Molecular Biology

Eukaryotes gene regulation

siRNA usually acts in:

Small interfering RNAs often guide heterochromatin formation in cis acting at locus producing homologous transcripts rather than diffusing. In fission yeast centromeric repeats transcribed into siRNA precursors processed into Ago1-loaded RITS remaining tethered to nascent transcript via base pairing, recruiting CLRC containing Clr4 methyltransferase to same domain. This cis-restricted recruitment ensures modification targeted exclusively to repeats producing dsRNA, not unrelated loci with limited similarity. In contrast cytoplasmic degradation by siRNAs acts in trans on distant transcripts. Du

Ref: Alberts et al., Molecular Biology of the Cell, 7th ed., Chapter 4: siRNA Functions in Cis for Heterochromatin Assembly

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Eukaryotes gene regulation

RdRP enhances RNAi by:

RNA-dependent RNA polymerase RdRP amplifies small RNA silencing in plants, nematodes, fungi including fission yeast. Primary siRNAs generated by Dicer recruit RdRP complex RDRC containing Rdp1 polymerase, Hrr1 helicase, Cid12 polyA polymerase via Ago1 to target single-stranded transcripts, synthesizing complementary strand forming dsRNA substrate for secondary Dicer cleavage producing secondary siRNAs distal to trigger. This spreads silencing beyond initial region and maintains signal when trigger diluted. RdRP requires Ago1 slicing providing primer hydroxyl. Amplification explains robust sust

Ref: NCBI Bookshelf, RNAi Pathways: RdRP Generates dsRNA for siRNA Amplification

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Eukaryotes gene regulation

Actinomycin D inhibits transcription by:

Actinomycin D chromopeptide antibiotic composed of phenoxazone ring with two cyclic pentapeptide lactones from Streptomyces antibioticus binds DNA via intercalation. Phenoxazone inserts between GC base pairs preferably dGpdC steps unwinding helix about 26 degrees, while lactone peptides occupy minor groove bonding to guanine amino groups stabilizing complex. Intercalation acts as roadblock preventing RNA polymerase II and I progression blocking promoter clearance and elongation. Low doses mainly inhibit transcription, higher doses impede replication. Used experimentally to halt transcription m

Ref: Lodish et al., Molecular Cell Biology, 9th ed., Chapter 6: Actinomycin D Intercalation Mechanism of Transcription Inhibition

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Eukaryotes gene regulation

α-Amanitin inhibits:

Alpha-amanitin is bicyclic octapeptide toxin from Amanita phalloides and related mushrooms selectively inhibiting RNA polymerases with highest affinity for Pol II. Toxin binds deep within funnel below bridge helix near trigger loop blocking translocation along DNA and nucleotide entry, trapping polymerase in pre-translocated state halting mRNA synthesis causing liver failure. Pol III inhibited at micromolar, Pol I resistant allowing discrimination. Amanitin used experimentally to stall complexes for cryo-EM, study transcription kinetics, and generate resistant Pol II mutants mapping binding po

Ref: Alberts et al., Molecular Biology of the Cell, 7th ed., Chapter 6: α-Amanitin Specific Inhibition of RNA Pol II

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Eukaryotes gene regulation

Erythromycin blocks which step?

Erythromycin macrolide contains 14-membered lactone ring with L-desosamine sugar binding nascent peptide exit tunnel of 50S subunit near peptidyl transferase center contacting 23S rRNA A2058, A2059. Binding does not prevent peptide bond formation initially but blocks nascent chain progression through tunnel after six to eight residues, inhibiting translocation where deacylated tRNA moves P to E and peptidyl-tRNA A to P via EF-G. Abortive peptidyl-tRNA drop-off occurs terminating translation prematurely. Resistance via erm methyltransferase methylating A2058 preventing interaction. Bacteriostat

Ref: Lodish et al., Molecular Cell Biology, 9th ed., Chapter 5: Erythromycin Block of Elongation-Translocation

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Eukaryotes gene regulation

Chloramphenicol inhibits:

Chloramphenicol binds domain V central loop of 23S rRNA in 50S subunit peptidyl transferase center overlapping A-site tRNA 3' end. Crystallography shows contacts with A2451, A2452, U2506 critical for aminoacyl positioning. Binding prevents proper orientation of incoming aminoacyl-tRNA inhibiting peptide bond formation arresting elongation. Low concentrations bacteriostatic, higher bactericidal. Mitochondrial ribosomes sensitive due to bacterial ancestry causing toxicity. Resistance conferred by cat gene encoding chloramphenicol acetyltransferase acetylating drug reducing ribosome affinity. Mec

Ref: NCBI Bookshelf, Antibiotics: Chloramphenicol Inhibition of 50S Peptidyl Transferase Activity

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Eukaryotes gene regulation

Puromycin inhibits translation by:

Puromycin is aminonucleoside antibiotic mimicking 3' terminus of aminoacyl-tRNA with aromatic group linked via stable amide not labile ester. Puromycin enters ribosomal A-site accepting nascent polypeptide from P-site via peptidyl transferase, forming peptidyl-puromycin adduct that dissociates prematurely as truncated peptide bearing puromycin at C-terminus causing chain release independent of release factors. Resulting peptide targeted for degradation. At low concentrations used experimentally to label nascent chains and probe translation status, puromycin provides tool for polysome analysis.

Ref: Alberts et al., Molecular Biology of the Cell, 7th ed., Chapter 6: Puromycin Mechanism – Premature Chain Termination

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Eukaryotes gene regulation

No-go decay occurs due to:

No-go decay NGD resolves stalled elongation complexes blocked by strong structures, damaged bases, rare codons, or adducts. Colliding ribosomes upstream recognized by Pelota Dom34 and Hbs1 GTPase resembling termination factors, facilitating endonucleolytic cleavage near stall site via Cue2 nuclease activated by ubiquitination of uS3, uS10 by Hel2 ligase. Resulting fragments degraded by exosome and Xrn1, nascent peptide ubiquitinated and degraded proteasomally. NGD prevents ribosome sequestration maintaining translational capacity and avoids accumulation of incomplete aggregation-prone polypept

Ref: Lodish et al., Molecular Cell Biology, 9th ed., Chapter 5: No-Go Decay Triggered by Ribosome Stalling

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Eukaryotes gene regulation

Nonsense-mediated decay targets mRNAs with:

Nonsense-mediated mRNA decay NMD is surveillance pathway eliminating transcripts harboring premature termination codons PTC to prevent synthesis of truncated proteins with potentially dominant-negative toxic effects. During splicing exon junction complex EJC deposited 20-24 nucleotides upstream of exon-exon borders. Normal termination in last exon lacks downstream EJC; PTC located more than 50-55 nucleotides upstream recruits Upf1 RNA helicase, Upf2, Upf3 after translation termination interacting with terminating ribosome and eRF1 eRF3. SMG1 kinase phosphorylates Upf1 triggering SMG6 endonucle

Ref: NCBI Bookshelf, RNA Surveillance: Nonsense-Mediated Decay Targeting Premature Stop Codons

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Eukaryotes gene regulation

Ferritin translation is regulated by:

Ferritin mRNAs contain iron responsive element IRE conserved hairpin in 5' UTR regulating translation via iron regulatory proteins IRP1 and IRP2. Low iron allows IRP binding blocking 43S scanning and 60S joining repressing synthesis. IRP1 holds Fe-S cluster converting to aconitase when iron sufficient; IRP2 degraded via FBXL5 sensing iron. High iron causes IRP dissociation permitting ferritin production storing iron in mineral core preventing Fenton reactions generating reactive oxygen species. This translational control complements transferrin receptor regulation via 3' UTR IREs stabilizing t

Ref: Alberts et al., Molecular Biology of the Cell, 7th ed., Chapter 7: Iron Regulation of Ferritin Translation via IRE-IRP

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Eukaryotes gene regulation

Telomeric silencing in yeast spreads due to:

Telomeric position effect in budding yeast involves Sir complex spreading from chromosome ends inward silencing subtelomeric genes. Rap1 protein binds TG1-3 telomere repeats recruiting Sir4 which interacts with Sir2 histone deacetylase. Sir2 deacetylates adjacent nucleosomal H4K16 and H3K9, generating high-affinity binding site for Sir3 chromodomain interacting with deacetylated tails, recruiting additional Sir2-Sir4 complexes iteratively propagating heterochromatin several kilobases. This histone deacetylation dependent polymerization requires continuous Sir2 NAD-dependent activity, blocked b

Ref: Lodish et al., Molecular Cell Biology, 9th ed., Chapter 8: Telomeric Silencing Spread via Histone Deacetylation

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Eukaryotes gene regulation

Sir2 protein mainly causes:

Sir2 founding member of sirtuin family is NAD-dependent class III histone deacetylase central to mating type and telomere silencing in Saccharomyces cerevisiae. Sir2 catalyzes deacetylation of acetyl-lysine producing deacetylated histone, nicotinamide, O-acetyl-ADP-ribose using NAD as co-substrate. Preferred substrates H4K16ac, H3K9ac, H3K14ac removal creates hypoacetylated nucleosomes high-affinity for Sir3 bromo adjacent homology domain and Sir4 binding, enabling spreading of SIR complex. Fission yeast Sir2 similarly deacetylates H3K9ac facilitating Clr4 methylation. Sir2 also deacetylates n

Ref: Alberts et al., Molecular Biology of the Cell, 7th ed., Chapter 4: Sir2 Histone Deacetylation and Heterochromatin Spreading

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