Transcription in Eukaryotes and Prokaryotes

Transcription is vitally important for each living cell. The word transcription comes from France and means writing. DNA protects and carries the information of proteins and it needs to read codes using elements. In this post, I will clarify these elements.

At the beginning, the cell needs to initiate the process. At this point, the process is diverted because we have different types of initiation between prokaryotes and eukaryotes. Also, genes are coded with special elements such as TATA box and Enhancer proteins. Firstly we will talk about the TATA box. The TATA box fulfills the purpose of recognition. TATA is the repetition of timin and adenin. Why adenin and timin? Adenin and timin have two hydrogen bonds, compared with guanine and gytosine which have three hydrogen bonds. T-A (timin and adenin) bonds break easier than G-C (guanine and cytosine) bonds. Prokaryote initiation is more simple than eukaryote and starts with sigma factor (sigma factor is a subunit of the RNA polymerase). Sigma factor helps RNA polymerase find TATA box. When the sigma factor binds to TATA box RNA polymerase automatically binds with TATA box and this binding makes a conformational change. During this process, DNA and RNA polymerase make an open complex and RNA polymerase transcribes some unnecessary RNA’s. RNA polymerase tests whether it can really read RNAs or not and this synthesis is named abortive initiation. After this, the abortive initiation elongation part starts. RNA polymerase transcribes the mRNA, following this, a special code such as gcgcgcgcgc finishes the elongation process and transcribes an RNA firket to start termination and it makes RNA polymerase slower. After the gcgcgcg point, there is another special code: atatatat. This code is unstable. RNA polymerase after the RNA firket exits atata. In prokaryotes the transcription initiation is as simple as that.

Transcription initiation in eukaryotes is a bit harder than the process described previously. The process I want to describe involves a series of agents. You can come back and read this part again to understand what is happening. We have three different RNA Polymerase such as RNA polymerase I (Transcribes especially rRNA’s genes), RNA polymerase II (transcribes all mRNA’s, only RNA polymerase II has the ctd tail), RNA polymerase III (transcribes especially tRNA’S genes). TFIID helps in TATA box recognition and starts the initiation. TFIID has a subunit called like TBP ( tata box binding protein). TAF; transcription association factor, helps to disassociate. TFIIB locates RNA polymerase correctly. TFIIF works like an eye for RNA polymerase and it recognizes the general transcription factor. Finally, TFIIE and TFIIH work together. TFIIE regulates TFIIH. TFIIH has two important jobs to do, which are kinases the CTD (C terminus domain of RNA polymerase), and carrying the helicase activity enzymes on CTD.

We talked about General Transcription Factors. Let’s start the transcription initiation process in eukaryotes. First of all, the process starts with TFIID. The subunit of TFIID, which is TBP, recognizes the TATA box and binds this region to make a conformational change. After that TAF and TFIIB become involved and bind the region for RNA polymerase. RNA polymerase includes TFIIF, TFIIE, and TFIIH and binds the TATA box region. When TFIID is locating the TATA box, RNA polymerase cannot start elongation. TFIIE recognizes the gene start point and after that regulates TFIIH. TFIIH directly kinases the CTD. It makes TAF active and all transcription factors are released. The final stage of iniatition is RNA polymerase starts elongation.

There are some special processes as well when we compare transcription initiation in eukaryotes with prokaryotes such as 5′ capping for the beginning of mRNA and 3′ poly-Adenylation for Ending of mRNA. This mechanism protects mRNA with a cell defense system. 5′ capping requires typical enzymes such as phosphatases, Guanyl transferase, Methyltransferase. 3′ polyadenylation is more complicated. This two type modification happens only while using RNA polymerase II because RNA polymerase II has a tail which is called CTD and it carries 5′ capping and 3′ polyadenylation enzymes (CstF and CSPF). When RNA polymerase reaches the stop codon sequence CSPF directly bind this mRNA region and helps to cleave. After cleaving, PAP (polyadenylation polymerase) begins and starts writing the AAAA region and to regulate this process, PABP (polyadenylation binding proteins) begins and binds each Adenin sequence. When it reaches a number close to 200, nucleotide bases PABP make a conformational change and PAP exits the sequence.

The most complicated part is the splicing of pre mRNA to become Mature mRNA. As you know genes encode exons and introns. Exons are important for protein-coding and we need to separate exons and introns from each other. Eukaryote cells are adapted for that and use splicing. Firstly, I will explain the agents of splicing. We have special agents for splicing such as snRNP’s(Spliceosomes, protein + snRNA combination) U1, U2, U4, U5, U6. U6 and U4 are haloenzymes, BEF (Branch point binding protein) and U2AF (U2 auxiliary factor). U1 is always located in the intron starting point and BEF and U2AF are always located in the intron ending point and exon starting point. When U2 spliceosome has reached this region, U2AF helps for rearrangement to reach BEF to U2. When U2 has bound the region U1 connects the U2 and U4-U6, U5 binds the region of the splicing point and makes a binding point. U4 and U6 separate from each other and U6 make a rearrangement with U1, and U1 and U4 are released from the region.They makes a lariat point and end of these lariat , Intron part just cleaved. U6 binds exons together.End of the process Exon juction factor joins.

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