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Polymerase Collisions: What Can a Cell Do
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bacterial chromosome could be transcribed away from the origin of replication ( g. 1). Brewer analyzed the orientation of genes on the E. coli chromosome; more recently, D. Zeigler and D. Dean did the same for the chromosome of Bacillus subtilis. In B. subtilis, 95% (91 of 96) of the genes analyzed were in the proper orientation to avoid a head-on collision of polymerases. Among the exceptions were sporulation genes, genes that would not be transcribed during DNA synthesis and whose orientation is thus not relevant to DNA polymerase activity. In E. coli, Brewer found that, overall, 74% (375 of 501) of the genes she looked at were oriented to avoid head-on collisions. Brewer s data were more impressive when she broke them down according to transcription function and activity. For genes that transcribe very actively most of the time, the orientation is about 90% in the safe direction. For regulatory genes that are transcribed only very rarely, the orientation is random (50% safe). For
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other genes, the orientation was 72% in the safe direction. Thus, an organization clearly exists within the bacterial chromosome that helps to avoid head-on collisions of the two polymerases. Brewer also provided evidence that a head-on collision between polymerases could be fatal to the cell. Studies selected inversions of the E. coli chromosome to see the effects of collision. (Inversions are regions that have been cut out and put back in the opposite orientation.) It was impossible to isolate inversion mutations that changed the orientation of genes in respect to oriC. Thus, it appears that a cell may not be able to resolve a head-on collision of polymerases and that evolution has solved the problem by having gene transcription generally oriented in the same direction as DNA replication. More amazingly, Alberts and his colleagues recently studied what happens when a replication fork catches up to a stalled RNA polymerase. Not only does the replication fork pass the transcription apparatus, but the RNA polymerase can resume transcription after the replication fork passes without loss of the transcript. Although there are contrary observations in other systems, it appears that gene orientation and the behavior of polymerases allow cells to survive with both replication and transcription occurring on the same DNA.
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terminator in gure 10.10 has the sequence AAAGGCTCC, 5 3 , from both the left on the coding strand and from the right on the template strand. A four-basepair sequence separates the inverted repeats. Inverted repeats can form a stem-loop structure by pairing complementary bases within the transcribed messenger RNA. Both rho-dependent and rho-independent terminators have the stem-loop structure in RNA just before the last base transcribed. Rho-independent terminators, as gure 10.10 shows, also have a sequence of thyminecontaining nucleotides after the inverted repeat, whereas rho-dependent terminators do not. Although the exact
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sequence of events at the terminator is not fully known, it appears that the RNA stem-loop structure forms and causes the RNA polymerase to pause just after completing it. This pause may then allow termination under two different circumstances. In rho-independent terminators, the pause may occur just after the sequence of uracils is transcribed ( g. 10.11). Uracil-adenine base pairs have two hydrogen bonds and are thus less stable thermodynamically than guanine-cytosine base pairs. Perhaps during the pause, the uracil-adenine base pairs spontaneously denature, releasing the transcribed RNA and the RNA polymerase,
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Tamarin: Principles of Genetics, Seventh Edition
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III. Molecular Genetics
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10. Gene Expression: Transcription
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Prokaryotic DNA Transcription
oriC
rpmH dnaA dnaN recF gyrB gyrA rrnO rrnA
rplP rpmC rpsQ rplN rplX rplE rps rps N H
am y ou E tm tB rB
gerA III gerA II gerA I citG
trx uvrB ask sdhC sdhA sdhB gerE ilvB ilvN ilvC A leu C leu B leu D leu
sE rp D rpm cY se fA in J rpm rpsM rpsK rpoA rplQ
rE pu rK pu rB pu rC pu Q r pu rL pu F pur purM purN purH purO
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rpmA B spoO obg B phe A e ph
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dn rp aE trp oD E trp D trp C trpF trpB trpA hisH tyrA aroE
sp fts oVE A
sp II sp oIIA o sp VA C oV A A sp oV B spo AC V spo AD VAE
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Location and orientation of gene transcription on the chromosome of Bacillus subtilis (arrows). DNA replication begins at oriC and terminates approximately 180 degrees from the origin of replication. Note that the overwhelming number of arrows point away from the origin of replication toward the termination point. (From D. R. Zeigler and D. H. Dean, Orientation of genes
in the Bacillus subtilis chromosome, Genetics, 125:703 8. Copyright 1990 Genetics Society of America.)
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