Transcription in Prokaryotes: Mechanisms and Factors Revealed
Explore transcription in prokaryotes, focusing on the bacterial RNA polymerase, core enzyme structure, sigma factor function, promoter binding, and initiation stages. Learn about the holoenzyme complex, different types of RNA polymerases in bacteria, and the stages of transcription - Initiation, Elongation, and Termination. Understand the role of promoters, consensus sequences, and the crucial -10 region in prokaryotic transcription.
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Transcription Transcription Dr. Rajveer Singh Chauhan Assistant Professor, Department of Botany, DDU Gorakhpur University, Gorakhpur, Uttar Pradesh
Transcription in prokaryotes Bacterial cells typically posses only one type of RNA polymerase molecule which catalyzes the synthesis of all classes of RNA i.e. mRNA, rRNA, tRNA. Bacterial RNA polymerase is a large multimeric enzyme. It has five subunits - alpha1, alpha2, beta, beta', and subunit that make up the core enzyme. The subunit is not essential for transcription but it helps to stabilize the enzyme . The bacterial core enzyme requires a specialized subunit called sigma ( ) factor which makes direct contact with the promoter sequence and thereby ensures that transcription begins at the proper position in the DNA.
The complex formed by the subunit and the polymerase core enzyme constitutes the bacterial holoenzyme. is required only for promoter binding and initiation. Many bacteria possess multiple types of . E.coli possess 28, 32, 54, 70. Each type of initiates the binding of RNA polymerase to a particular set of protein 32 binds to the promoter of gene that protects bacteria against environmental stress. 54 binds to promoter of genes used during nitrogen starvation and 70 binds to many different promoters.
Transcription can be convinently divided into 3 stages- Initiation Elongation Termination In initiation transcription factors assemble to promoter and begins the synthesis of RNA. Transcription initiation requires that transcription apparatus recognize and bind to promotes that determine which parts of DNA template are to be transcribed. Promoters are DNA sequences that are recognized by the transcription apparatus and are required for transcription to take place.
In bacteria promoters are usually adjacent to an RNA coding sequence. In promoters there are short stretches of bases, that are called, boxes or elements. The nucleotide sequences of these boxes are sometimes called consensus sequence. The term consensus sequences refers to the sequences that posses considerable similarity. The most commonly found consensus sequences in almost all bacterial promoter is located just upstream of the transcription start site (TSS) centered on position -10.
-10 sequence is sometimes called Pribnow box and its sequence is 5'-TATAAT-3' but is often written simply TATAAT. In most prokaryotic promoters the actual sequence is not TATAAT. The -10 sequence is the region of contact for the core enzyme and is necessary for the initial melting of DNA to expose the template strand. Another consensus sequence common to most bacterial promoters is 5'-TTGACA-3' which lies approximately -35 nucleotides upstream of start site and is termed the -35 consensus sequence.
RNA polymerase binds to -35 and -10 sequences in the promoter via the s subunit. An additional upstream (UP) element may be bound by the a subunits. While tightly bound to the promoter, the polymerase pulls additional DNA toward itself ( scrunching ). Eventually, a sufficiently long RNA is produced that the polymerase escapes the promoter, releasing the s subunit. Transcription Initiation
The factor associates with the core enzyme to form a holoenzyme which binds to the -35 and -10 consensus sequences in the DNA promoters. RNA polymerase holoenzyme can bind to a few promoters that lack a -35 box, it can do so because these promoters have a supplementary sequence element, 5'-TG-3' located one bp upstream from -10 box, known as the extended -10 element . Some bacterial genes that are transcribed at a high rate contain an additional AT rich sequence called the UP element, to the upstream site of the -35 region.
The UP element serves as binding site for the carboxy terminal domain (CTD) of alpha subunit of RNA polymerase, thereby strengthing the binding of RNA polymerase to the DNA.
Elongation of Transcription in prokaryotes Chain elongationnow continues as RNA polymerase moves along the DNA molecule, untwisting the helix bit by bit and adding one complementary nucleotide at a time to the growing RNA chain. The b subunits contain regions that act like pincers that bind DNA and move it into the active site of the enzyme. As RNA polymerase moves along DNA, different channels in the enzyme allow components to enter (incoming DNA, ribonucleotides) and leave (DNA that has already been transcribed, newly formed RNA) the polymerase as it moves along the enzyme moves along the template DNA strand from the 3' end toward the 5' end.
As the RNA chain grows, the most recently added nucleotides remain base-paired with the DNA template strand, forming a short RNA-DNA hybrid about 8 9 bp long. As the polymerase moves forward, the DNA ahead of the enzyme is unwound to permit the RNA-DNA hybrid to form. At the same time, the DNA behind the moving enzyme is rewound into a double helix. The supercoiling that would otherwise be generated by this unwinding and rewinding is released through the action of topoisomerases, just as in DNA replication.
Termination of Transcription in prokaryotes Elongation of the growing RNA chain proceeds until RNA polymerase copies a special sequence, called a termination signal, that triggers the end of transcription. In bacteria, two classes of termination signals can be distinguished based on whether they require the participation of a protein called rho ( ) factor. RNA molecules terminated without the aid of the rho factor contain a short GC-rich sequence followed by several U residues near their 3' end. This configuration promotes termination in the following way:
First, the GC region contains sequences that are complementary to each other, causing the RNA to spontaneously fold into a hairpin loop that tends to pull the RNA molecule away from the DNA. Then the weaker bonds between the sequence of U residues and the DNA template are broken, releasing the newly formed RNA molecule. In contrast, RNA molecules that do not form a GC-rich hairpin loop require participation of the rho factor for termination.
