Key Concepts of Section 9.1

• Gene expression in both prokaryotes and eukaryotes is regulated primarily by mechanisms that control gene transcription.

• The first step in the initiation of transcription in E. coli is the binding of a σ-factor complexed with an RNA polymerase to a promoter.

• The nucleotide sequence of a promoter determines its strength, that is, how frequently different RNA polymerase molecules can bind and initiate transcription per minute.

• Repressors are proteins that bind to operator sequences that overlap or lie adjacent to promoters. Binding of a repressor to an operator inhibits transcription initiation or elongation.

• The DNA-binding activity of most bacterial repressors is modulated by small-molecule ligands. This allows bacterial cells to regulate transcription of specific genes in response to changes in the concentration of various nutrients in the environment and metabolites in the cytoplasm.

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• The lac operon and some other bacterial genes are also regulated by activator proteins that bind next to a promoter and increase the frequency of transcription initiation by interacting directly with RNA polymerase bound to that promoter.

• The major sigma factor in E. coli is σ⁷⁰, but several other, less abundant sigma factors are also found, each recognizing different consensus promoter sequences or interacting with different activators.

• Transcription initiation by all E. coli RNA polymerases, except those containing σ⁵⁴, can be regulated by repressors and activators that bind near the transcription start site (see Figure 9-4).

• Genes transcribed by σ⁵⁴-RNA polymerase are regulated by activators that bind to enhancers located about 100 base pairs upstream from the start site. When the activator and σ⁵⁴-RNA polymerase interact, the DNA between their binding sites forms a loop (see Figure 9-5).

• In two-component regulatory systems, one protein acts as a sensor, monitoring the level of nutrients or other components in the environment. Under appropriate conditions, the γ-phosphate of an ATP is transferred first to a histidine in the sensor protein and then to an aspartic acid in a second protein, the response regulator. The phosphorylated response regulator then performs a specific function in response to the stimulus, such as binding to DNA regulatory sequences, thereby stimulating or repressing transcription of specific genes (see Figure 9-6).

• Transcription in bacteria can also be regulated by control of transcriptional elongation in the promoter-proximal region. This control can be exerted by ribosome binding to the nascent mRNA, as in the case of the E. coli trp operon (see Figure 9-7), or by riboswitches, RNA sequences that bind small molecules, as for the B. subtilis xpt-pbuX operon (see Figure 9-8), to determine whether a stem-loop followed by a string of uracils forms, causing the bacterial RNA polymerase to pause and terminate transcription.