Mechanism of Transcription in Prokaryotes

Explain The Process of Transcription in Prokaryotes

Transcription is the process of RNA synthesis using DNA as a template, catalyzed by RNA polymerase. It is also the first step of gene expression. While it is a common process occurring in both prokaryotes and eukaryotes, the mechanism is different in each. 

Mechanism of Transcription in Prokaryotes

In prokaryotes, transcription starts with the recognition of the promoter gene or the specific sequence on the DNA by the RNA polymerase. 

• When the enzyme recognises the promoter gene, it binds itself to the single strand or the template strand of DNA.
• It is the sigma factor of RNA polymerase that recognizes the promoter, binds to the DNA< and initiates transcription or RNA synthesis.
• The promoter sequence serves as the landing site for the RNA polymerase.
• When the enzyme binds to the promoter, the DNA duplex is opened and unwound to form the transcription bubble.
• It is within this transcription bubble where the RNA synthesis takes place.
• The double-stranded DNA gets separated to form single strands and serves as the template strand.

Enzymes Involved In Transcription In Prokaryotes

There are various enzymes involved in the transcription process in prokaryotes. Enzymes used for prokaryotic transcription fall under the category of RNA polymerase. 

The bacterial RNA polymerase is one of the extensively studied enzymes. It has a molecular weight of 450k and has 5 subunits. It is these subunits that control the transcription process. 

Subunits of RNA Polymerase

The bacterial RNA polymerase consists of 

• 2 ⍺ subunits
• One ꞵ subunit
• One ꞵ’ subunit
• One sigma subunit

These subunits together form the holoenzyme. This holoenzyme is separated into 2 compartments known as the core enzyme and the sigma factor. 

• The two ⍺ subunits, ꞵ and ꞵ’ subunits, together form the core enzyme, while the sigma subunit is the sigma factor.
• Moreover, the ꞵ and ꞵ’ subunits together make the catalytic centre.

Once the initiation process starts, the sigma factor dissociates itself from the RNA polymerase and makes itself available for other holoenzyme formation. The further process of transcription is catalysed by the core enzyme. 

Steps of Transcription in Prokaryotes

Transcription happens in three steps- initiation, elongation, and termination.  

Initiation

Initiation is the process where the RNA polymerase identifies the promoter gene sequence and binds itself loosely to the template DNA strand. 

• While the holoenzyme of RNA polymerase can initiate transcription, only the sigma factor recognizes and binds the RNA polymerase to the promoter site to initiate the transcription process.
• The sigma factor not only recognises the promoter sequence but can also ensure that the enzyme stays bound to the DNA template for hours.
• When the RNA polymerase binds to DNA, it is called a closed complex.
• The enzyme creates an opening on the template strand to convert it into an open promoter complex.
• The RNA polymerase melts a small region of DNA within the transcription bubble.
• Opening the DNA strand increases the affinity of RNA polymerase, and binding becomes tighter.
• The core enzyme is responsible for adding the RNA precursors and elongating the chain.
• At a time, 10-12 nucleotides of the RNA chain will be bonded to the DNA template.
• RNA chain grows with the addition of 2-9 bases, and this short chain is released to make way for the addition of more base pairs.
• As the RNA chain starts growing, the sigma factors detach themselves, and the initiation process comes to an end.

Elongation

Elongation is the process of lengthening the RNA chain by the addition of more nucleotides by polymerization. 

• As each nucleotide is polymerized, the core enzyme moves along the template DNA, and the chain elongates.
• The elongation of the RNA chain happens simultaneously with the separation of the two strands of the DNA for a continuous synthesis of RNA.
• While the DNA strand is separated in one direction, the renaturation of DNA happens at the other end, keeping the DNA helix intact.
• RNA synthesis happens in the 5’ to 3’ direction.
• The elongation process continues until the core enzyme of RNA polymerase reaches the termination sequence.

Termination

Termination is the culmination of RNA synthesis and the detachment of the RNA polymerase enzyme.  The template DNA strand contains specific sequences known as termination sequences that mark the end of a code. 

As the RNA polymerase reaches such a sequence, the elongation process stops. At this point, it stops adding any more nucleotides to the growing RNA chain. 

Termination Sequence in E. coli

In E. coli, there are two identified termination sequences.

1. Intrinsic termination

Intrinsic Termination has two special features- a hairpin-shaped structure and a U-shaped structure. The former is rich in the G-C region, helping to identify the termination sequence. 

2. Rho factor

Rho factor is a protein that helps the RNA polymerase identify termination sequences. 

• In such cases, the termination sequence will be 60-90 base pairs long, rich in C residues.
• The Rho factor attaches to the RNA polymerase, runs along the enzyme, and reaches the sequence.
• While the enzyme pauses RNA synthesis, termination happens only when the Rho factor reaches the termination sequence.

In the absence of RNA polymerase, the Rho factor can act as a helicase and break the H-bond between the DNA and RNA. This will be an ATP-dependent reaction followed by the renaturation of the DNA duplex.

References

Chhakchhuak, Passong & Khatri, Ajay & Sen, Ranjan. (2018). Mechanism of Action of Bacterial Transcription Terminator Rho. Proceedings of the Indian National Science Academy. 84. 10.16943/ptinsa/2018/49436.

Additional Topics

• Distinguish Between Prokaryotic and Eukaryotic Cells