Question

List several reasons why promoters and transcription are more complex and eukaryotes compared to prokaryotes.

Answer 1

Eukaryotic promoters are much more complex and diverse than prokaryotic promoters. Eukaryotic promoters span a wide range of DNA sequences. It is not unusual to have several regulatory elements such as enhancers several kilobases away from the TSS. Eukaryotic promoters are so complex in structure that the DNA tends to fold back on itself which helps to explain how many physically distant DNA sequences can affect transcription of a given gene. The TATA-binding protein binds the TATA box and helps in the subsequent binding of the RNA polymerase. A transcription complex is constructed from the RNA polymerase and several transcription factor proteins.

Eukaryotic transcription is more complex than prokaryotic transcription. For instance, in eukaryotes the genetic material (DNA), and therefore transcription, is primarily localized to the nucleus, where it is separated from the cytoplasm (in which translation occurs) by the nuclear membrane. This allows for the temporal regulation of gene expression through the sequestration of the RNA in the nucleus, and allows for selective transport of mature RNAs to the cytoplasm. Bacteria do not have a distinct nucleus that separates DNA from ribosome and mRNA is translated into protein as soon as it is transcribed. The coupling between the two processes provides an important mechanism for prokaryotic gene regulation.

At the level of initiation, RNA polymerase in prokaryotes (bacteria in particular) binds strongly to the promoter region and initiates a high basal rate of transcription. No ATP hydrolysis is needed for the close-to-open transition, promoter melting is driven by binding reactions that favor the melted conformation. Chromatin greatly impedes transcription in eukaryotes. Assembly of large multi-protein preinitiation complex is required for promoter-specific initiation. Promoter melting in eukaryotes requires hydrolysis of ATP. As a result, eukaryotic RNA polymerases exhibit a low basal rate of transcription initiation.

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