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Additional methods of regulation in bacteria: attenuation and riboswitches

Although most gene expression is regulated at the level of transcription initiation in prokaryotes, there are also mechanisms to control both the completion of transcription as well as translation concurrently. Since their discovery, these mechanisms have been shown to control the completion of transcription and translation of many prokaryotic operons. Because these mechanisms link the regulation of transcription and translation directly, they are specific to prokaryotes, because these processes are physically separated in eukaryotes.

One such regulatory system is attenuation , whereby secondary stem-loop structure s formed within the 5’ end of an mRNA being transcribed determine if transcription to complete the synthesis of this mRNA will occur and if this mRNA will be used for translation. Beyond the transcriptional repression mechanism already discussed, attenuation also controls expression of the trp operon in E. coli ( [link] ). The trp operon regulatory region contains a leader sequence called trpL between the operator and the first structural gene, which has four stretches of RNA that can base pair with each other in different combinations. When a terminator stem-loop forms, transcription terminates, releasing RNA polymerase from the mRNA. However, when an antiterminator stem-loop forms, this prevents the formation of the terminator stem-loop, so RNA polymerase can transcribe the structural genes.

A related mechanism of concurrent regulation of transcription and translation in prokaryotes is the use of a riboswitch , a small region of noncoding RNA found within the 5’ end of some prokaryotic mRNA molecules ( [link] . A riboswitch may bind to a small intracellular molecule to stabilize certain secondary structures of the mRNA molecule. The binding of the small molecule determines which stem-loop structure forms, thus influencing the completion of mRNA synthesis and protein synthesis.

a) At high level of tryptophan a complete polypeptide is made from mRNA regions 1 and 2. Regions 3 and 4 form a terminator stem loop and RNA polymerase stops transcription. B) At low levels of tryptophan an incomplete polypeptide is produced from region 1. Regions 2 and 3 form an antiterminator stem loop which causes the ribosome to stall. This allows RNA polymerase to transcribe the trp regulated genes.
When tryptophan is plentiful, translation of the short leader peptide encoded by trpL proceeds, the terminator loop between regions 3 and 4 forms, and transcription terminates. When tryptophan levels are depleted, translation of the short leader peptide stalls at region 1, allowing regions 2 and 3 to form an antiterminator loop, and RNA polymerase can transcribe the structural genes of the trp operon.
a) The mRNA forms a loop called a riboswitch and a loop called an antiterminator stem loop. RNA polymerase can proceed transcription. This is labeled “on”. A small molecule binds to the mRNA at the riboswitch location. The shifts the second loop to the terminator stem loop position and no transcription occurs. This is labeled off. B) The mRNA forms a loop called a riboswitch and another unlabeled loop. The ribosome binds at the ribosome binding site after the second loop and a translation proceeds. This is “on”. A small molecule binds to the mRNA at the riboswitch location. The shifts the second loop to the ribosome binding site location with blocks this ribosome binding site. This is now “off”.
Riboswitches found within prokaryotic mRNA molecules can bind to small intracellular molecules, stabilizing certain RNA structures, influencing either the completion of the synthesis of the mRNA molecule itself (left) or the protein made using that mRNA (right).

Other factors affecting gene expression in prokaryotes and eukaryotes

Although the focus on our discussion of transcriptional control used prokaryotic operons as examples, eukaryotic transcriptional control is similar in many ways. As in prokaryotes, eukaryotic transcription can be controlled through the binding of transcription factors including repressor s and activator s. Interestingly, eukaryotic transcription can be influenced by the binding of proteins to regions of DNA, called enhancer s, rather far away from the gene, through DNA looping facilitated between the enhancer and the promoter ( [link] ). Overall, regulating transcription is a highly effective way to control gene expression in both prokaryotes and eukaryotes. However, the control of gene expression in eukaryotes in response to environmental and cellular stresses can be accomplished in additional ways without the binding of transcription factors to regulatory regions.

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Source:  OpenStax, Microbiology. OpenStax CNX. Nov 01, 2016 Download for free at http://cnx.org/content/col12087/1.4
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