Biology:Transcription preinitiation complex

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Short description: Complex of proteins necessary for gene transcription in eukaryotes and archaea
Cluster of ovals representing the transcription preinitiation complex is sandwiched inside a curved strand of DNA, between the promoter region on one end and the enhancer region on the other.
Transcription preinitiation complex, represented by the central cluster of proteins, causes RNA polymerase to bind to target DNA site. The PIC is able to bind both the promoter sequence near the gene to be transcribed and an enhancer sequence in a different part of the genome, allowing enhancer sequences to regulate a gene distant from it.

The preinitiation complex (abbreviated PIC) is a complex of approximately 100 proteins that is necessary for the transcription of protein-coding genes in eukaryotes and archaea. The preinitiation complex positions RNA polymerase II (Pol II) at gene transcription start sites, denatures the DNA, and positions the DNA in the RNA polymerase II active site for transcription.[1][2][3][4]

The minimal PIC includes RNA polymerase II and six general transcription factors: TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIIH. Additional regulatory complexes (such as the mediator coactivator[5] and chromatin remodeling complexes) may also be components of the PIC.

Preinitiation complexes are also formed during RNA Polymerase I and RNA Polymerase III transcription.

Assembly (RNA Polymerase II)

A classical view of PIC formation at the promoter involves the following steps:

  • TATA binding protein (TBP, a subunit of TFIID) binds the promoter, creating a sharp bend in the promoter DNA.[6]
    • Animals have some TBP-related factors (TRF; TBPL1/TBPL2). They can replace TBP in some special contexts.[7]
  • TBP recruits TFIIA, then TFIIB, to the promoter.
  • TFIIB recruits RNA polymerase II and TFIIF to the promoter.
  • TFIIE joins the growing complex and recruits TFIIH which has protein kinase activity (phosphorylates RNA polymerase II within the CTD) and DNA helicase activity (unwinds DNA at promoter). It also recruits nucleotide-excision repair proteins.
  • Subunits within TFIIH that have ATPase and helicase activity create negative superhelical tension in the DNA.
  • Negative superhelical tension causes approximately one turn of DNA to unwind and form the transcription bubble.
  • The template strand of the transcription bubble engages with the RNA polymerase II active site.
  • RNA synthesis begins.
  • After synthesis of ~10 nucleotides of RNA, and an obligatory phase of several abortive transcription cycles, RNA polymerase II escapes the promoter region to transcribe the remainder of the gene.

An alternative hypothesis of PIC assembly postulates the recruitment of a pre-assembled "RNA polymerase II holoenzyme" directly to the promoter (composed of all, or nearly all GTFs and RNA polymerase II and regulatory complexes), in a manner similar to the bacterial RNA polymerase (RNAP).

Other preinitiation complexes

In Archaea

Archaea have a preinitiation complex resembling that of a minimized Pol II PIC, with a TBP and an Archaeal transcription factor B (TFB, a TFIIB homolog). The assembly follows a similar sequence, starting with TBP binding to the promoter. An interesting aspect is that the entire complex is bound in an inverse orientation compared to those found in eukaryotic PIC.[8] They also use TFE, a TFIIE homolog, which assists in transcription initiation but is not required.[9][10]

RNA Polymerase I (Pol I)

Formation of the Pol I preinitiation complex requires the binding of selective factor 1 (SL1 or TIF-IB) to the core element of the rDNA promoter.[11] SL1 is a complex composed of TBP and at least three TBP-associated factors (TAFs). For basal levels of transcription, only SL1 and the initiation-competent form of Pol I (Pol Iβ), characterized by RRN3 binding, are required.[12][13]

For activated transcription levels, UBTF (UBF) is also required. UBTF binds as a dimer to both the upstream control element (UCE) and core element of the rDNA promoter, bending the DNA to form an enhanceosome.[13][12] SL1 has been found to stabilize the binding of UBTF to the rDNA promoter.[11]

The subunits of the Pol I PIC differ between organisms.[14]

RNA Polymerase III (Pol III)

Pol III has three classes of initiation, which start with different factors recognizing different control elements but all converging on TFIIIB (similar to TFIIB-TBP; consists of TBP/TRF, a TFIIB-related factor, and a B″ unit) recruiting the Pol III preinitiation complex. The overall architecture resembles that of Pol II. Only TFIIIB needs to remain attached during elongation.[15]

References

  1. ↑ "Transcription of eukaryotic protein-coding genes". Annual Review of Genetics 34: 77–137. 2000. doi:10.1146/annurev.genet.34.1.77. PMID 11092823. 
  2. ↑ "The molecular basis of eukaryotic transcription". Proceedings of the National Academy of Sciences of the United States of America 104 (32): 12955–61. August 2007. doi:10.1073/pnas.0704138104. PMID 17670940. Bibcode: 2007PNAS..10412955K. 
  3. ↑ "Trajectory of DNA in the RNA polymerase II transcription preinitiation complex". Proceedings of the National Academy of Sciences of the United States of America 94 (23): 12268–73. November 1997. doi:10.1073/pnas.94.23.12268. PMID 9356438. Bibcode: 1997PNAS...9412268K. 
  4. ↑ "Mechanism of ATP-dependent promoter melting by transcription factor IIH". Science 288 (5470): 1418–22. May 2000. doi:10.1126/science.288.5470.1418. PMID 10827951. Bibcode: 2000Sci...288.1418K. 
  5. ↑ "The Mediator complex: a central integrator of transcription". Nature Reviews. Molecular Cell Biology 16 (3): 155–66. 2015. doi:10.1038/nrm3951. PMID 25693131. 
  6. ↑ Ossipow, Vincent; Fonjallaz, Philippe; Schibler, Ueli (1999-02-01). "An RNA Polymerase II Complex Containing All Essential Initiation Factors Binds to the Activation Domain of PAR Leucine Zipper Transcription Factor Thyroid Embryonic Factor" (in en). Molecular and Cellular Biology 19 (2): 1242–1250. doi:10.1128/MCB.19.2.1242. ISSN 1098-5549. PMID 9891058. PMC 116053. https://www.tandfonline.com/doi/full/10.1128/MCB.19.2.1242. 
  7. ↑ Duttke, SH (March 2015). "Evolution and diversification of the basal transcription machinery.". Trends in Biochemical Sciences 40 (3): 127–9. doi:10.1016/j.tibs.2015.01.005. PMID 25661246. 
  8. ↑ Bell, SD; Jackson, SP (June 1998). "Transcription and translation in Archaea: a mosaic of eukaryal and bacterial features.". Trends in Microbiology 6 (6): 222–8. doi:10.1016/S0966-842X(98)01281-5. PMID 9675798. 
  9. ↑ Hanzelka, BL; Darcy, TJ; Reeve, JN (March 2001). "TFE, an archaeal transcription factor in Methanobacterium thermoautotrophicum related to eucaryal transcription factor TFIIEalpha.". Journal of Bacteriology 183 (5): 1813–8. doi:10.1128/JB.183.5.1813-1818.2001. PMID 11160119. 
  10. ↑ Gehring, Alexandra M.; Walker, Julie E.; Santangelo, Thomas J.; Margolin, W. (15 July 2016). "Transcription Regulation in Archaea". Journal of Bacteriology 198 (14): 1906–1917. doi:10.1128/JB.00255-16. PMID 27137495. 
  11. ↑ 11.0 11.1 Friedrich, J. Karsten; Panov, Kostya I.; Cabart, Pavel; Russell, Jackie; Zomerdijk, Joost C.B.M. (August 2005). "TBP-TAF Complex SL1 Directs RNA Polymerase I Pre-initiation Complex Formation and Stabilizes Upstream Binding Factor at the rDNA Promoter". Journal of Biological Chemistry 280 (33): 29551–29558. doi:10.1074/jbc.m501595200. ISSN 0021-9258. PMID 15970593. 
  12. ↑ 12.0 12.1 Russell, Jackie; Zomerdijk, Joost C.B.M. (February 2005). "RNA-polymerase-I-directed rDNA transcription, life and works". Trends in Biochemical Sciences 30 (2): 87–96. doi:10.1016/j.tibs.2004.12.008. ISSN 0968-0004. PMID 15691654. PMC 3858833. http://dx.doi.org/10.1016/j.tibs.2004.12.008. 
  13. ↑ 13.0 13.1 Goodfellow, Sarah J.; Zomerdijk, Joost C. B. M. (2012-06-28), Basic Mechanisms in RNA Polymerase I Transcription of the Ribosomal RNA Genes, Subcellular Biochemistry, 61, Dordrecht: Springer Netherlands, pp. 211–236, doi:10.1007/978-94-007-4525-4_10, ISBN 978-94-007-4524-7, PMID 23150253, PMC 3855190, http://dx.doi.org/10.1007/978-94-007-4525-4_10, retrieved 2023-10-30 
  14. ↑ Grummt, Ingrid (15 July 2003). "Life on a planet of its own: regulation of RNA polymerase I transcription in the nucleolus". Genes & Development 17 (14): 1691–1702. doi:10.1101/gad.1098503R. PMID 12865296. 
  15. ↑ Han, Y; Yan, C; Fishbain, S; Ivanov, I; He, Y (2018). "Structural visualization of RNA polymerase III transcription machineries.". Cell Discovery 4: 40. doi:10.1038/s41421-018-0044-z. PMID 30083386. 

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