DNA is a special part of the cell. Without DNA, there would not have been life, evolution, survival, and existence. The base of synthesizing RNA starts from a DNA strand. Hence, DNA has a strict impact on the processes occurring in the body. DNA gets transcribed into RNA. Studying transcription helps to investigate how mutations affecting transcription cause inherited diseases. The first step involved in gene expression is transcription. Interested in cloning or treating a genetic disorder with DNA? Then keeping updates regarding transcription processes is helpful. RNA is a key nucleic acid involved in synthesizing proteins. Watson and Crick proposed the central dogma. It is a two-step process denoted as DNA leading to transcription of RNA and RNA leading to translation of the protein. Not all genes encode for proteins. Hence, not all DNA gets transcribed to RNA.
A gist of DNA replication:
Initiation of replication starts at a point where the unwinding of DNA takes place. Enzymes synthesize an RNA primer and the fragments so that new nucleotides get added. The segments get elongated through a process of elongation followed by removal of the primers. The unjoined fragments get ligated to end the process of replication. Using DNA as a template, the transcription starts.
RNA synthesis:
Genes are known as ordered sequences of nucleotide bases encoding polypeptide chains via RNA molecules. They are nothing but the pieces of DNA that consist of specific information for making a particular protein. Each gene associates with regulatory sequences known as gene regulatory elements. They are involved in regulation of transcription. The process of transcription starts with denaturation of the DNA double helix. The enzyme known as RNA polymerase catalyzes the process of transcription. In prokaryotes, RNA polymerase is responsible for unwinding. The process of unwinding in eukaryotes occurs with the help of other proteins. The DNA starts unwinding next to the gene involved the process. Hence, RNA polymerase starts catalyzing the RNA synthesis. The RNA gets synthesized from 5’-3’ direction along the 3’-5’ template strand. Out of the two DNA strands, only one strand participates in the process of transcription. Total four nucleotide phosphates act as precursors for transcription. They include ATP, GTP, CTP, and UTP. Recall that DNA synthesis requires RNA primers. However, RNA synthesis does not require primers. RNA polymerases are efficient in initiating the synthesis of new polynucleotide chains without any primers. Participant molecules in RNA synthesis are DNA strand, RNA polymerases, nucleoside triphosphates, elongation and termination factors. Also, there is a requirement of specific gene sequences for the initiation of transcription. In both prokaryotes and eukaryotes, the process of transcription occurs in three consecutive steps such as initiation, elongation, and termination. The eukaryotic transcription needs an understanding of prokaryotic transcription first.
A prokaryotic gene responsible for transcription needs the three following sequences:
A prokaryotic gene responsible for transcription needs the three following sequences:
· The promoter sequence is an upstream sequence present at the start of the RNA coding gene sequences.
· RNA coding gene sequences are known as DNA sequences capable of getting transcribed to RNA.
· The terminator specifies the destination point of transcription.
The genes specifying the initiation process have two promoter sequences known as -35 and -10. Each promoter has a specific consensus sequence.
Promoter region
|
No. of base pairs upstream
|
Consensus sequence
|
-35
|
35
|
5’-TTGACA-3’
|
-10
|
10
|
5’-TATAAT-3’
|
Table: Promoters -35 and -10 respectively.
Initiation:
RNA synthesis gets initiated by the recruitment of RNA polymerase holoenzyme. It binds to the promoter region. The holoenzyme consists of the core enzyme form of RNA polymerase. It has four polypeptides such as two α, one β, and one β’ polypeptides bound to a sigma factor. It recognizes both the promoter regions. It first recognizes -35 region where the DNA is a close promoter complex. Then the holoenzyme unwinds the DNA. The untwisted form of the promoter is known as an open promoter complex. The RNA polymerase orients itself to the Pribnow box for further process. Thus, the process of initiation includes two main steps. First, RNA polymerase gets attached to its core promoter. Second, the closed promoter gets converted into an open promoter complex. Then the RNA gets synthesized. For a successful initiation, RNA polymerase now moves away from the promoter region.
Image: Transcription in prokaryotes
Elongation and termination
The RNA polymerase approximately includes a 30 base pair of DNA. It includes a transcription bubble of 12-14 base pairs. The RNA gets attached to the template strand of the DNA. RNA-DNA base pairs assist the RNA in the attachment. The main feature of RNA polymerase observed during the elongation process does not constantly synthesize the transcript. Instead, it follows a discontinuous synthesis. The process of elongation although rapid gets interspersed by brief pauses. During brief pauses, the active site of the polymerase undergoes a slight structural conformation or gets rearranged. A pause lasts for a few milliseconds and accompanies backtracking thereby occurring randomly. A pause helps in termination of the transcript synthesis. The termination of transcription follows a signal given by terminator sequences. An important protein involved in the process of termination is known as rho (ρ). Hence, there are two types of terminator sequences known as Rho-dependent and Rho-independent terminators. The Rho-dependent terminators are known as type II terminators. They lack A-T string and avoid forming hairpin loops. Rho has RNA binding ATPase domain. Rho-independent terminators, on the other hand, form hairpin loops and consist of inverted repeat sequences. A string of AT base pairs transcribes a string of Us. When the inverted palindrome (with a hairpin loop) gets transcribed, there arises RNA-RNA base pairing. Studies revealed the presence of a flap structure on the surface of RNA polymerase which mediates in termination.
Anti-termination:
It is a process beyond termination. There is an anti-termination process too common in prokaryotes. Anti-termination occurs when RNA polymerase ignores a terminator signal and continues to elongate the transcript until the next signal. Anti-termination provides a mechanism through which few genes at the end of the operon get switched off. Anti-termination protein attaches to the DNA and transfers to the RNA polymerase. However, the reason behind switching off those genes remains unclear.
Premature termination and attenuation:
The primary transcript produced by RNA polymerase is known as a mature mRNA. The bacteria involve coupled transcription and translation. It allows a special type of control known as attenuation. It is a process in which the expression of amino acid biosynthesis gets regulated. Some of the bacteria get bacteriophage infection. Bacteriophages transcribe their genomes using bacterial RNA polymerases.
References:
[1] Transcription, William M. Brown, Philip M. Brown
[2] Molecular Biology of the Cell, Bruce Alberts
[2] Molecular Biology of the Cell, Bruce Alberts
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