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Initiation of Transcription in Bacteria
Bacteria do not have membrane-enclosed nuclei. Therefore, the processes of transcription, translation, and mRNA degradation can all occur simultaneously. The intracellular level of a bacterial protein can quickly be amplified by multiple transcription and translation events that occur concurrently on the same DNA template. Bacterial genomes are very compact. To maximize efficiency, genes with related functions are often grouped together on the DNA under the control of a single promoter. This functional cluster is called an operon. Because the entire operon is transcribed together in a single run, the resulting mRNA transcript covers more than one gene or cistron (a coding sequence for a single protein). These polycistronic mRNAs are then translated to produce multiple distinct types of proteins at the same time.
Figure 3.4 Structure of the genes in the alpha operon of e. coli. All of these genes are under the control of one promoter and would be transcribed into one mRNA, and then translated into separate proteins.
Our discussion here will exemplify transcription by describing this process in Escherichia coli, a well-studied model species. An understanding of E. coli transcription can be applied to virtually all bacterial species.
Bacterial RNA Polymerase
Bacteria use the same RNA polymerase to transcribe all of their genes. In E. coli, the polymerase is composed of six polypeptide subunits: two identical \(\alpha \) subunits, one \(\beta \) subunit, one \(\beta ^{\prime }\) subunit, and a small stabilizing \(\omega \) subunit. These subunits make up the core enzyme and assemble every time a gene is transcribed, and they disassemble once transcription is complete. Each subunit has a unique role; the two α-subunits are necessary to assemble the polymerase on the DNA; the β-subunit binds to the ribonucleoside triphosphate that will become part of the nascent mRNA molecule; the β' subunit binds the DNA template strand; and the \(\omega \) subunit stabilizes the core enzyme. The sixth subunit, σ (sigma) factor, is involved only in transcription initiation. It confers transcriptional specificity so that the polymerase begins to synthesize mRNA at the correct initiation site. Without the σ subunit, the core enzyme would transcribe from random sites and would produce mRNA molecules that specified protein gibberish. The polymerase comprised of all five subunits is called the holoenzyme.
Because the core enzyme handles the actual synthesis of all RNA molecules, bacteria require only a single type of RNA polymerase to transcribe all of their genes. To change which genes are being transcribed, the cell simply switches out the σ factor. The primary σ factor (such as σ⁷⁰ in E. coli) directs the holoenzyme to standard housekeeping genes needed for everyday growth. However, under environmental stress, such as starvation or extreme heat, the cell can synthesize alternative σ factors. These alternative factors displace the primary σ factor, shifting the holoenzyme’s focus to a completely new set of promoters to help the cell survive.
Bacterial Promoters
A promoter is a DNA sequence onto which the transcription machinery, including RNA polymerase, binds and initiates transcription. In most cases, promoters exist upstream of the genes they regulate. The specific sequence of a promoter is very important because it determines whether the corresponding gene is transcribed all the time, some of the time, or infrequently. Although promoters vary among bacterial genomes, a few elements are evolutionarily conserved in many species. At the -10 and -35 regions upstream of the initiation site, there are two promoter consensus sequences, or regions that are similar across all promoters and across various bacterial species (Figure 3.5). The -10 sequence, called the -10 region, or Pribnow Box, has the consensus sequence TATAAT. The -35 sequence has the consensus sequence TTGACA. These consensus sequences are recognized and bound by σ. Once this interaction is made, the subunits of the core enzyme bind to the site. The A–T-rich -10 region facilitates unwinding of the DNA template. Before the holoenzyme can move down the DNA, it often goes through a trial-and-error process called abortive initiation. Because the holoenzyme is tightly bound to the promoter, it repeatedly synthesizes and releases short RNA fragments (approximately 10 nucleotides long) without moving forward. The initiation phase officially ends only when the enzyme successfully builds a slightly longer transcript, breaks its grip on the promoter and releases the sigma factor.
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View this MolecularMovies animation to see the transcription process as it happens in the cell.
Elongation
The transcription elongation phase begins with the release of the σ subunit from the polymerase. The dissociation of σ allows the core enzyme to proceed along the DNA template, synthesizing mRNA in the 5' to 3' direction at a rate of approximately 40 nucleotides per second. As elongation proceeds, the DNA is continuously unwound ahead of the core enzyme and rewound behind it. The hydrogen bonds between the template DNA and the newly formed RNA strand are too weak to hold the heavy transcription machinery together on their own. Instead, the RNA polymerase itself acts as a bridge, tightly gripping both the DNA template and the nascent RNA. By physically anchoring these strands within its protein core, the enzyme prevents the fragile complex from falling apart prematurely during elongation.
Bacterial Termination Signals
Once a gene is transcribed, the RNA polymerase needs to be instructed to dissociate from the DNA template and liberate the newly made mRNA. Depending on the gene being transcribed, there are two kinds of termination signals. One is protein-based and the other is RNA-based. Rho-dependent termination is controlled by the rho protein, which tracks along behind the polymerase on the growing mRNA chain. Near the end of the gene, the polymerase encounters a run of G nucleotides on the DNA template and it stalls. As a result, the rho protein collides with the polymerase. The interaction with rho releases the mRNA from the transcription bubble.
Rho-independent termination, also called intrinsic termination, is controlled by specific sequences in the DNA template strand. As the polymerase nears the end of the gene being transcribed, it encounters a region rich in C–G nucleotides. The mRNA folds back on itself, and the complementary C–G nucleotides bind together. The result is a stable hairpin that causes the polymerase to stall as soon as it begins to transcribe a region rich in A–T nucleotides. The complementary U–A region of the mRNA transcript forms only a weak interaction with the template DNA. This, coupled with the stalled polymerase, induces enough instability for the core enzyme to break away and liberate the new mRNA transcript.
Figure 3.6 Comparison of Rho-independent (A) and Rho-dependent (B) termination
Upon termination, the process of transcription is complete. By the time termination occurs, the bacterial transcript would already have been used to begin synthesis of numerous copies of the encoded protein because transcription and translation can occur concurrently. The unification of transcription, translation, and even mRNA degradation is possible because all of these processes occur in the same 5' to 3' direction, and because there is no membranous compartmentalization in the prokaryotic cell (Figure 15.9). In contrast, the presence of a nucleus in eukaryotic cells precludes simultaneous transcription and translation.
Key Terms
Polycistronic mRNA
An mRNA molecule that encodes multiple proteins.
Operon
A cluster of genes transcribed together from a single promoter.
Sigma (σ) Factor
A protein that directs bacterial RNA polymerase to promoter sequences.
RNA Polymerase Holoenzyme
The bacterial RNA polymerase core enzyme bound to a sigma factor.
Promoter
A DNA sequence where transcription begins.
–10 Region (Pribnow Box)
An AT-rich promoter sequence recognized during transcription initiation.
–35 Region
A conserved promoter sequence recognized by sigma factors.
Rho-Independent Termination
Termination caused by the formation of an RNA hairpin followed by a string of uracils.
Rho-Dependent Termination
Termination requiring the Rho helicase protein.
Check Your Understanding
- Why do bacteria require only one RNA polymerase?
- What is the function of a sigma factor?
- What are the –10 and –35 promoter regions?
- What happens to the sigma factor after transcription begins?
- Compare rho-independent and rho-dependent termination.
- Why can transcription and translation occur simultaneously in bacteria?
- What is a polycistronic mRNA?
- Why are operons beneficial to bacterial cells?
This page titled 1.3.2: Bacterial Transcription was last modified on Thu, 20 Aug 2026 01:22:11 GMT and is shared under a CC BY 4.0 license and was authored, remixed, and/or curated by OpenStax via source content that was edited to the style and standards of the LibreTexts platform.
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