Transcription preinitiation complex

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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. Figure 16 04 01.jpg
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]

Contents

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:

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]

Related Research Articles

In molecular biology, the TATA box is a sequence of DNA found in the core promoter region of genes in archaea and eukaryotes. The bacterial homolog of the TATA box is called the Pribnow box which has a shorter consensus sequence.

RNA polymerase 1 is, in higher eukaryotes, the polymerase that only transcribes ribosomal RNA, a type of RNA that accounts for over 50% of the total RNA synthesized in a cell.

<span class="mw-page-title-main">General transcription factor</span> Class of protein transcription factors

General transcription factors (GTFs), also known as basal transcriptional factors, are a class of protein transcription factors that bind to specific sites (promoter) on DNA to activate transcription of genetic information from DNA to messenger RNA. GTFs, RNA polymerase, and the mediator constitute the basic transcriptional apparatus that first bind to the promoter, then start transcription. GTFs are also intimately involved in the process of gene regulation, and most are required for life.

<span class="mw-page-title-main">TATA-binding protein</span> Protein-coding gene in the species Homo sapiens

The TATA-binding protein (TBP) is a general transcription factor that binds specifically to a DNA sequence called the TATA box. This DNA sequence is found about 30 base pairs upstream of the transcription start site in some eukaryotic gene promoters.

Transcription factor II D (TFIID) is one of several general transcription factors that make up the RNA polymerase II preinitiation complex. RNA polymerase II holoenzyme is a form of eukaryotic RNA polymerase II that is recruited to the promoters of protein-coding genes in living cells. It consists of RNA polymerase II, a subset of general transcription factors, and regulatory proteins known as SRB proteins. Before the start of transcription, the transcription Factor II D (TFIID) complex binds to the core promoter DNA of the gene through specific recognition of promoter sequence motifs, including the TATA box, Initiator, Downstream Promoter, Motif Ten, or Downstream Regulatory elements.

<span class="mw-page-title-main">Eukaryotic transcription</span> Transcription is heterocatalytic function of DNA

Eukaryotic transcription is the elaborate process that eukaryotic cells use to copy genetic information stored in DNA into units of transportable complementary RNA replica. Gene transcription occurs in both eukaryotic and prokaryotic cells. Unlike prokaryotic RNA polymerase that initiates the transcription of all different types of RNA, RNA polymerase in eukaryotes comes in three variations, each translating a different type of gene. A eukaryotic cell has a nucleus that separates the processes of transcription and translation. Eukaryotic transcription occurs within the nucleus where DNA is packaged into nucleosomes and higher order chromatin structures. The complexity of the eukaryotic genome necessitates a great variety and complexity of gene expression control.

Transcription factor TFIIA is a nuclear protein involved in the RNA polymerase II-dependent transcription of DNA. TFIIA is one of several general (basal) transcription factors (GTFs) that are required for all transcription events that use RNA polymerase II. Other GTFs include TFIID, a complex composed of the TATA binding protein TBP and TBP-associated factors (TAFs), as well as the factors TFIIB, TFIIE, TFIIF, and TFIIH. Together, these factors are responsible for promoter recognition and the formation of a transcription preinitiation complex (PIC) capable of initiating RNA synthesis from a DNA template.

<span class="mw-page-title-main">Transcription factor II B</span> Mammalian protein found in Homo sapiens

Transcription factor II B (TFIIB) is a general transcription factor that is involved in the formation of the RNA polymerase II preinitiation complex (PIC) and aids in stimulating transcription initiation. TFIIB is localised to the nucleus and provides a platform for PIC formation by binding and stabilising the DNA-TBP complex and by recruiting RNA polymerase II and other transcription factors. It is encoded by the TFIIB gene, and is homologous to archaeal transcription factor B and analogous to bacterial sigma factors.

Transcription factor II E (TFIIE) is one of several general transcription factors that make up the RNA polymerase II preinitiation complex. It is a tetramer of two alpha and two beta chains and interacts with TAF6/TAFII80, ATF7IP, and varicella-zoster virus IE63 protein.

Transcription factor II F (TFIIF) is one of several general transcription factors that make up the RNA polymerase II preinitiation complex.

<span class="mw-page-title-main">TAF2</span> Protein-coding gene in the species Homo sapiens

Transcription initiation factor TFIID subunit 2 is a protein that in humans is encoded by the TAF2 gene.

<span class="mw-page-title-main">TAF1C</span> Protein-coding gene in the species Homo sapiens

TATA box-binding protein-associated factor RNA polymerase I subunit C is an enzyme that in humans is encoded by the TAF1C gene.

<span class="mw-page-title-main">TAF1A</span> Protein-coding gene in the species Homo sapiens

TATA box-binding protein-associated factor RNA polymerase I subunit A is an enzyme that in humans is encoded by the TAF1A gene.

<span class="mw-page-title-main">TAF1B</span> Protein-coding gene in the species Homo sapiens

TATA box-binding protein-associated factor RNA polymerase I subunit B is an enzyme that in humans is encoded by the TAF1B gene.

RNA polymerase II holoenzyme is a form of eukaryotic RNA polymerase II that is recruited to the promoters of protein-coding genes in living cells. It consists of RNA polymerase II, a subset of general transcription factors, and regulatory proteins known as SRB proteins.

<span class="mw-page-title-main">B recognition element</span>

The B recognition element (BRE) is a DNA sequence found in the promoter region of most genes in eukaryotes and Archaea. The BRE is a cis-regulatory element that is found immediately near TATA box, and consists of 7 nucleotides. There are two sets of BREs: one (BREu) found immediately upstream of the TATA box, with the consensus SSRCGCC; the other (BREd) found around 7 nucleotides downstream, with the consensus RTDKKKK.

<span class="mw-page-title-main">TBP-associated factor</span> Protein domains

The TBP-associated factors (TAF) are proteins that associate with the TATA-binding protein in transcription initiation. It is a part of the transcription initiation factor TFIID multimeric protein complex. It also makes up many other factors, including SL1. They mediate the formation of the transcription preinitiation complex, a step preceding transcription of DNA to RNA by RNA polymerase II.

<span class="mw-page-title-main">Archaeal transcription factor B</span> Protein family

Archaeal transcription factor B is a protein family of extrinsic transcription factors that guide the initiation of RNA transcription in organisms that fall under the domain of Archaea. It is homologous to eukaryotic TFIIB and, more distantly, to bacterial sigma factor. Like these proteins, it is involved in forming transcription preinitiation complexes. Its structure includes several conserved motifs which interact with DNA and other transcription factors, notably the single type of RNA polymerase that performs transcription in Archaea.

<span class="mw-page-title-main">Selective factor 1</span> Mammalian protein found in Homo sapiens

Selective factor 1 is a transcription factor that binds to the promoter of genes and recruits a preinitiation complex to which RNA polymerase I will bind to and begin the transcription of ribosomal RNA (rRNA).

<span class="mw-page-title-main">Archaeal transcription</span>

Archaeal transcription is the process in which a segment of archaeal DNA is copied into a newly synthesized strand of RNA using the sole Pol II-like RNA polymerase (RNAP). The process occurs in three main steps: initiation, elongation, and termination; and the end result is a strand of RNA that is complementary to a single strand of DNA. A number of transcription factors govern this process with homologs in both bacteria and eukaryotes, with the core machinery more similar to eukaryotic transcription.

References

  1. ↑ Lee TI, Young RA (2000). "Transcription of eukaryotic protein-coding genes". Annual Review of Genetics. 34: 77–137. doi:10.1146/annurev.genet.34.1.77. PMID   11092823.
  2. ↑ Kornberg RD (August 2007). "The molecular basis of eukaryotic transcription". Proceedings of the National Academy of Sciences of the United States of America. 104 (32): 12955–61. Bibcode:2007PNAS..10412955K. doi: 10.1073/pnas.0704138104 . PMC   1941834 . PMID   17670940.
  3. ↑ Kim TK, Lagrange T, Wang YH, Griffith JD, Reinberg D, Ebright RH (November 1997). "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. Bibcode:1997PNAS...9412268K. doi: 10.1073/pnas.94.23.12268 . PMC   24903 . PMID   9356438.
  4. ↑ Kim TK, Ebright RH, Reinberg D (May 2000). "Mechanism of ATP-dependent promoter melting by transcription factor IIH". Science. 288 (5470): 1418–22. Bibcode:2000Sci...288.1418K. doi:10.1126/science.288.5470.1418. PMID   10827951.
  5. ↑ Allen BL, Taatjes DJ (2015). "The Mediator complex: a central integrator of transcription". Nature Reviews. Molecular Cell Biology. 16 (3): 155–66. doi:10.1038/nrm3951. PMC   4963239 . 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". Molecular and Cellular Biology. 19 (2): 1242–1250. doi:10.1128/MCB.19.2.1242. ISSN   1098-5549. PMC   116053 . PMID   9891058.
  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. PMC   4410091 . 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. PMC   95073 . 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. PMC   4936096 . PMID   27137495.
  11. 1 2 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. PMC   3858828 . PMID   15970593.
  12. 1 2 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. PMC   3858833 . PMID   15691654.
  13. 1 2 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, vol. 61, Dordrecht: Springer Netherlands, pp. 211–236, doi:10.1007/978-94-007-4525-4_10, ISBN   978-94-007-4524-7, PMC   3855190 , PMID   23150253 , retrieved 2023-10-30
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  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. PMC   6066478 . PMID   30083386.
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