RNA polymerase I

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RNA polymerase 1 (also known as Pol I) is, in higher eukaryotes, the polymerase that only transcribes ribosomal RNA (but not 5S rRNA, which is synthesized by RNA polymerase III), a type of RNA that accounts for over 50% of the total RNA synthesized in a cell. [1]

Contents

Structure and Function

Pol I is a 590 kDa enzyme that consists of 14 protein subunits (polypeptides), and its crystal structure in the yeast Saccharomyces cerevisiae was solved at 2.8Å resolution in 2013. [2] Twelve of its subunits have identical or related counterparts in RNA polymerase II (Pol II) and RNA polymerase III (Pol III). The other two subunits are related to Pol II initiation factors and have structural homologues in Pol III.

Ribosomal DNA transcription is confined to the nucleolus, where about 400 copies of the 42.9-kb rDNA gene are present, arranged as tandem repeats in nucleolus organizer regions. Each copy contains a ~13.3 kb sequence encoding the 18S, the 5.8S, and the 28S RNA molecules, interlaced with two internal transcribed spacers, ITS1 and ITS2, and flanked upstream by a 5' external transcribed spacer and a downstream 3' external transcribed spacer. [3] [4] These components are transcribed together to form the 45S pre-rRNA. [5] The 45S pre-rRNA is then post-transcriptionally cleaved by C/D box and H/ACA box snoRNAs, [6] removing the two spacers and resulting in the three rRNAs by a complex series of steps. [7] The 5S ribosomal RNA is transcribed by Pol III. Because of the simplicity of Pol I transcription, it is the fastest-acting polymerase and contributes up to 60% of cellular transcription levels in exponentially growing cells.

In Saccharomyces cerevisiae , the 5S rDNA has the unusual feature of lying inside the rDNA repeat. It is flanked by non-transcribed spacers NTS1 and NTS2, and is transcribed backwards by Pol III, separately from the rest of the rDNA. [7]

Regulation of rRNA transcription

The rate of cell growth is directly dependent on the rate of protein synthesis, which is itself intricately linked to ribosome synthesis and rRNA transcription. Thus, intracellular signals must coordinate the synthesis of rRNA with that of other components of protein translation. Myc is known to bind to human ribosomal DNA in order to stimulate rRNA transcription by RNA polymerase I. [8] Two specific mechanisms have been identified, ensuring proper control of rRNA synthesis and Pol I-mediated transcription.

Given the large numbers of rDNA genes (several hundreds) available for transcription, the first mechanism involves adjustments in the number of genes being transcribed at a specific time. In mammalian cells, the number of active rDNA genes varies between cell types and level of differentiation. In general, as a cell becomes more differentiated, it requires less growth and, therefore, will have a decrease in rRNA synthesis and a decrease in rDNA genes being transcribed. When rRNA synthesis is stimulated, SL1 (selectivity factor 1) will bind to the promoters of rDNA genes that were previously silent, and recruit a pre-initiation complex to which Pol I will bind and start transcription of rRNA.

Changes in rRNA transcription can also occur via changes in the rate of transcription. While the exact mechanism through which Pol I increases its rate of transcription is as yet unknown, evidence has shown that rRNA synthesis can increase or decrease without changes in the number of actively transcribed rDNA.

Transcription cycle

In the process of transcription (by any polymerase), there are three main stages:

  1. Initiation: the construction of the RNA polymerase complex on the gene's promoter with the help of transcription factors
  2. Elongation: the actual transcription of the majority of the gene into a corresponding RNA sequence
  3. Termination: the cessation of RNA transcription and the disassembly of the RNA polymerase complex.

Initiation

Pol I requires no TATA box in the promoter, instead relying on an upstream control element (UCE) located between −200 and −107, and a core element located between −45 and +20. [9] [10]

  1. The dimeric eukaryotic upstream binding factor (UBF) binds the UCE and the core element.
  2. UBF recruits and binds a protein complex called SL1 in humans (or TIF-IB in mouse), composed of the TATA-binding protein (TBP) and three TBP-associated factors (TAFs). [11] [12]
  3. The UBF dimer contains several high-mobility-group boxes (HMG-boxes) that introduce loops into the upstream region, allowing the UCE and the core elements to come into contact.
  4. RRN3/TIF-IA is phosphorylated and binds Pol I.
  5. Pol I binds to the UBF/SL1 complex via RRN3/TIF-IA, and transcription starts.

Note that this process is variable in different organisms. [10]

Elongation

As Pol I escapes and clears the promoter, UBF and SL1 remain-promoter bound, ready to recruit another Pol I. Indeed, each active rDNA gene can be transcribed multiple times simultaneously, as opposed to Pol II-transcribed genes, which associate with only one complex at a time. While elongation proceeds unimpeded in vitro, it is unclear at this point whether this process happens in a cell, given the presence of nucleosomes. Pol I does seem to transcribe through nucleosomes, either bypassing or disrupting them, perhaps assisted by chromatin-remodeling activities. In addition, UBF might also act as positive feedback, enhancing Pol I elongation through an anti-repressor function. An additional factor, TIF-IC, can also stimulate the overall rate of transcription and suppress pausing of Pol I. As Pol I proceeds along the rDNA, supercoils form both ahead of and behind the complex. These are unwound by topoisomerase I or II at regular intervals, similar to what is seen in Pol II-mediated transcription.[ citation needed ]

Elongation is likely to be interrupted at sites of DNA damage. Transcription-coupled repair occurs similarly to Pol II-transcribed genes and requires the presence of several DNA repair proteins, such as TFIIH, CSB, and XPG.

Termination

In higher eukaryotes, TTF-I binds and bends the termination site at the 3' end of the transcribed region. This will force Pol I to pause. TTF-I, with the help of transcript-release factor PTRF and a T-rich region, will induce Pol I into terminating transcription and dissociating from the DNA and the new transcript. Evidence suggests that termination might be rate-limiting in cases of high rRNA production. TTF-I and PTRF will then indirectly stimulate the reinitiation of transcription by Pol I at the same rDNA gene. In organisms such as budding yeast the process seems to be much more complicated and is still not completely elucidated.[ citation needed ]

Recombination hotspot

Recombination hotspots are DNA sequences that increase local recombination. The HOT1 sequence in yeast is one of the most well studied mitotic recombination hotspots. The HOT1 sequence includes an RNA polymerase I transcription promoter. In a yeast mutant strain defective in RNA polymerase I the HOT1 activity in promoting recombination is abolished. The level of RNA polymerase I transcription activity that is dependent on the promoter in the HOT1 sequence appears to determine the level of nearby mitotic recombination. [13]

See also

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Nucleolus Largest structure in the nucleus of eukaryotic cells

The nucleolus is the largest structure in the nucleus of eukaryotic cells. It is best known as the site of ribosome biogenesis. Nucleoli also participate in the formation of signal recognition particles and play a role in the cell's response to stress. Nucleoli are made of proteins, DNA and RNA and form around specific chromosomal regions called nucleolar organizing regions. Malfunction of nucleoli can be the cause of several human conditions called "nucleolopathies" and the nucleolus is being investigated as a target for cancer chemotherapy.

Transcription (biology) Process of copying a segment of DNA into RNA

Transcription is the process of copying a segment of DNA into RNA. The segments of DNA transcribed into RNA molecules that can encode proteins are said to produce messenger RNA (mRNA). Other segments of DNA are copied into RNA molecules called non-coding RNAs (ncRNAs). Averaged over multiple cell types in a given tissue, the quantity of mRNA is more than 10 times the quantity of ncRNA. The general preponderance of mRNA in cells is valid even though less than 2% of the human genome can be transcribed into mRNA, while at least 80% of mammalian genomic DNA can be actively transcribed, with the majority of this 80% considered to be ncRNA.

RNA polymerase

In molecular biology, RNA polymerase, is an enzyme that synthesizes RNA from a DNA template.

In molecular biology and genetics, transcriptional regulation is the means by which a cell regulates the conversion of DNA to RNA (transcription), thereby orchestrating gene activity. A single gene can be regulated in a range of ways, from altering the number of copies of RNA that are transcribed, to the temporal control of when the gene is transcribed. This control allows the cell or organism to respond to a variety of intra- and extracellular signals and thus mount a response. Some examples of this include producing the mRNA that encode enzymes to adapt to a change in a food source, producing the gene products involved in cell cycle specific activities, and producing the gene products responsible for cellular differentiation in multicellular eukaryotes, as studied in evolutionary developmental biology.

A sigma factor is a protein needed for initiation of transcription in bacteria. It is a bacterial transcription initiation factor that enables specific binding of RNA polymerase (RNAP) to gene promoters. It is homologous to archaeal transcription factor B and to eukaryotic factor TFIIB. The specific sigma factor used to initiate transcription of a given gene will vary, depending on the gene and on the environmental signals needed to initiate transcription of that gene. Selection of promoters by RNA polymerase is dependent on the sigma factor that associates with it. They are also found in plant chloroplasts as a part of the bacteria-like plastid-encoded polymerase (PEP).

In genetics, a transcription terminator is a section of nucleic acid sequence that marks the end of a gene or operon in genomic DNA during transcription. This sequence mediates transcriptional termination by providing signals in the newly synthesized transcript RNA that trigger processes which release the transcript RNA from the transcriptional complex. These processes include the direct interaction of the mRNA secondary structure with the complex and/or the indirect activities of recruited termination factors. Release of the transcriptional complex frees RNA polymerase and related transcriptional machinery to begin transcription of new mRNAs.

Ribosomal DNA

Ribosomal DNA (rDNA) is a DNA sequence that codes for ribosomal RNA. These sequences regulate transcription initiation and amplification, and contain both transcribed and non-transcribed spacer segments.

Transcription preinitiation complex Complex of proteins necessary for gene transcription in eukaryotes and archaea

The preinitiation complex 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 at gene transcription start sites, denatures the DNA, and positions the DNA in the RNA polymerase II active site for transcription.

RNA polymerase II Protein complex that transcribes DNA

RNA polymerase II is a multiprotein complex that transcribes DNA into precursors of messenger RNA (mRNA) and most small nuclear RNA (snRNA) and microRNA. It is one of the three RNAP enzymes found in the nucleus of eukaryotic cells. A 550 kDa complex of 12 subunits, RNAP II is the most studied type of RNA polymerase. A wide range of transcription factors are required for it to bind to upstream gene promoters and begin transcription.

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.

In eukaryote cells, RNA polymerase III transcribes DNA to synthesize ribosomal 5S rRNA, tRNA and other small RNAs.

Ribosome biogenesis Cellular process

Ribosome biogenesis is the process of making ribosomes. In prokaryotes, this process takes place in the cytoplasm with the transcription of many ribosome gene operons. In eukaryotes, it takes place both in the cytoplasm and in the nucleolus. It involves the coordinated function of over 200 proteins in the synthesis and processing of the three prokaryotic or four eukaryotic rRNAs, as well as assembly of those rRNAs with the ribosomal proteins. Most of the ribosomal proteins fall into various energy-consuming enzyme families including ATP-dependent RNA helicases, AAA-ATPases, GTPases, and kinases. About 60% of a cell's energy is spent on ribosome production and maintenance.

Transcription bubble

A transcription bubble is a molecular structure formed during DNA transcription when a limited portion of the DNA double strand is unwound. The size of a transcription bubble ranges from 12-14 base pairs. A transcription bubble is formed when the RNA polymerase enzyme binds to a promoter and causes two DNA strands to detach. It presents a region of unpaired DNA, where a short stretch of nucleotides are exposed on each strand of the double helix.

Bacterial transcription

Bacterial transcription is the process in which a segment of bacterial DNA is copied into a newly synthesized strand of messenger RNA (mRNA) with use of the enzyme RNA polymerase. The process occurs in three main steps: initiation, elongation, and termination; and the end result is a strand of mRNA that is complementary to a single strand of DNA. Generally, the transcribed region accounts for more than one gene. In fact, many prokaryotic genes occur in operons, which are a series of genes that work together to code for the same protein or gene product and are controlled by a single promoter. Bacterial RNA polymerase is made up of four subunits and when a fifth subunit attaches, called the σ-factor, the polymerase can recognize specific binding sequences in the DNA, called promoters. The binding of the σ-factor to the promoter is the first step in initiation. Once the σ-factor releases from the polymerase, elongation proceeds. The polymerase continues down the double stranded DNA, unwinding it and synthesizing the new mRNA strand until it reaches a termination site. There are two termination mechanisms that are discussed in further detail below. Termination is required at specific sites for proper gene expression to occur. Gene expression determines how much gene product, such as protein, is made by the gene. Transcription is carried out by RNA polymerase but its specificity is controlled by sequence-specific DNA binding proteins called transcription factors. Transcription factors work to recognize specific DNA sequences and based on the cells needs, promote or inhibit additional transcription.

Eukaryotic transcription 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.

UBTF

Nucleolar transcription factor 1 is a protein that in humans is encoded by the UBTF gene.

TAF1C

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

Selective factor 1

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).

References

  1. ↑ Russell, Jackie; Zomerdijk, Joost C B M (2006). "The RNA polymerase I transcription machinery". Biochemical Society Symposium. 73 (73): 203–16. doi:10.1042/bss0730203. PMC   3858827 . PMID   16626300.
  2. ↑ Engel, Christoph; Sainsbury, Sarah; Cheung, Alan C.; Kostrewa, Dirk; Cramer, Patrick (23 October 2013). "RNA polymerase I structure and transcription regulation". Nature. 502 (7473): 650–655. Bibcode:2013Natur.502..650E. doi:10.1038/nature12712. hdl: 11858/00-001M-0000-0015-3B48-5 . PMID   24153182. S2CID   205236187.
  3. ↑ Zentner, Gabriel E; Saiakhova, Alina; Manaenkov, Pavel; Adams, Mark D; Scacheri, Peter C (25 February 2011). "Integrative genomic analysis of human ribosomal DNA". Nucleic Acids Research. 39 (12): 4949–4960. doi:10.1093/nar/gkq1326. PMC   3130253 . PMID   21355038.
  4. ↑ Edger, Patrick P; Tang, Michelle; Bird, Kevin A; Mayfield, Dustin R; Conant, Gavin; Mummenhoff, Klaus; Koch, Marcus A; Pires, J Chris (1 July 2014). "Secondary structure analyses of the nuclear rRNA internal transcribed spacers and assessment of its phylogenetic utility across the Brassicaceae (mustards)". PLOS ONE. 9 (7): e101341. Bibcode:2014PLoSO...9j1341E. doi: 10.1371/journal.pone.0101341 . PMC   4077792 . PMID   24984034.
  5. ↑ Appling, Dean; Anthony-Cahill, Spencer; Mathews, Christopher (2016). Biochemistry: Concepts and Connections. Hoboken, New Jersey: Pearson. p. 742. ISBN   978-0-321-83992-3.
  6. ↑ Watkins, Nicholas J.; Bohnsack, Markus T. (May 2012). "The box C/D and H/ACA snoRNPs: key players in the modification, processing and the dynamic folding of ribosomal RNA". Wiley Interdisciplinary Reviews: RNA. 3 (3): 397–414. doi:10.1002/wrna.117. PMID   22065625. S2CID   25766812.
  7. 1 2 Venema, Jaap; Tollervey, David (December 1999). "Ribosome Synthesis in Saccharomyces cerevisiae". Annual Review of Genetics. 33 (1): 261–311. doi:10.1146/annurev.genet.33.1.261. PMID   10690410.
  8. ↑ Grandori, Carla; Gomez-Roman, Natividad; Felton-Edkins, Zoe A.; Ngouenet, Celine; Galloway, Denise A.; Eisenman, Robert N.; White, Robert J. (20 February 2005). "c-Myc binds to human ribosomal DNA and stimulates transcription of rRNA genes by RNA polymerase I". Nature Cell Biology. 7 (3): 311–318. doi:10.1038/ncb1224. PMID   15723054. S2CID   8913931.
  9. ↑ Jantzen, Hans-Michael; Admon, Arie; Bell, Stephen P.; Tjian, Robert (26 April 1990). "Nucleolar transcription factor hUBF contains a DNA-binding motif with homology to HMG proteins". Nature. 344 (6269): 830–836. Bibcode:1990Natur.344..830J. doi:10.1038/344830a0. PMID   2330041. S2CID   4280039.
  10. 1 2 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 . Retrieved 16 December 2014.
  11. ↑ Learned, R Marc; Cordes, Sabine; Tjian, Robert (June 1985). "Purification and characterization of a transcription factor that confers promoter specificity to human RNA polymerase I". Molecular and Cellular Biology. 5 (6): 1358–69. doi:10.1128/MCB.5.6.1358. PMC   366865 . PMID   3929071.
  12. ↑ Clos, Joachim; Buttgereit, Detlev; Grummt, Ingrid (February 1986). "A purified transcription factor (TIF-IB) binds to essential sequences of the mouse rDNA promoter". Proceedings of the National Academy of Sciences of the United States of America. 83 (3): 604–8. Bibcode:1986PNAS...83..604C. doi: 10.1073/pnas.83.3.604 . PMC   322912 . PMID   3456157.
  13. ↑ Serizawa N, Horiuchi T, Kobayashi T (2004). "Transcription-mediated hyper-recombination in HOT1". Genes Cells. 9 (4): 305–15. doi: 10.1111/j.1356-9597.2004.00729.x . PMID   15066122.
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