RNA polymerases have been found in all species, but the number and composition of these proteins vary across taxa. For instance, bacteria contain a single type of RNA polymerase, while eukaryotes multicellular organisms and yeasts contain three distinct types. In spite of these differences, there are striking similarities among transcriptional mechanisms. For example, all species require a mechanism by which transcription can be regulated in order to achieve spatial and temporal changes in gene expression.
In order to fully understand what this means, it is first necessary to examine the mechanisms of RNA transcription in more detail. In all species, transcription begins with the binding of the RNA polymerase complex or holoenzyme to a special DNA sequence at the beginning of the gene known as the promoter. Activation of the RNA polymerase complex enables transcription initiation, and this is followed by elongation of the transcript.
In turn, transcript elongation leads to clearing of the promoter, and the transcription process can begin yet again. Transcription can thus be regulated at two levels: the promoter level cis regulation and the polymerase level trans regulation.
These elements differ among bacteria and eukaryotes. In bacteria, all transcription is performed by a single type of RNA polymerase. This polymerase contains four catalytic subunits and a single regulatory subunit known as sigma s. Interestingly, several distinct sigma factors have been identified, and each of these oversees transcription of a unique set of genes. Sigma factors are thus discriminatory, as each binds a distinct set of promoter sequences.
A striking example of the specialization of sigma factors for different gene promoters is provided by bacterial sporulation in the species Bacillus subtilis. This bacterium exists in two states: vegetative growing and sporulating. Genes involved in spore formation are not normally expressed during vegetative growth. Remarkably, expression of a gene encoding a novel sigma factor turns on the first genes for sporulation. Each of these sigma factors recognizes the promoters of the genes in its group, not those "seen" by other sigma factors.
This simple example illustrates how transcription can be regulated in both cis and trans to cause changes in cell function. Therefore, while bacteria accomplish transcription of all genes using a single kind of RNA polymerase, the use of different sigma factor subunits provides an extra level of control. Interestingly, RNA pol II is uniquely sensitive to amatoxins, such as a-amanitin of the extremely toxic Amanita genus of mushrooms Weiland, , a fact that researchers have been able to exploit for the purposes of polymerase studies - although recreational mushroom hunters should beware!
Thus, while eukaryotic transcription is far more complex than bacterial transcription, the main difference between the two types of transcription lies in RNA polymerase. Hahn, S. Nature Structural and Molecular Biology 11 , — link to article.
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Ramsay, E. Acta , — Rehfeld, F. Enhancers and silencers affect the efficiency of transcription but are not necessary for transcription to proceed. The evolution of genes may be a familiar concept. Mutations can occur in genes during DNA replication, and the result may or may not be beneficial to the cell. By altering an enzyme, structural protein, or some other factor, the process of mutation can transform functions or physical features. However, eukaryotic promoters and other gene regulatory sequences may evolve as well.
For instance, consider a gene that, over many generations, becomes more valuable to the cell. Maybe the gene encodes a structural protein that the cell needs to synthesize in abundance for a certain function. Scientists examining the evolution of promoter sequences have reported varying results. In part, this is because it is difficult to infer exactly where a eukaryotic promoter begins and ends.
Some promoters occur within genes; others are located very far upstream, or even downstream, of the genes they are regulating. However, when researchers limited their examination to human core promoter sequences that were defined experimentally as sequences that bind the preinitiation complex, they found that promoters evolve even faster than protein-coding genes.
It is still unclear how promoter evolution might correspond to the evolution of humans or other higher organisms. However, the evolution of a promoter to effectively make more or less of a given gene product is an intriguing alternative to the evolution of the genes themselves. These sequences alone are sufficient for transcription initiation to occur, but promoters with additional sequences in the region from to upstream of the initiation site will further enhance initiation.
Genes that are transcribed by RNA polymerase III have upstream promoters or promoters that occur within the genes themselves. Eukaryotic transcription is a tightly regulated process that requires a variety of proteins to interact with each other and with the DNA strand. Although the process of transcription in eukaryotes involves a greater metabolic investment than in prokaryotes, it ensures that the cell transcribes precisely the pre-mRNAs that it needs for protein synthesis. As discussed previously, RNA polymerase II transcribes the major share of eukaryotic genes, so this section will focus on how this polymerase accomplishes elongation and termination.
Although the enzymatic process of elongation is essentially the same in eukaryotes and prokaryotes, the DNA template is more complex. When eukaryotic cells are not dividing, their genes exist as a diffuse mass of DNA and proteins called chromatin.
The DNA is tightly packaged around charged histone proteins at repeated intervals.
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