General transcription factor
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 (a multi-protein complex) 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.
A transcription factor is a protein that binds to specific DNA sequences (enhancer or promoter), either alone or with other proteins in a complex, to control the rate of transcription of genetic information from DNA to messenger RNA by promoting (serving as an activator) or blocking (serving as a repressor) the recruitment of RNA polymerase. As a class of protein, general transcription factors bind to promoters along the DNA sequence or form a large transcription preinitiation complex to activate transcription. General transcription factors are necessary for transcription to occur.
In archaea and eukaryotes, transcription initiation requires an RNA polymerase and a set of multiple GTFs to form a transcription preinitiation complex. The Transcription initiation by eukaryotic RNA polymerase II involves the following GTFs:
Function and mechanism
A sigma factor is a protein needed only for initiation of RNA synthesis in bacteria. Sigma factors provide promoter recognition specificity to the RNA polymerase (RNAP) and contribute to DNA strand separation, then dissociating from the RNA polymerase core enzyme following transcription initiation. The RNA polymerase core associates with the sigma factor to form RNA polymerase holoenzyme. Sigma factor reduces the affinity of RNA polymerase for nonspecific DNA while increasing specificity for promoters, allowing transcription to initiate at correct sites. The core enzyme of RNA polymerase has five subunits (protein subunits) (~400 kDa). Because of the RNA polymerase association with sigma factor, the complete RNA polymerase therefore has 6 subunits: the sigma subunit-in addition to the two alpha (α), one beta (β), one beta prime (β'), and one omega (ω) subunits that make up the core enzyme(~450 kDa). In addition, many bacteria can have multiple alternative σ factors. The level and activity of the alternative σ factors are highly regulated and can vary depending on environmental or developmental signals.
In archaea and eukaryotes
The transcription preinitiation complex is a large complex of proteins that is necessary for the transcription of protein-coding genes in eukaryotes and archaea. It attaches to the promoter of the DNA (e.i., TATA box) and helps position the RNA polymerase II to the gene transcription start sites, denatures the DNA, and then starts transcription.
Transcription preinitiation complex assembly
The assembly of transcription preinitiation complex follows these steps:
- TATA binding protein (TBP), a subunit of TFIID (the largest GTF) binds to the promoter (TATA box), creating a sharp bend in the promoter DNA. Then the TBP-TFIIA interactions recruit TFIIA to the promoter.
- TBP-TFIIB interactions recruit TFIIB to the promoter. RNA polymerase II and TFIIF assemble to form the Polymerase II complex. TFIIB helps the Pol II complex bind correctly.
- TFIIE and TFIIH then bind to the complex and form the transcription preinitiation complex. TFIIA/B/E/H leave once RNA elongation begins. TFIID will stay until elongation is finished.
- Subunits within TFIIH that have ATPase and helicase activity create negative superhelical tension in the DNA. This 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, then RNA synthesis starts.
- Pierce, Benjamin A. (2012). Genetics a conceptual approach (4th ed.). New York: W.H. Freeman. pp. 364–367. ISBN 978-1-4292-3250-0.
- Dillon, Niall (2006). "Gene regulation and large-scale chromatin organization in the nucleus". Chromosome Research. 14 (1): 117–26. doi:10.1007/s10577-006-1027-8. PMID 16506101.
- Latchman, David S. (December 1997). "Transcription factors: an overview". The International Journal of Biochemistry & Cell Biology. 29 (12): 1305–12. doi:10.1016/S1357-2725(97)00085-X. PMC 2002184. PMID 9570129.
- Karin, M. (February 1990). "Too many transcription factors: positive and negative interactions". The New Biologist. 2 (2): 126–31. PMID 2128034.
- Roeder, Robert G. (September 1996). "The role of general initiation factors in transcription by RNA polymerase II". Trends in Biochemical Sciences. 21 (9): 327–35. doi:10.1016/S0968-0004(96)10050-5. PMID 8870495.
- Nikolov, D.B.; Burley, S.K. (1997). "RNA polymerase II transcription initiation: A structural view". Proceedings of the National Academy of Sciences of the United States of America. 94 (1): 15–22. Bibcode:1997PNAS...94...15N. doi:10.1073/pnas.94.1.15. PMC 33652. PMID 8990153.
- Lee, Tong Ihn; Young, Richard A. (2000). "Transcription of eukaryotic protein-coding genes". Annual Review of Genetics. 34 (1): 77–137. doi:10.1146/annurev.genet.34.1.77. PMID 11092823.
- Weinzierl, Robert O.J. (1999). Mechanisms of Gene Expression: Structure, Function and Evolution of the Basal Transcriptional Machinery. London: Imperial College Press. ISBN 978-1-86094-126-9.
- Reese, Joseph C. (April 2003). "Basal transcription factors". Current Opinion in Genetics & Development. 13 (2): 114–8. doi:10.1016/S0959-437X(03)00013-3. PMID 12672487.
- Shilatifard, Ali; Conaway, Ronald C.; Conaway, Joan Weliky (2003). "The RNA polymerase II elongation complex". Annual Review of Biochemistry. 72 (1): 693–715. doi:10.1146/annurev.biochem.72.121801.161551. PMID 12676794.
- Orphanides, George; Lagrange, Thierry; Reinberg, Danny (November 1996). "The general transcription factors of RNA polymerase II". Genes & Development. 10 (21): 2657–83. doi:10.1101/gad.10.21.2657. PMID 8946909.
- Gruber, Tanja M.; Gross, Carol A. (October 2003). "Multiple sigma subunits and the partitioning of bacterial transcription space". Annual Review of Microbiology. 57: 441–66. doi:10.1146/annurev.micro.57.030502.090913. PMID 14527287.
- Borukhov, Sergei; Nudler, Evgeny (April 2003). "RNA polymerase holoenzyme: structure, function and biological implications". Current Opinion in Microbiology. 6 (2): 93–100. doi:10.1016/S1369-5274(03)00036-5. ISSN 1369-5274. PMID 12732296.
- Ebright, Richard H. (December 2000). "RNA polymerase: structural similarities between bacterial RNA polymerase and eukaryotic RNA polymerase II". Journal of Molecular Biology. 304 (5): 687–98. doi:10.1006/jmbi.2000.4309. PMID 11124018.
- Chandrangsu, Pete; Helmann, John D. (March 2014). "Sigma factors in gene expression". Encyclopedia of Life Sciences. Chichester: John Wiley & Sons Ltd. doi:10.1002/9780470015902.a0000854.pub3. ISBN 978-0-470-01590-2.
- Kornberg, Roger D. (7 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.
- Kim, Tae-Kyung; Lagrange, Thierry; Wang, Yuh-Hwa; Griffith, Jack D.; Reinberg, Danny; Ebright, Richard H. (11 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.
- Kim, Tae-Kyung; Ebright, Richard H.; Reinberg, Danny (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.