Prokaryotic transcription regulation

We begin by examining the interactions between proteins and DNA that are the key to transcriptional regulation. We next discuss the specific proteins that influence the expression of specific genes, first in prokaryotic and then in eukaryotic cells. Information about posttranscriptional and translational regulation is included in the discussion, where relevant, to provide a more complete overview of the rich complexity of regulatory mechanisms. 

Transcription and transcriptional regulation is more complicated in eukaryotes than in prokaryotes. The very much larger amount of DNA in eukaryotes is organized with histones... 

Pennella MA, Giedroc DP. Structural determinants of metal selectivity in prokaryotic metal-responsive transcriptional regulators. BioMetals 2005 18 413-428. 

We have seen how interactions between DNA-binding proteins such as CAP and RNA polymerase can activate transcription in prokaryotic cells (Section 31.1.6). Such protein-protein interactions play a dominant role in eukaryotic gene regulation. In contrast with those of prokaryotic transcription, few eukaryotic transcription factors have any effect on transcription on their own. Instead, each factor recruits other proteins to build up large complexes that interact with the transcriptional machinery to activate or repress Panscription. 

More complex transcriptional regulation. Like prokaryotes, eukaryotes rely on conserved sequences in DN A to regulate the initiation of transcription. But prokaryotes have only three promoter elements (the —10. -33. and UP elements), whereas eukaryotes use a variety of types of promoter elements, each identified by its own conserved sequence. Not all possible types will he present together in the same promoter. n eukaryotes, elements that regulate transcription can be found at a variety of locations in DNA, upstream or downstream of the start site and sometimes at distances much farther from the start site than in prokaryotes. For example, enhancer elements located on DNA far from the start site increase the promoter activity of specific genes. 

Key Words Transcriptional regulation pattern discovery pattern matching phylogenetic footprinting prokaryotes RSAT get-orthologs retrieve-seq dyad-analysis. 

Fig. 3.3-2 Prokaryotic regulators of transcription have been adapted for use as eukaryotic transcriptional regulators ...

Frequency of transcription is controlled by the promoter sequence. Additional sequences upstream can also be involved in regulating prokaryotic transcription. These sequences are called enhancers or silencers, and they stimulate or inhibit transcription, respectively. Proteins called transcription factors can bind to these enhancer or silencer elements. Many prokaryotic genes that produce proteins that are part of a pathway are controlled in groups called operons, and expression of some genes is controlled by transcription attenuation. 

The phenomenon of attenuation of translation of the trp operon in bacteria is provided as an example of posttranscriptional gene regulation. This mechanism, which is used by several amino acid biosynthetic operons, relies on alternative RNA secondary structures and on the coupling of transcription and translation in prokaryotes. The regulation of iron metabolism in animals is presented to show how RNA secondary structures can by bound specifically by proteins and thereby regulate translation. 

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