1. Gene expression

1.2. Prokaryotic Transcription

The process of  transcription occurs in the nucleus of the cell in eukaryotes  and the mRNA transcript must be transported to the cytoplasm for protein synthesis . In prokaryotes, which lack membrane-bound nuclei and other organelles, transcription occurs in the cytoplasm of the cell. Therefore, the processes of transcription and  translation,  can all occur simultaneously. This is referred to as  . The intracellular level of a bacterial protein can quickly be amplified by multiple transcription and translation events occurring concurrently on the same DNA template. Prokaryotic transcription often covers more than one gene and produces polycistronic mRNAs that specify more than one protein.
The Process of Prokaryotic Transcription

The first step in transcription is initiation, when the RNA pol binds to the DNA upstream (5′) of the gene at a specialized sequence called a promoter .

Prokaryotic Promoters
  • The DNA sequence onto which the proteins and enzymes involved in transcription bind to initiate the process is called a. Promoters usually exist upstream of the genes they regulate. The specific sequence of a promoter determines whether the corresponding gene is transcribed all of the time, some of the time, or hardly at all. The structure and function of a prokaryotic promoter is relatively simple 
  • The -10 consensus sequence or the Pribnow box  : In prokaryotes, most genes have a sequence called the Pribnow box, with the consensus sequence TATAAT positioned about ten base pairs away from the site . This serves as the location of transcription initiation. Not all Pribnow boxes have this exact nucleotide sequence; these nucleotides are simply the most common ones found at each site.
  • The -35 consensus sequence : Many genes also have the consensus sequence TTGCCA at -35  position, upstream of the start site
  • Upstream element  : an A-T rich region 40 to 60 nucleotides upstream that enhances the rate of transcription

The process of transcription starts with the binding of  the RNA pol “holoenzyme” binding to the template DNA and  unwinds  the DNA double helix in order to facilitate access to the gene. The sigma subunit conveys promoter specificity to RNA polymerase; that is, it instructs the  RNA polymerase where to bind. There are a number of different sigma subunits that bind to different promoters. These sigma subunits assist in turning genes on and off as conditions change.

The mRNA product is complementary to the template strand and is almost identical to the other DNA strand, called the non-template strand, with the exception that RNA contains a uracil (U) in place of the thymine (T) found in DNA. Like DNA polymerase, RNA polymerase adds new nucleotides onto the 3′-OH group of the previous nucleotide. This means that the growing mRNA strand is being synthesized in the 5′ to 3′ direction.

Elongation

Once transcription is initiated, the DNA double helix unwinds and RNA polymerase reads the template strand. 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 .

Nucleotides  are added to the 3′ end of the growing chain . At a temperature of 370 C new nucleotides are added at an estimated rate of about 42-54 nucleotides per second in bacteria. As elongation proceeds, the DNA is continuously unwound ahead of the core enzyme and rewound behind it. The base pairing between DNA and RNA is not stable enough to maintain the stability of the mRNA synthesis components. Instead, the RNA polymerase acts as a stable linker between the DNA template and the nascent RNA strands to ensure that elongation is not interrupted prematurely.

Termination

Once a gene is transcribed, the prokaryotic 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 namely :

  1. Rho-dependent or Extrinsic termination : Termination is controlled by the rho protein.The rho protein 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. Rho unwinds the DNA-RNA hybrid formed during transcription and releases the mRNA from the transcription bubble.
  2. Rho-independent or Intrinsic termination is controlled by  C–G nucleotide sequences in the DNA template strand at the end of the gene being transcribed. Due to the self complementary nature of the C-G nucleotides . The mRNA folds back on itself, and form a stable hairpin . This causes the polymerase to stall and  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 fact together  with the stalled polymerase, induces enough instability for the core enzyme to break away and liberate the new mRNA transcript.

Upon termination, the process of transcription is complete. By the transcription would end the prokaryotic transcript would  have already commenced the   synthesis of numerous copies of the encoded protein .