.-Y. Wu. 1998. A promoter relay mechanism for sequential gene activation. J. Bacteriol. 180:626633.
15. Fang, M.,, and H.-Y. Wu. 1998. Suppression of leu-500 mutation in topA+ Salmonella typhimurium strains. J. Biol. Chem. 273:2992929934.
16. Forsberg, Å. J.,, G. D. Pavitt,, and C. F. Higgins. 1994. Use of transcriptional fusions to monitor gene expression: a cautionary tale. J. Bacteriol. 176:21282132.
17. Friedman, D. I. 1988. Integration host factor: a protein for all reasons. Cell 55:545554.
18. Gowrishankar, J.,, and D. Manna. 1996. How is osmotic regulation of transcription of the Escherichia coli proU operon achieved? Genetica 97:363378.
19. Higgins, C. F.,, C. J. Dorman,, and N. Ni Bhriain,. 1990. Environmental influences on DNA supercoiling: a novel mechanism for the regulation of gene expression, p. 421432. In K. Drlica,, and M. Riley (ed.), The Bacterial Chromosome. American Society for Microbiology, Washington, D.C..
20. Higgins, N. P.,, X. Yang,, Q. Fu,, and J. R. Roth. 1996. Surveying a supercoil domain by using the γ δ resolution system in Salmonella typhimurium. J. Bacteriol. 178:28252835.
21. Hsieh, L.-S.,, R. M. Burger,, and K. Drlica. 1991. Bacterial DNA supercoiling and [ATP]/ [ADP]: changes associated with a transition to anaerobic growth. J. Mot. Biol. 219:443450.
22. Hsieh, L.-S.,, J. Rouviere-Yaniv,, and K. Drlica. 1991. Bacterial DNA supercoiling and [ATP]/[ADP] ratio: changes associated with salt shock. J. Bacteriol. 173:39143917.
23. Hyde, J. E.,, and J. E. Hearst. 1978. Binding of psoralen derivatives to DNA and chromatin: influence of the ionic environment on dark binding and photoreactivity. Biochemistry 17:12511257.
24. Kellenberger, E.,, and B. Arnold-Schulz-Gahmen. 1992. Chromatins of low-protein content: special features of their compaction and condensation. FEMS Microbiol. Lett. 100:361370.
25. Laundon, C. H.,, and J. D. Griffith. 1988. Curved helix segments can uniquely orient the topology of supertwisted DNA. Cell 52:545549.
26. Liu, L. F.,, and J. C. Wang. 1987. Supercoiling of the DNA template during transcription. Proc. Natl. Acad. Sci. USA 84:70247027.
27. Lodge, J. K.,, T. Kazic,, and D. E. Berg. 1989. Formation of supercoiling domains in plasmidpBR322. J. Bacteriol. 171:21812187.
28. Matthews, K. S. 1992. DNA looping. Microbiol. Rev. 56:123136.
29. Miller, W. G.,, and R. W. Simons. 1993. Chromosomal supercoiling in Escherichia coli. Mol. Microbiol. 10:675684.
30. Mojica, F. J. M.,, and C. F. Higgins. 1996. Localized domains of DNA supercoiling: topological coupling between promoters. Mol. Microbiol. 22:919928.
31. Mojica, F. J. M.,, and C. F. Higgins. 1997. In vivo supercoiling of plasmid and chromosomal DNA in an Escherichia coli hns mutant. J. Bacteriol. 179:35283533.
32. Mukai, F. H.,, and P. Margolin. 1963. Analysis of unlinked suppressors of an O° mutation in Salmonella. Proc. Natl. Acad. Sci. USA 50:140148.
33. Owen-Hughes, T.,, G. D. Pavitt,, D. S. Santos,, J. Sidebotham,, C. S. J. Hulton,, J. C. D. Hinton,, and C. F. Higgins. 1992. Interaction of H-NS with curved DNA influences DNA topology and gene expression. Cell 71:255265.
34. Pavitt, G. D.,, and C. F. Higgins. 1993. Chromosomal domains of supercoiling in Salmonella typhimurium. Mol. Microbiol. 10:685696.
35. Pérez-Martin, J.,, F. Rojo,, and V. Lorenzo. 1994. Promoters responsive to DNA bending: a common theme in prokaryotic gene expression. Microbiol. Rev. 58:268290.
36. Pettijohn, E.,, and O. Pfenninger. 1980. Supercoils in prokaryotic DNA restrained in vivo. Proc. Natl. Acad. Sci. USA 77:13311335.
37. Rahmouni, A. R.,, and R. D. Wells. 1992. Direct evidence for the effect of transcription on local DNA supercoiling in vivo. J. Mol. Biol. 223: 131144.
38. Reich, Z.,, S. Levin-Zaidman,, S. B. Gut-man,, T. Arad,, and A. Minsky. 1994. Supercoiling-regulated liquid-crystalline packaging of topologically-constrained, nucleosome-free DNA molecules. Biochemistry 33:1417714184.
39. Richardson, S. M. H.,, C. F. Higgins,, and D. M. J. Lilley. 1988. DNA supercoiling and the leu-500 promoter mutation of Salmonella typhimurium. EMBO J. 7:18631869.
40. Robinow, C.,, and E. Kellenberger. 1994. The bacterial nucleoid revisited. Microbiol. Rev. 58:211232.
41. Rohde, J. R.,, J. M. Fox,, and S. A. Minnich. 1994. Thermoregulation in Yersinia enterocolitica is coincident with changes in DNA supercoiling. Mol. Microbiol. 12:187199.
42. Ryter, A.,, and A. Chang. 1975. Localization of transcribing genes in the bacterial cell by means of high resolution autoradiography. J. Mol. Biol. 98:797810.
43. Sinden, R. R.,, J. O. Carlson,, and D. E. Pettijohn. 1980. Torsional tension in the DNA double helix measured with trimethylpsoralen in living E. coli cells: analogous measurements in insect and human cells. Cell 21:773783.
44. Sinden, R. R.,, and D. E. Pettijohn. 1981. Chromosomes in living E. coli cells are segregated into domains of supercoiling. Proc. Natl. Acad. Sci. USA 78:224228.
45. Spirito, F.,, and L. Bossi. 1996. Long-distance effect of downstream transcription on activity of the supercoiling-sensitive leu-500 promoter in a topA mutant of Salmonella typhimurium. J. Bacteriol. 178:71297137.
46. Staczek, P.,, and P. Higgins. 1998. Gyrase and topo IV modulate chromosome domain size in vivo. Mol. Miaobiol. 29:14351448.
47. Steck, T. R.,, R. J. Franco,, J.-Y. Wang,, and K. Drlica. 1993. Topoisomerase mutations affect the relative abundance of many Escherichia coli proteins. Mol. Microbiol. 10:473481.
48. Takayanagi, S.,, S. Morimura,, H. Kusaoke,, Y. Yokoyama,, K. Kano,, and M. Shioda. 1992. Chromosomal structure of the halophilic archaebacterium Halobacterium salinarium. J. Bacteriol. 174:72077216.
49. Tan, J.,, L. Shu,, and H.-Y. Wu. 1994. Activation of the leu-500 promoter by adjacent transcription. J. Bacteriol. 176:10771086.
50. ten Heggeler-Bordier, B.,, W. Wahli,, M. Adrian,, A. Stasiak,, and J. Dubochet. 1992. The apical localization of transcribing RNA polymerases on supercoiled DNA prevents their rotation around the template. EMBO J. 11:667672.
51. Tupper, A. E.,, T. A. Owen-Hughes,, D. W. Ussery,, D. S. Santos,, D. J. P. Ferguson,, J. M. Sidebotham,, J. C. D. Hinton,, and C. F. Higgins. 1994. The chromatin-associated protein H-NS alters DNA topology in vitro. EMBO J. 13:258268.
52. Worcel, A.,, and E. Burgi. 1972. On the structure of the folded chromosome of E. coli. J. Mol. Biol. 71:127147.
53. Wu, H.-Y.,, S. Shyy,, J. C. Wang,, and L. F. Liu. 1988. Transcription generates positively and negatively supercoiled domains in the template. Cell 53:433440.
54. Wu, H.-Y.,, J. Tan,, and M. Fang. 1995. Long-range interaction between two promoters: activation of the leu-500 promoter by a distant upstream promoter. Cell 82:445451.


Generic image for table

Counts of distances between adjacent ORFs separated by less than 250 bp of DNA occurring on opposite strands

Citation: St. Jean A. 1999. Local Genetic Context, Supercoiling, and Gene Expression, p 203-215. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch12

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