BIOL 366 Lecture 14: Post-transcriptional Regulation
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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</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</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</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</p> Signup and view all the answers

    Which characteristic is NOT true of riboswitches?

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

    What major mechanism do resistant bacteria utilize to counteract antibiotics?

    <p>Enhancing degradation of antibiotics</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.</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.</p> Signup and view all the answers

    How many genes typically encode r-proteins in bacteria?

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

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

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

    What structural component is critical for the function of riboswitches?

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

    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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    Lecture 14 (PT Reg Bacterial Gen Exp, ch 20) PDF

    Description

    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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