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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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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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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