Prokaryotic_vs_Eukaryotic_Transcription_Expanded.pptx

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1. Prokaryotic vs. Eukaryotic Transcription RNA Polymerases, Promoters, Sigma Factors, and Transcription Factors Molecular Biology - Master's Level

2. Outline • Overview of Transcription • Prokaryotic Transcription • Eukaryotic Transcription • RNA Polymerases Comparison • Promoters • Sigma Factors vs. Transcription Factors • Key Differences • References

3. Overview of Transcription • Transcription is the process of synthesizing RNA from a DNA template. • Fundamental in gene expression and regulation. • Involves RNA polymerase, promoter recognition, and initiation factors. • Mechanisms differ significantly between prokaryotes and eukaryotes.

4. Prokaryotic Transcription • Occurs in the cytoplasm. • Single RNA polymerase (holoenzyme). • Requires sigma factors for promoter recognition. • Promoters: -10 (Pribnow box) and -35 consensus sequences. • Coupled transcription and translation.

5. Eukaryotic Transcription • Occurs in the nucleus. • Three RNA polymerases: - RNA Pol I: rRNA (except 5S) - RNA Pol II: mRNA, snRNA, miRNA - RNA Pol III: tRNA, 5S rRNA • Requires general transcription factors (TFII proteins). • Promoters: TATA box, CAAT box, GC-rich regions.

6. RNA Polymerases: Prokaryotic vs. Eukaryotic Prokaryotes: • Single RNA polymerase for all RNA types. Eukaryotes: • Multiple RNA polymerases (I, II, III) with specialized roles. • Complex regulation and additional cofactors required.

7. Promoters Prokaryotic Promoters: • -10 (Pribnow box) and -35 elements recognized by sigma factor. Eukaryotic Promoters: • TATA box (commonly recognized by TATA-binding protein). • CAAT box and GC-rich regions for enhancer regulation. • More diverse and modular than prokaryotic promoters.

8. Sigma Factors vs. Transcription Factors Prokaryotes: • Sigma factors (σ) guide RNA polymerase to specific promoters. • Alternative sigma factors allow differential gene expression. Eukaryotes: • General transcription factors (TFIIA, TFIIB, TFIID, etc.). • Regulatory transcription factors bind enhancers/silencers. • Enable complex regulation of gene expression.

9. Key Differences • Location: cytoplasm (prokaryotes) vs. nucleus (eukaryotes). • RNA polymerases: single (prokaryotes) vs. multiple (eukaryotes). • Initiation factors: sigma factors vs. transcription factors. • Promoters: simple (-10, -35) vs. complex (TATA, CAAT, enhancers). • Coupled transcription-translation (prokaryotes) vs. compartmentalized (eukaryotes).

10. References • Alberts B. et al., Molecular Biology of the Cell, 6th Edition. • Lodish H. et al., Molecular Cell Biology, 8th Edition. • Nelson DL & Cox MM, Lehninger Principles of Biochemistry, 8th Edition. • Brow DA, “RNA polymerase transcription,” Cold Spring Harbor Perspectives, 2011. • Kornberg RD, “The molecular basis of eukaryotic transcription,” PNAS, 2007.

11. Figure: Bacterial Promoter Architecture Consensus −35 (TTGACA) and −10 (TATAAT) elements with optimal 16–18 bp spacing; UP elements enhance α-CTD binding; +1 marks transcription start site.

12. Figure: Eukaryotic Core Promoter Motifs Modular motifs: TATA (~−25), BREu/BREd (TFIIB), Inr at +1, DPE (~+28–+32). TBP binds TATA as part of TFIID; many human promoters are TATA-less (often CpG islands) with Inr±DPE.

13. Figure: Sigma Factor vs. Eukaryotic PIC Bacteria: a single, swappable σ factor seeds promoter recognition. Eukaryotes: a multi-factor PIC integrates signals from activators via Mediator before Pol II initiation.

14. Figure: Transcription Cycle—Key Divergences At each stage—recognition, opening, escape, elongation, termination—bacteria and eukaryotes use distinct factors and strategies tailored to their cellular context.

15. References (Selected) • Alberts B, Johnson A, Lewis J, et al. Molecular Biology of the Cell. 6th ed. Garland Science. • Lodish H, Berk A, Kaiser C, et al. Molecular Cell Biology. 8th ed. W.H. Freeman. • Kadonaga JT. Perspectives on the RNA Polymerase II Core Promoter. Cold Spring Harb Perspect Biol. 2012. • Cramer P. Organization and Regulation of Gene Transcription. Nat Rev Mol Cell Biol. 2019. • Porrua O, Libri D. Transcription termination in eukaryotes. Nat Rev Mol Cell Biol. 2015. • Hahn S. Structure and mechanism of the RNA polymerase II transcription machinery. Nat Rev Mol Cell Biol. 2004. • Thomas MC, Chiang CM. The general transcription machinery and general cofactors. Genes Dev. 2006. • Gourse RL, Ross W, Gaal T. UP elements and bacterial promoter control. Annu Rev Microbiol. 2000. • Kornberg RD. The molecular basis of eukaryotic transcription. Annu Rev Biochem. 2007. • Vannini A, Cramer P. Conservation and specialization in transcription machineries. Nat Rev Mol Cell Biol. 2012. • Peters JM, et al. Rho and NusG influence on transcription-translation coupling. Science. 2012. • Campbell EA, et al. Structural mechanism for rifampicin inhibition of bacterial RNA polymerase. Cell. 2001.