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Ch. 16 - Regulation of Gene Expression in Bacteria
All textbooksKlug 12th EditionCh. 16 - Regulation of Gene Expression in BacteriaProblem 16
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Chapter 16, Problem 16

Both attenuation of the trp operon in E. coli and riboswitches in B. subtilis rely on changes in the secondary structure of the leader regions of mRNA to regulate gene expression. Compare and contrast the specific mechanisms in these two types of regulation with that involving short noncoding RNAs (sRNAs).

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Understand the concept of attenuation in the trp operon: In E. coli, the trp operon is regulated by attenuation, which involves the formation of alternative secondary structures in the leader region of the mRNA. When tryptophan levels are high, a terminator structure forms, halting transcription. When tryptophan is low, an anti-terminator structure forms, allowing transcription to continue.
Explore riboswitches in B. subtilis: Riboswitches are regulatory segments of mRNA that bind small molecules, causing a change in the mRNA's secondary structure. This change can either promote or inhibit the expression of downstream genes. In B. subtilis, riboswitches can control gene expression by altering the accessibility of the ribosome binding site or by forming transcription terminator structures.
Examine the role of short noncoding RNAs (sRNAs): sRNAs are small RNA molecules that regulate gene expression post-transcriptionally. They typically function by base-pairing with target mRNAs, affecting their stability or translation. sRNAs can either promote degradation of the mRNA or block the ribosome binding site, preventing translation.
Compare the mechanisms: Both attenuation and riboswitches involve changes in mRNA secondary structure to regulate gene expression, but attenuation is primarily a transcriptional control mechanism, while riboswitches can affect both transcription and translation. sRNAs, on the other hand, regulate gene expression post-transcriptionally by interacting with mRNA directly.
Contrast the regulatory outcomes: Attenuation and riboswitches rely on the presence or absence of specific metabolites to induce structural changes in mRNA, leading to either termination or continuation of transcription. sRNAs do not rely on metabolite binding but instead use complementary base-pairing to modulate mRNA stability or translation, providing a different layer of gene regulation.

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Key Concepts

Here are the essential concepts you must grasp in order to answer the question correctly.

Attenuation in the trp operon

Attenuation is a regulatory mechanism in the trp operon of E. coli that controls gene expression based on tryptophan levels. It involves the formation of different secondary structures in the mRNA leader sequence, which can either promote or inhibit transcription. When tryptophan is abundant, a structure that terminates transcription is favored, while low levels allow for a structure that permits transcription to continue.
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Riboswitches in B. subtilis

Riboswitches are segments of mRNA that can change their secondary structure in response to specific metabolites, thereby regulating gene expression. In B. subtilis, the binding of a metabolite to the riboswitch can lead to the formation of a structure that either sequesters the ribosome binding site or promotes transcription termination, effectively controlling the synthesis of proteins based on the cellular environment.
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Short noncoding RNAs (sRNAs)

Short noncoding RNAs (sRNAs) are regulatory RNA molecules that can modulate gene expression by base-pairing with target mRNAs. They often influence the stability and translation of mRNAs by altering their secondary structures or by recruiting proteins that affect mRNA degradation. Unlike attenuation and riboswitches, which are intrinsic to the mRNA itself, sRNAs act as trans-acting factors that can regulate multiple targets.
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Textbook Question
Attenuation of the trp operon was viewed as a relatively inefficient way to achieve genetic regulation when it was first discovered in the 1970s. Since then, however, attenuation has been found to be a relatively common regulatory strategy. Assuming that attenuation is a relatively inefficient way to achieve genetic regulation, what might explain its widespread occurrence?
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Textbook Question
Neelaredoxin is a 15-kDa protein that is a gene product common in anaerobic bacteria. It has superoxide-scavenging activity, and it is constitutively expressed. In addition, its expression is not further induced during its exposure to O₂ or H₂O₂ [Silva, G. et al. (2001). J. Bacteriol. 183:4413–4420]. What do the terms constitutively expressed and induced mean in terms of neelaredoxin synthesis?
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Textbook Question
The creation of milk products such as cheeses and yogurts is dependent on the conversion by various anaerobic bacteria, including several Lactobacillus species, of lactose to glucose and galactose, ultimately producing lactic acid. These conversions are dependent on both permease and β-galactosidase as part of the lac operon. After selection for rapid fermentation for the production of yogurt, one Lactobacillus subspecies lost its ability to regulate lac operon expression [Lapierre, L., et al. (2002). J. Bacteriol. 184:928–935]. Would you consider it likely that in this subspecies the lac operon is on or off? What genetic events would likely contribute to the loss of regulation as described above?
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Textbook Question
Keeping in mind the life cycle of bacteriophages discussed earlier in the text (see Chapter 6), consider the following problem: During the reproductive cycle of a temperate bacteriophage, the viral DNA inserts into the bacterial chromosome where the resultant prophage behaves much like a Trojan horse. It can remain quiescent, or it can become lytic and initiate a burst of progeny viruses. Several operons maintain the prophage state by interacting with a repressor that keeps the lytic cycle in check. Insults (ultraviolet light, for example) to the bacterial cell lead to a partial breakdown of the repressor, which in turn causes the production of enzymes involved in the lytic cycle. As stated in this simple form, would you consider this system of regulation to be operating under positive or negative control?
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Textbook Question
Bacterial strategies to evade natural or human-imposed antibiotics are varied and include membrane-bound efflux pumps that export antibiotics from the cell. A review of efflux pumps [Grkovic, S., et al. (2002)] states that, because energy is required to drive the pumps, activating them in the absence of the antibiotic has a selective disadvantage. The review also states that a given antibiotic may play a role in the regulation of efflux by interacting with either an activator protein or a repressor protein, depending on the system involved. How might such systems be categorized in terms of negative control (inducible or repressible) or positive control (inducible or repressible)?
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Textbook Question
In a theoretical operon, genes A, B, C, and D represent the repressor gene, the promoter sequence, the operator gene, and the structural gene, but not necessarily in the order named. This operon is concerned with the metabolism of a theoretical molecule (tm). From the data provided in the accompanying table, first decide whether the operon is inducible or repressible. Then assign A, B, C, and D to the four parts of the operon. Explain your rationale. (AE=active enzyme; IE=inactive enzyme; NE=no enzyme.) Genotype tm Present tm Absent A⁺B⁺C⁺D⁺ AE NE A⁻B⁺C⁺D⁺ AE AE A⁺B⁻C⁺D⁺ NE NE A⁺B⁺C⁻D⁺ IE NE A⁺B⁺C⁺D⁻ AE AE A⁻B⁺C⁺D⁺/F'A⁺B⁺C⁺D⁺ AE AE A⁺B⁻C⁺D⁺/F'A⁺B⁺C⁺D⁺ AE NE A⁺B⁺C⁻D⁺/F'A⁺B⁺C⁺D⁺ AE+IE NE A⁺B⁺C⁺D⁻/F'A⁺B⁺C⁺D⁺ AE NE
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