The DNA sequence below is a segment of a protein coding gene. It includes the promoter region and the beginning of the
sequence to be transcribed. The transcription start site is indicated by the +1. To begin, drag and drop the appropriate
icons onto the DNA to establish the -35 and -10 promoter sequences.
Bacterial RNA polymerase cannot associate with DNA on its own; it requires an additional factor to help it recognize specific
regulatory sequences. Locate this factor in the palette and bring it to the RNA polymerase.
The RNA polymerase complex is now ready to go! Drag and drop the complex onto the region of DNA that it recognizes. [Note:
The RNA polymerase complex shown here is not drawn to scale—in reality it spans approximately 100 bp of DNA.]
Once the σ70-RNA polymerase complex binds to the promoter region of DNA, spontaneous isomerization converts the complex from a closed
state to an open state, where a bubble of the duplex DNA is separated in preparation for transcription.
Congratulations, you’ve formed the open complex and are ready to begin RNA synthesis! Your next task is to synthesize RNA. The
floating green letters represent RNA nucleotides. Using one DNA strand as a template, drag and drop the RNA nucleotides to the template,
to initiate formation of the RNA transcript.
The polymerase, after abortive initiation, has reset to the transcription start site and RNA synthesis is attempted again. Your task
is to drag and drop RNA nucleotides (floating green letters) to the template to reinitiate formation of the RNA transcript.
Transcription initiation was successful! The polymerase complex has stabilized. Transcription has entered the elongation phase,
and will continue along the DNA until the polymerase reaches a termination signal. For clarity, the RNA transcript simulated
here is short. Actual bacterial transcripts are many hundreds of bases.
Simulating RNA transcription elongation....the simulation will stop when the sequence that signifies the termination type is visible. When this happens, it is your task to drag-and-drop the correct symbol for the termination type onto the signature sequence.
The RNA polymerase has transcribed a termination sequence, and transcription has paused. Examine the RNA transcript to determine the
type of termination that will occur. From the palette, identify the factor required for this type of termination and bring it to the
appropriate sequence in the RNA transcript.
Great job! You you correctly identified the termination type as ρ-dependent. The hexameric ρ-helicase uses ATP to move along the
RNA transcript toward the RNA polymerase, which results in release of the RNA transcript from the DNA template and the polymerase.
Great job! You correctly identified the termination type as ρ-independent. Formation of the hairpin in the RNA transcript disrupts
interactions between the RNA, DNA template, and RNA polymerase, leading to release of the RNA transcript.
RNA transcript is released from the DNA and polymerase. The resulting RNA transcript contains the transcription of the gene and the termination sequence.
Congratulations! You have successfully transcribed the bacterial protein-coding gene. Your score shows you have a solid understanding
of bacterial transcription. Click the button below to begin the Tutorial Comprehension Quiz.
Congratulations! You have successfully transcribed the bacterial protein-coding gene. However, your score indicates you have some
uncertainty with bacterial transcription. Consider reviewing your text, and then try the exercise again before taking the Tutorial
Comprehension Quiz.
Abortive initiation has occurred! In the initial stages of transcription, the association between the RNA, template, and polymerase
complex is tenuous. The polymerase often releases the nascent transcript without extending it further. The polymerase resets to the
transcription start site and RNA synthesis is attempted again.
Transcription Simulation
Transcription is the process of synthesizing RNA by using DNA as a template. This simulation explores the initiation, elongation,
and termination steps of bacterial transcription.
The promoter region of a bacterial protein coding gene is upstream of the transcription start site, and controls the timing of
transcription. Short stretches of sequence are conserved between many bacterial promoters, and these regions of consensus sequence are
known as the -10 region and the -35 region. The negative numbers represent their general distance (in base pairs) away from the
transcription start site. The consensus sequence for the -10 region is TATAAT. The consensus sequence for the -35 region is TTGACA.
Bacterial RNA polymerase cannot associate with DNA on its own. It requires a special protein called a sigma factor that recognizes
sequences in the -10 and -35 regions of the promoter. Different sigma factors recognize different sequences in these regions, and
therefore facilitate transcription of different sets of genes. The most common sigma factor in bacteria is σ70. The majority of bacterial
genes have -10 and -35 promoter sequences that are recognized by σ70.
RNA polymerases synthesize RNA 5´ to 3´. Therefore, the DNA strand used as a template is the one that is antiparallel to the growing RNA
strand.
Bacteria have two main types of termination sequences. The first is a CA-rich sequence called a rut site. ρ-helicase associates
with the rut site to facilitate release of the RNA transcript from the DNA template and the polymerase. The second type of termination
sequence has two distinguishing features—a region of the RNA transcript that is self-complementary, permitting formation of a hairpin,
and a highly conserved segment of three A residues in the template strand that are transcribed into U residues near the hairpin.
Hairpin formation disrupts RNA, DNA, and polymerase interactions, leading to release of the RNA transcript.
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Prerequisite skills needed:
DNA/RNA Structure and Base Pairing
Relevant book section: pages 1036-1042
By completing this simulation, you will:
Understand the chemical reactions underlying transcription in bacteria
Understand how the different components of transcription come together to transcribe DNA into RNA
Distinguish between two possible modes of transcription termination
