Transcription (part -2) Prokaryotic V/S Eukaryotic transcription

The general process of transcription can be applied to both prokaryotic cells and eukaryotic cells. The basic biochemistry for each is the same; however, the specific mechanisms and regulation of transcription differ between prokaryotes and eukaryotes. 

Transcription of eukaryotic genes is far more a complicated process than prokaryotes. The important points of differences are as follows:

1) Location

• In prokaryotes (bacteria), transcription occurs in the cytoplasm (figure-1-A)
• Translation of the mRNA into proteins also occurs in the cytoplasm (figure-1-B)
• In eukaryotes, transcription occurs in the cell’s nucleus. mRNA then moves to the cytoplasm for translation.

                    

(A)            

                   

                                                   

 

 

 

(B)

Figure-1- (A)- Showing eukaryotic transcription, (B)- Prokaryotic transcription

2) Genome size

• The genome size is much larger in eukaryotes,
•  Greater specificity is needed for the transcription of eukaryotic genes.

3) Chromatin structure

• DNA in prokaryotes is much more accessible to RNA polymerase than DNA in eukaryotes.
• Eukaryotic DNA is wrapped around proteins called histones to form structures called nucleosomes (Figure-2)
• Eukaryotic DNA is packed to form chromatin (Figure-2).
• While RNA polymerase interacts directly with prokaryotic DNA, other proteins mediate the interaction between RNA polymerase and DNA in eukaryotes.

Figure-2- showing chromatin structure.

4)  RNA polymerases

• There are three distinct classes of RNA polymerases in eukaryotic cells. All are large enzymes with multiple subunits. Each class of RNA polymerase recognizes particular types of genes.
• RNA polymerase I- Synthesizes the precursor of the large ribosomal RNAs (28S, 18S, and 5.8S).
• RNA polymerase II – Synthesizes the precursors of messenger RNA and small nuclear RNAs(snRNAs).
• RNA polymerase III- synthesizes small RNA, including t RNAs, small 5S RNA, and some snRNAs.

 5) Promoter regions

• Eukaryotic promoters are more complex.
• Two types of sequence elements are promoter-proximal and distal regulatory elements.
• There are two elements in promoter-proximal, One of these defines where transcription is to commence along the DNA, and the other contributes to the mechanisms that control how frequently this event is to occur.(Figure-3)
• Most mammalian genes have a TATA box that is usually located 25–30 bp upstream from the transcription start site.
• The consensus sequence for a TATA box is TATAAA, though numerous variations have been characterized. 
• Sequences farther upstream from the start site determine how frequently the transcription event occurs.
• Typical of these DNA elements are the GC and CAAT boxes, (Figure-3) so named because of the DNA sequences involved.
• Each of these boxes binds a specific protein.
• Distal regulatory elements enhance or decrease the rate of transcription.
• They include the enhancer/ silencer regions and other regulatory elements (figure-3).

Figure-3- showing that a gene can be divided into its coding and regulatory regions, as defined by the transcription start site (arrow; +1). The coding region contains the DNA sequence that is transcribed into mRNA, which is ultimately translated into protein. The regulatory region consists of two classes of elements. One class is responsible for ensuring basal expression. These elements generally have two components. The proximal component, generally the TATA box, or Inr or DPE elements direct RNA polymerase II to the correct site (fidelity). In TATA-less promoters, an initiator (Inr) element that spans the initiation site (+1) may direct the polymerase to this site. Another component, the upstream elements, specifies the frequency of initiation. Among the best studied of these is the CAAT box, but several other elements may be used in various genres. The distal regulatory elements consist of enhancers and repressors and other regulatory regions. Enhancers and repressors enhance or repress expression and mediate the response to various signals, including hormones, heat shock, heavy metals, and chemicals. 

6) Promoter identification

• In contrast to the situation in prokaryotes, eukaryotic RNA polymerases alone are not able to discriminate between promoter sequences and other regions of DNA
• The TATA box is bound by 34 kDa TATA-binding protein (TBP), which in turn binds several other proteins called TBP-associated factors (TAFs).
• This complex of TBP and TAFs is referred to as TFIID (Figure-4).

Figure-4-The eukaryotic basal transcription complex. The formation of the basal transcription complex begins when TFIID binds to the TATA box. It directs the assembly of several other components by protein-DNA and protein-protein interactions. The entire complex spans DNA from position -30 to +30 relative to the initiation site.

• Binding of TFIID to the TATA box sequence is thought to represent the first step in the formation of the transcription complex on the promoter.(Figure-4)
• Another set of proteins—coactivators—help regulate the rate of transcription initiation by interacting with transcription activators that bind to upstream DNA elements (figure-5)

7) Enhancers and Repressors

• A third class of sequence elements can either increase or decrease the rate of transcription initiation of eukaryotic genes (Figure-4)
•  These elements are called either enhancers or repressors (or silencers), depending on which effect they have.
• They have been found in a variety of locations both upstream and downstream of the transcription start site and even within the transcribed portions of some genes.
• In contrast to proximal and upstream promoter elements, enhancers and silencers can exert their effects when located hundreds or even thousands of bases away from transcription units located on the same chromosome.
• Hormone response elements (for steroids, T₃, retinoic acid, peptides, etc) act as—or in conjunction with—enhancers or silencers

Figure-5- Showing promoter identification and formation of basal transcription complex. The basal transcription complex is assembled on the promoter after the TBP subunit of TFIID is bound to the TATA box. Several TAFs (coactivators) are associated with TBP. TAFs, since they are required for the action of activators, are often called coactivators. There are thus three classes of transcription factors involved in the regulation of class II genes: basal factors, coactivators, and activator-repressors.

7) Termination of transcription

• The signals for the termination of transcription by eukaryotic RNA polymerase II are very poorly understood.

8) Processing of primary  transcript

• mRNA produced as a result of transcription is not modified in prokaryotic cells. Eukaryotic cells modify mRNA by RNA splicing, 5′ end capping, and addition of a polyA tail.
• Most eukaryotic RNAs are synthesized as precursors that contain excess sequences that are removed prior to the generation of mature, functional RNA.

 To be continued…