BIOL 366 Lecture 14: Post-transcriptional Regulation
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Questions and Answers

What is the primary function of a riboswitch when a specific metabolite is present?

  • To enhance transcription levels significantly
  • To modify the mRNA for increased stability
  • To sequester the Shine-Dalgarno sequence and halt translation (correct)
  • To promote the synthesis of additional ribosomes

In which part of the mRNA does the THI box riboswitch primarily function?

  • Within the promoter region of the gene
  • In the 5′ untranslated region (5' UTR) (correct)
  • In the 3′ untranslated region (3' UTR)
  • In the coding sequence of the mRNA

How does the presence of thiamine pyrophosphate (TPP) affect gene expression?

  • It accelerates mRNA degradation
  • It enhances the binding of ribosomes to mRNA
  • It inhibits translation when levels of vitamin B1 are high (correct)
  • It augments the transcription process of mRNA

Which process is disrupted by the binding of a specific metabolite to a riboswitch?

<p>Translation initiation (B)</p> Signup and view all the answers

What is the role of the glmS riboswitch in regulating mRNA stability?

<p>It promotes degradation of specific mRNAs when bound by a metabolite (A)</p> Signup and view all the answers

What is the primary role of the translational repressor in r-protein operons?

<p>To block the translation of the operon's mRNA (D)</p> Signup and view all the answers

Under what condition does translation of the r-protein mRNA proceed without inhibition?

<p>When r-protein levels are low relative to rRNA levels (B)</p> Signup and view all the answers

Which characteristic is NOT true of riboswitches?

<p>They are primarily found in mammals (D)</p> Signup and view all the answers

What best describes the composition of ribosomal proteins in rapidly growing cells?

<p>They can make up to 45% of total cellular proteins (C)</p> Signup and view all the answers

How does the presence of excess r-protein affect the translational repressor's function?

<p>It causes the repressor to bind both rRNA and mRNA (C)</p> Signup and view all the answers

What is the typical role of the ribosomal protein designated L4 in the regulation of r-protein operons?

<p>To function as a translational repressor (D)</p> Signup and view all the answers

What defines the structure of r-protein operons?

<p>They typically include 52 genes organized into approximately 20 operons (D)</p> Signup and view all the answers

What is the primary function of a riboswitch in bacterial gene regulation?

<p>To detect specific molecular signals and regulate gene expression accordingly (A)</p> Signup and view all the answers

Which mechanism is primarily involved in rapid regulation of protein synthesis in response to environmental signals?

<p>Translational feedback control via ribosomal proteins (D)</p> Signup and view all the answers

In the context of the trp operon, what is the role of attenuation?

<p>To prematurely terminate transcription based on tryptophan levels (B)</p> Signup and view all the answers

What is a characteristic feature of translational repressors in bacterial regulation?

<p>They bind to mRNA and prevent the ribosome from initiating translation (D)</p> Signup and view all the answers

How does the ara operon demonstrate both positive and negative regulation using the same proteins?

<p>Through the action of regulatory proteins that can either activate or inhibit transcription (A)</p> Signup and view all the answers

Which of the following best explains the stringent response in bacteria?

<p>Regulation of ribosomal RNA synthesis to adapt to amino acid starvation (C)</p> Signup and view all the answers

What role do r-proteins play in feedback regulation of ribosome synthesis?

<p>They act as translational repressors to fine-tune ribosomal protein production (C)</p> Signup and view all the answers

What general concept do operons like lac and trp illustrate in bacteria?

<p>The integration of multiple signals for coordinated gene regulation (A)</p> Signup and view all the answers

Which statement is true regarding the post-transcriptional control of gene expression?

<p>It enables rapid responses to signals through mechanisms like riboswitches and translational repressors (A)</p> Signup and view all the answers

What is the primary mechanism by which bacteria respond to increased demand for protein synthesis?

<p>Increasing the number of ribosomes (A)</p> Signup and view all the answers

What distinguishes the regulation of the ara operon compared to other operons like the lac operon?

<p>It can employ both positive and negative regulation with the same set of proteins (A)</p> Signup and view all the answers

In terms of control of gene expression, what does 'translational feedback' primarily refer to?

<p>The regulation of translation involving r-proteins adjusting ribosome production (D)</p> Signup and view all the answers

Which factor plays a crucial role in the stringent response mechanism in bacteria?

<p>Decreased amino acid availability (D)</p> Signup and view all the answers

What is the function of the riboswitch in bacterial gene expression?

<p>To allow immediate changes in translation based on metabolite presence (B)</p> Signup and view all the answers

What is a key characteristic of ribosomal proteins in rapidly growing bacterial cells?

<p>Their synthesis is tightly regulated to match ribosomal RNA levels (A)</p> Signup and view all the answers

Which factor contributes to the riboswitch's ability to discriminate between chemically related molecules?

<p>Stereochemistry and functional group presence (D)</p> Signup and view all the answers

What is the consequence of glucosamine 6-phosphate binding to glmS pre-mRNA?

<p>Degradation of the glmS pre-mRNA (C)</p> Signup and view all the answers

Which of the following statements best describes the conservation of upstream sequences in riboswitch-regulated mRNAs?

<p>They show significant conservation across various organisms. (B)</p> Signup and view all the answers

Which of the following best describes the classification of riboswitches?

<p>According to the ligand they bind and their secondary structure (C)</p> Signup and view all the answers

What major mechanism do resistant bacteria utilize to counteract antibiotics?

<p>Enhancing degradation of antibiotics (B)</p> Signup and view all the answers

Which of the following is NOT a characteristic of riboswitch-regulated mRNAs?

<p>They require protein binding for regulation. (A)</p> Signup and view all the answers

What is the function of the translational repressor in r-protein operons when the concentration of r-protein is low?

<p>The repressor binds solely to rRNA to allow translation. (C)</p> Signup and view all the answers

How many genes typically encode r-proteins in bacteria?

<p>52 genes in approximately 20 operons. (C)</p> Signup and view all the answers

Under what condition does L4 protein begin to repress translation of its mRNA?

<p>With an excess of r-protein leading to saturation of rRNA. (A)</p> Signup and view all the answers

What is the primary characteristic of riboswitches found in bacteria?

<p>They are mainly found within the 5′ untranslated region of mRNA. (A)</p> Signup and view all the answers

How does the r-protein operon ensure the balance of r-protein to rRNA levels?

<p>Through translational feedback where excess r-protein inhibits its own synthesis. (B)</p> Signup and view all the answers

In which scenario does translation of r-protein mRNA occur without any repression?

<p>When r-protein levels are low compared to rRNA levels. (C)</p> Signup and view all the answers

Which of the following is NOT true regarding the function of ribosomal proteins in bacteria?

<p>They are synthesized independently of rRNA levels. (B)</p> Signup and view all the answers

What role do riboswitches play in gene regulation within bacteria?

<p>They modulate gene expression in response to specific metabolites. (A)</p> Signup and view all the answers

What happens to transcription when a specific metabolite binds to a riboswitch?

<p>Transcription is terminated. (C)</p> Signup and view all the answers

What is the primary effect of the TPP riboswitch when thiamine pyrophosphate (TPP) is absent?

<p>Translation proceeds normally. (D)</p> Signup and view all the answers

Which feature is characteristic of riboswitches, specifically regarding their mechanism of action?

<p>They change their conformation upon metabolite binding. (A)</p> Signup and view all the answers

How do riboswitches regulate gene expression at the level of translation?

<p>By altering the secondary structure of mRNA to obstruct the Shine-Dalgarno sequence. (D)</p> Signup and view all the answers

What distinguishes the THI box riboswitch in terms of its conservation across organisms?

<p>It is one of the few riboswitches found across most organisms. (C)</p> Signup and view all the answers

How do riboswitches like the glmS riboswitch affect mRNA stability?

<p>They can cause specific mRNA degradation in response to metabolites. (B)</p> Signup and view all the answers

In the absence of specific metabolites, what occurs at the level of transcription for riboswitches?

<p>Transcription occurs as usual. (A)</p> Signup and view all the answers

What structural component is critical for the function of riboswitches?

<p>The specific metabolite-binding element. (D)</p> Signup and view all the answers

Which of the following best describes the Shine-Dalgarno sequence's role in the context of a riboswitch?

<p>It is essential for ribosome recruitment during translation. (A)</p> Signup and view all the answers

What is an effect of the conformational change in the riboswitch upon metabolite binding?

<p>It leads to the formation of alternative secondary structures. (D)</p> Signup and view all the answers

Flashcards

Ribosomal protein synthesis regulation

Bacteria control the production of ribosomal proteins (r-proteins), coordinated with ribosomal RNA (rRNA) levels, via operons and translational feedback.

r-protein operons

Groups of genes encoding ribosomal proteins, typically containing 1-11 genes each.

Translational repressor

A protein (like L4) that binds rRNA or mRNA to control translation of ribosomal protein genes.

Feedback mechanism (ribosomal proteins)

A process where high levels of ribosome proteins repress further protein synthesis, while low levels allow production to continue.

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Riboswitches

Regulatory regions within mRNA (5'UTR) that control gene expression based on cellular conditions.

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5' UTR

Untranslated region at the 5' end of messenger RNA.

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rRNA vs. r-protein levels

The relative levels of ribosomal RNA (rRNA) and ribosomal proteins (r-proteins) determine whether translation of r-protein genes is encouraged or stopped.

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Riboswitch function: Transcriptional Control

A riboswitch can directly affect transcription by altering the RNA structure, leading to termination of transcription when the specific metabolite binds.

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Riboswitch function: Translational Control

A riboswitch can bind to a specific metabolite and alter the mRNA structure, preventing translation by sequestering the Shine-Dalgarno sequence needed for ribosome binding.

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THI box / THI element

A specific riboswitch that binds thiamine pyrophosphate (TPP), a coenzyme involved in vitamin B1 metabolism.

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glmS riboswitch

A riboswitch that can impact mRNA stability, controlling the lifespan of a particular mRNA molecule depending on the presence of a metabolite (glucosamine-6-phosphate).

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Translational feedback

A regulatory mechanism where the amount of a protein produced directly influences its own further production.

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Stringent response

A cellular stress response triggered by amino acid starvation, leading to reduced protein synthesis and increased synthesis of amino acid biosynthetic enzymes.

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Stringent factor (RelA)

An enzyme that synthesizes a signaling molecule (ppGpp) to initiate the stringent response.

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ppGpp

A signaling molecule produced by RelA during the stringent response, triggering changes in gene expression.

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How does the rRNA/r-protein ratio influence translation?

The relative levels of rRNA and r-proteins dictate whether translation of r-protein genes is encouraged or halted. If rRNA levels are high and r-protein levels are low, translation is encouraged, and vice versa.

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Post-transcriptional regulation

Control of gene expression that happens after mRNA is made, affecting the translation or stability of mRNA.

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How do riboswitches control translation?

Riboswitches bind specific metabolites, causing structural changes in mRNA, either blocking or allowing ribosome binding.

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r-proteins

Proteins that are essential components of ribosomes, the cellular machinery responsible for protein synthesis.

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rRNA

Ribosomal RNA, a type of RNA that forms the structural and functional core of ribosomes.

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How does L4 control r-protein synthesis?

L4, a ribosomal protein, serves as a translational repressor. When rRNA levels are low, L4 binds to rRNA, allowing translation of r-protein genes. When rRNA levels are high, L4 binds to mRNA, inhibiting translation. This feedback loop ensures the balance of r-proteins and rRNA.

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Shine-Dalgarno sequence

A short sequence in mRNA that helps ribosomes bind to the correct start codon and initiate translation.

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How do riboswitches affect gene expression?

Riboswitches directly bind to small molecules, triggering changes in RNA structure. These structural changes can lead to either the termination of transcription or the blocking of translation.

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What is the role of the THI box in vitamin B1 metabolism?

The THI box is a riboswitch that binds thiamine pyrophosphate (TPP). When TPP levels are high, the THI box inhibits translation of genes involved in vitamin B1 biosynthesis, ensuring that the cell does not produce excess vitamin B1.

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How does the glmS riboswitch influence mRNA stability?

When glucosamine-6-phosphate binds to the glmS riboswitch, it triggers the cleavage of mRNA, leading to its degradation. This mechanism regulates the lifespan of the mRNA.

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How does the glmS riboswitch regulate gene expression?

The glmS riboswitch regulates gene expression by controlling the stability of the glmS mRNA. When glucosamine 6-phosphate binds to the riboswitch, it triggers a conformational change in the mRNA, leading to its self-degradation. This prevents the production of more GlcN6-P synthesizing enzyme.

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What makes riboswitches specific?

Riboswitches can be very specific in recognizing their target ligands. This specificity is based on structural features, including atomic charge, stereochemistry, and the presence or absence of specific functional groups.

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How are riboswitches classified?

Riboswitches are classified based on the specific metabolite they bind and their secondary structure. There are over 15 known classes of riboswitches, each named after the ligand it recognizes.

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Utility of riboswitches in controlling bacterial growth

Riboswitches can be used to control the production of essential enzymes in bacteria, which can be exploited for developing new antibiotics. This is especially important as bacteria are becoming resistant to existing antibiotics.

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Study Notes

BIOL 366 Lecture 14: Post-transcriptional Regulation

  • Post-transcriptional regulation involves controlling gene expression after transcription.
  • Key readings include text sections 20.2.1-20.2.2 and specific articles available on reserve.
  • Key terms include riboswitch, translational repressor, stringent response, and stringent factor.
  • Relevant problems for the chapter include 10, 11, 13, 14, 15, 17, and 18.

Review of Last Lecture

  • Transcriptional control in bacteria examples
    • lac operon: positive and negative regulation with different proteins
    • ara operon: positive and negative regulation with the same proteins
    • trp operon: Attenuation

Post-transcriptional Control of Gene Expression

  • Focuses on rapid up- or down-regulation of protein synthesis in response to molecular signals.

Regulation via Translational Feedback: r-protein Operons

  • In bacteria, increasing protein synthesis demand is met by increasing ribosome numbers.
  • Ribosomal proteins can comprise up to 45% of total cellular proteins in rapidly growing cells.
  • Bacteria coordinate ribosomal component synthesis (r-proteins and r-RNAs).

Regulation via Translational Feedback: The r-protein Operons (Details)

  • r-proteins are encoded by 52 genes in ~20 operons (each with 1-11 genes).
  • Each operon's r-protein functions as a translational repressor.
  • The repressor can bind rRNA (preferred) or the operon's mRNA, blocking translation.

Regulation of an r-protein Operon via Translational Feedback Mechanism

  • When r-protein concentration is low relative to rRNA, the translational repressor (L4) binds only to rRNA. The unbound L4 protein is available to bind r-protein mRNA. This allows translation to proceed.
  • When r-protein concentration is high relative to rRNA (no need for more r-protein), L4 proteins saturate rRNA. Some L4 proteins then bind mRNA, repressing translation.

Riboswitches

  • RNA elements within the 5' untranslated region (5'UTR) of mRNA.
  • Present in bacteria and some eukaryotes (not typically mammals).
  • Contain a regulatory region and a small molecule/metabolite-binding element.

Riboswitches: Function at the Transcriptional Level

  • Transcription continues when mRNA is unbound to the metabolite.
  • A specific metabolite binding to the molecule-binding element changes the shape of the entire RNA molecule.
  • When bound, transcription is terminated.

Riboswitches: Function at the Translational Level

  • When no specific metabolite is present, translation proceeds.
  • A specific metabolite binding alters the mRNA structure and sequesters the Shine-Dalgarno sequence.
  • This prevents translation.

Example: The Thiamine Pyrophosphate (TPP)-binding Riboswitch (THI box/element)

  • Located in the 5'UTR of mRNAs involved in vitamin B1 biosynthesis.
  • Controls gene expression by inhibiting translation when vitamin B1 levels are high.
  • Found in most organisms (archaea, some eukaryotes, and bacteria).

Mode of Action of the TPP Riboswitch

  • When TPP is present, it binds the riboswitch, changing its conformation and sequestering the Shine-Dalgarno sequence, preventing translation.
  • When TPP is NOT present, translation proceeds without the riboswitch's interference.

Riboswitches Can Affect mRNA Stability, Example glmS riboswitch

  • The glmS gene encodes an enzyme catalyzing the reaction: Fructose 6-phosphate + glutamine → glucosamine 6-phosphate.
  • Glucosamine 6-phosphate controls the expression of the glmS mRNA.
  • Binding of GlcN6-P triggers the glmS pre-mRNA to degrade itself (a ribozyme), preventing enzyme production.
  • Discrimination is based on atomic charge, stereochemistry, and functional groups.
  • The glmS riboswitch, for example, specifically recognizes GlcN6P.

Riboswitches and Specificity

  • Riboswitches exhibit high specificity for their ligands.
  • The glmS mRNA is degraded specifically by different ligands, as demonstrated in an agarose gel electrophoresis.

Some Properties of Riboswitch-Regulated mRNAs

  • Unusually long upstream sequences are essential for forming the riboswitch structure.
  • These sequences are well conserved across different bacterial species (and sometimes archaea, plants, and fungi).
  • Riboswitches do not require protein binding partners, enabling direct gene expression regulation.

Types of Riboswitches

  • Over 15 classes, categorized based on ligand type and secondary structure.
  • Example classes: FMN, THI box, B12, S box, L box, lysine, glycine, cyclic di-GMP, glmS, preQ1, magnesium, and others.

Utility of riboswitches in controlling bacterial growth

  • Many bacteria are developing resistance to antibiotics, and ribosomal regulation is a factor in this process.

Overview of Metabolic Pathways Targets for Some Common Antibiotics

  • Diagram depicting pathways targeted by antibiotics.
    • DNA synthesis inhibitors: quinolones (e.g., levofloxacin)
    • Transcription inhibitors: Rifamycins
    • Translation inhibitors: Aminoglycosides, tetracyclines, chloramphenicol
    • Folate synthesis inhibitors: sulfonamides, trimethoprim

Major Mechanisms of Antibiotic Resistance Development

  • Influx/efflux of antibiotics: decrease antibiotic influx, increase efflux pump expression/mutation
  • Modification of antibiotics: degradation by enzymes or modification by adding chemical groups.
  • Modification of antibiotic target: protecting antibiotic target or producing an alternative protein.

Utility of Riboswitches: The FMN (Flavin Mononucleotide) Riboswitch

  • Controls the expression of genes involved in riboflavin biosynthesis.
  • Riboflavin is a precursor to cofactors like FMN.
  • The pathway is essential in Mycobacterium tuberculosis.

Background on Riboflavin Biosynthesis

  • In bacteria like E. coli and B. subtilis, riboflavin is synthesized from GTP and ribulose-5-phosphate via enzymatic reactions.
  • Specific enzymes (RibA, RibB, RibDG, RibH, RibE, RibCF) are involved.
  • The genes are part of a single transcription unit.
  • Regulation is achieved by the FMN riboswitch located in the 5'UTR of the mRNA.

Utility of Riboswitches: The FMN Riboswitch

  • In the absence of FMN, riboflavin synthesis enzymes/mRNA is produced and translated.
  • Binding of FMN to the riboswitch changes conformation and forms a terminator loop, stopping gene expression.
  • Transcription and translation are inhibited by the FMN riboswitch binding to its ligand.

Additional Notes

  • Note inhibitors of vitamin B2 and FMN synthesis (Roseoflavin, Ribocil-C) act as mimics of the metabolite to bind and inhibit riboswitch function.

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Explore the mechanisms of post-transcriptional regulation in gene expression with a focus on bacterial systems. Key terms include riboswitches and translational repressors, along with related operon examples. This quiz will test your understanding of the dynamic control of protein synthesis.

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