Any protein that propels itself alone along a DNA strand of a double helix, such as a DNA helicase or an RNA polymerase, tends to generate superhelical tension. In eukaryotes, DNA topoisomerase enzymes rapidly remove this superhelical tension (see pp. 251–253). But in bacteria a specialized topoisomerase called DNA gyrase uses the energy of ATP hydrolysis to pump supercoils continuously into the DNA, thereby maintaining the DNA under constant tension. These are negative supercoils, having the opposite handedness from the positive supercoils that form when a region of DNA helix opens (see Figure 6–19B). Whenever a region of helix opens, it removes these negative supercoils from bacterial DNA, reducing the superhelical tension. DNA gyrase therefore makes the opening of the DNA helix in bacteria energetically favorable compared with helix opening in DNA that is not supercoiled. For this reason, it facilitates those genetic processes in bacteria, such as the initiation of transcription by bacterial RNA polymerase, that require helix opening (see Figure 6–11).
Transcription Elongation in Eukaryotes Is Tightly Coupled to RNA Processing
We have seen that bacterial mRNAs are synthesized by the RNA polymerase starting and stopping at specific spots on the genome. The situation in eukaryotes is substantially different. In particular, transcription is only the first of several steps needed to produce a mature mRNA molecule. Other critical steps are the covalent modification of the ends of the RNA and the removal of intron sequences that are discarded from the middle of the RNA transcript by the process of RNA splicing (Figure 6–20).
Both ends of eukaryotic mRNAs are modified: by capping on the 5ʹ end and by polyadenylation of the 3ʹ end (Figure 6–21). These special ends allow the cell to assess whether both ends of an mRNA molecule are present (and if the message is therefore intact) before it exports the RNA from the nucleus and translates it
Figure 6–20 Comparison of the steps leading from gene to protein in eukaryotes and bacteria. The final level of a protein in the cell depends on the efficiency of each step and on the rates of degradation of the RNA and protein molecules. (A) In eukaryotic cells, the mRNA molecule resulting from transcription contains both coding (exon) and noncoding (intron) sequences. Before it can be translated into protein, the two ends of the RNA are modified, the introns are removed by an enzymatically catalyzed RNA splicing reaction, and the resulting mRNA is transported from the nucleus to the cytoplasm. For convenience, the steps in this figure are depicted as occurring one at a time; in reality, many occur concurrently. For example, the RNA cap is added and splicing begins before transcription has been completed. Because of the coupling between transcription and RNA processing, intact primary transcripts—the full-length RNAs that would, in theory, be produced if no processing had occurred—are found only rarely. (B) In prokaryotes, the production of mRNA is much simpler. The 5ʹ end of an mRNA molecule is produced by the initiation of transcription, and the 3ʹ end is produced by the termination of transcription. Since prokaryotic cells lack a nucleus, transcription and translation take place in a common compartment, and the translation of a bacterial mRNA often begins before its synthesis has been completed.
prokaryotic mRNA 5˜ end of coding noncoding 7-methylguanosine primary transcript sequence sequence