RNA polymerase III

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In eukaryote cells, RNA polymerase III (also called Pol III) is a protein that transcribes DNA to synthesize 5S ribosomal RNA, tRNA, and other small RNAs.

Contents

The genes transcribed by RNA Pol III fall in the category of "housekeeping" genes whose expression is required in all cell types and most environmental conditions. Therefore, the regulation of Pol III transcription is primarily tied to the regulation of cell growth and the cell cycle and thus requires fewer regulatory proteins than RNA polymerase II. Under stress conditions, however, the protein Maf1 represses Pol III activity. [1] Rapamycin is another Pol III inhibitor via its direct target TOR. [2]

Transcription

The process of transcription (by any polymerase) involves three main stages:

Initiation

Pol III is unusual (compared to Pol II) by requiring no control sequences upstream of the gene, instead normally relying on internal control sequences - sequences within the transcribed section of the gene (although upstream sequences are occasionally seen, e.g. U6 snRNA gene has an upstream TATA box as seen in Pol II Promoters).

There are three classes of Pol III initiation, corresponding to 5S rRNA, tRNA, and U6 snRNA initiation. In all cases, the process starts with transcription factors binding to control sequences and ends with TFIIIB (Transcription Factor for polymerase IIIB) being recruited to the complex and assembling Pol III. TFIIIB consists of three subunits: TATA binding protein (TBP), a TFIIB-related factor (BRF1, or BRF2 for transcription of a subset of Pol III-transcribed genes in vertebrates), and a B-double-prime (BDP1) unit. The overall architecture bears similarities to that of Pol II. [3]

Class I

Typical stages in 5S rRNA (also termed class I) gene initiation:

  • TFIIIA (Transcription Factor for polymerase IIIA) binds to the intragenic (lying within the transcribed DNA sequence) 5S rRNA control sequence, the C Block (also termed box C).
  • TFIIIA serves as a platform that replaces the A and B Blocks for positioning TFIIIC in an orientation with respect to the start site of transcription that is equivalent to what is observed for tRNA genes.
  • Once TFIIIC is bound to the TFIIIA-DNA complex, the assembly of TFIIIB proceeds as described for tRNA transcription.

Class II

Typical stages in a tRNA (also termed class II) gene initiation:

  • TFIIIC (Transcription Factor for polymerase IIIC) binds to two intragenic (lying within the transcribed DNA sequence) control sequences, the A and B Blocks (also termed box A and box B).
  • TFIIIC acts as an assembly factor that positions TFIIIB to bind to DNA at a site centered approximately 26 base pairs upstream of the start site of transcription.
  • TFIIIB is the transcription factor that assembles Pol III at the start site of transcription. Once TFIIIB is bound to DNA, TFIIIC is no longer required. TFIIIB also plays an essential role in promoter opening.

Class III

Typical stages in a U6 snRNA (also termed class III) gene initiation (documented in vertebrates only):

  • SNAPc (SNRNA Activating Protein complex; subunits: 1, 2, 3, 4, 5) (also termed PBP and PTF) binds to the PSE (Proximal Sequence Element) centered approximately 55 base pairs upstream of the start site of transcription. This assembly is greatly stimulated by the Pol II transcription factors Oct1 and STAF that bind to an enhancer-like DSE (Distal Sequence Element) at least 200 base pairs upstream of the start site of transcription. These factors and promoter elements are shared between Pol II and Pol III transcription of snRNA genes.
  • SNAPc acts to assemble TFIIIB at a TATA box centered 26 base pairs upstream of the start site of transcription. It is the presence of a TATA box that specifies that the snRNA gene is transcribed by Pol III rather than Pol II.
  • The TFIIIB for U6 snRNA transcription contains a smaller Brf1 paralogue, Brf2.
  • TFIIIB is the transcription factor that assembles Pol III at the start site of transcription. Sequence conservation predicts that TFIIIB containing Brf2 also plays a role in promoter opening.

Elongation

TFIIIB remains bound to DNA following the initiation of transcription by Pol III, unlike bacterial σ factors and most of the basal transcription factors for Pol II transcription. This leads to a high rate of transcriptional reinitiation of Pol III-transcribed genes. One study conducted on Saccharomyces cerevisiae found the average rate of chain elongation was 21 to 22 nucleotides per second, with the fastest being 29 nucleotides per second. These rates were comparable to elongation rates of RNA polymerase II found by an in vivo study conducted on Drosophila. The analysis of the individual steps of RNA chain elongation depicted that adding U and A to U-terminated RNA chains was slow. [4]

Termination

Polymerase III terminates transcription at small polyUs stretch (5-6). In eukaryotes, a hairpin loop is not required, but may enhance termination efficiency in humans. [5] In Saccharomyces cerevisiae, it was found that termination of transcription occurred in the sequence T7GT6 and was progressive. The presence of transcripts with five, six, and seven U residues and the slow readthrough of the T7 stretch suggest that the incorporation of a single G into the RNA chain served to reset elongation rates either entirely or substantially. [4]

Transcribed RNAs

The types of RNAs transcribed from RNA polymerase III include: [6]

Role in DNA repair

RNA polymerase III appears to be essential for homologous recombinational repair of DNA double-strand breaks. [8] RNA polymerase III catalyzes the formation of a transient RNA-DNA hybrid at double strand breaks, an essential intermediate step in homologous recombination mediated double-strand break repair. [8] This step protects the 3’ overhanging DNA strand from degradation. [8] After the transient RNA-DNA hybrid intermediate is formed, the RNA strand is replaced by the RAD51 protein, which then catalyzes the ssDNA invasion step of homologous recombination.

See also

Related Research Articles

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<span class="mw-page-title-main">Transcription (biology)</span> Process of copying a segment of DNA into RNA

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<span class="mw-page-title-main">RNA polymerase</span> Enzyme that synthesizes RNA from DNA

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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.

<span class="mw-page-title-main">Transcription preinitiation complex</span> 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.

<span class="mw-page-title-main">SR protein</span>

SR proteins are a conserved family of proteins involved in RNA splicing. SR proteins are named because they contain a protein domain with long repeats of serine and arginine amino acid residues, whose standard abbreviations are "S" and "R" respectively. SR proteins are ~200-600 amino acids in length and composed of two domains, the RNA recognition motif (RRM) region and the RS domain. SR proteins are more commonly found in the nucleus than the cytoplasm, but several SR proteins are known to shuttle between the nucleus and the cytoplasm.

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">RNA polymerase II</span> 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.

In molecular biology, a termination factor is a protein that mediates the termination of RNA transcription by recognizing a transcription terminator and causing the release of the newly made mRNA. This is part of the process that regulates the transcription of RNA to preserve gene expression integrity and are present in both eukaryotes and prokaryotes, although the process in bacteria is more widely understood. The most extensively studied and detailed transcriptional termination factor is the Rho (ρ) protein of E. coli.

<span class="mw-page-title-main">Transcription bubble</span>

A transcription bubble is a molecular structure formed during DNA transcription when a limited portion of the DNA double helix is unwound. The size of a transcription bubble ranges from 12 to 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.

Antitermination is the prokaryotic cell's aid to fix premature termination of RNA synthesis during the transcription of RNA. It occurs when the RNA polymerase ignores the termination signal and continues elongating its transcript until a second signal is reached. Antitermination provides a mechanism whereby one or more genes at the end of an operon can be switched either on or off, depending on the polymerase either recognizing or not recognizing the termination signal.

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

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.

<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.

<span class="mw-page-title-main">Intrinsic termination</span>

Intrinsic, or rho-independent termination, is a process to signal the end of transcription and release the newly constructed RNA molecule. In bacteria such as E. coli, transcription is terminated either by a rho-dependent process or rho-independent process. In the Rho-dependent process, the rho-protein locates and binds the signal sequence in the mRNA and signals for cleavage. Contrarily, intrinsic termination does not require a special protein to signal for termination and is controlled by the specific sequences of RNA. When the termination process begins, the transcribed mRNA forms a stable secondary structure hairpin loop, also known as a stem-loop. This RNA hairpin is followed by multiple uracil nucleotides. The bonds between uracil (rU) and adenine (dA) are very weak. A protein bound to RNA polymerase (nusA) binds to the stem-loop structure tightly enough to cause the polymerase to temporarily stall. This pausing of the polymerase coincides with transcription of the poly-uracil sequence. The weak adenine-uracil bonds lower the energy of destabilization for the RNA-DNA duplex, allowing it to unwind and dissociate from the RNA polymerase. Overall, the modified RNA structure is what terminates transcription.

<span class="mw-page-title-main">BRF1 (gene)</span> Protein-coding gene in the species Homo sapiens

Transcription factor IIIB 90 kDa subunit is a protein that in humans is encoded by the BRF1 gene.

<span class="mw-page-title-main">POLR3F</span> Protein-coding gene in the species Homo sapiens

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<span class="mw-page-title-main">Transcription factor IIIB 50 kDa subunit</span> Protein-coding gene in the species Homo sapiens

Transcription factor IIIB 50 kDa subunit (TFIIIB50) also known as b-related factor 2 (BRF-2) is a protein that in humans is encoded by the BRF2 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">5′ flanking region</span>

The 5′ flanking region is a region of DNA that is adjacent to the 5′ end of the gene. The 5′ flanking region contains the promoter, and may contain enhancers or other protein binding sites. It is the region of DNA that is not transcribed into RNA. Not to be confused with the 5′ untranslated region, this region is not transcribed into RNA or translated into a functional protein. These regions primarily function in the regulation of gene transcription. 5′ flanking regions are categorized between prokaryotes and eukaryotes.

Georges André Sentenac is a French molecular biologist specializing in gene transcription.

References

  1. ↑ Vannini, Alessandro; Ringel, Rieke; Kusser, Anselm G.; Berninghausen, Otto; Kassavetis, George A.; Cramer, Patrick (2010). "Molecular Basis of RNA Polymerase III Transcription Repression by Maf1". Cell. 143 (1): 59–70. doi: 10.1016/j.cell.2010.09.002 . hdl: 11858/00-001M-0000-0015-820B-0 . ISSN   0092-8674. PMID   20887893.
  2. ↑ Lee, JaeHoon; Moir, Robyn D.; Willis, Ian M. (2009-05-08). "Regulation of RNA Polymerase III Transcription Involves SCH9-dependent and SCH9-independent Branches of the Target of Rapamycin (TOR) Pathway". Journal of Biological Chemistry. 284 (19): 12604–12608. doi: 10.1074/jbc.c900020200 . ISSN   0021-9258. PMC   2675989 . PMID   19299514.
  3. ↑ Han, Yan; Yan, Chunli; Fishbain, Susan; Ivanov, Ivaylo; He, Yuan (2018). "Structural visualization of RNA polymerase III transcription machineries". Cell Discovery. 4: 40. doi:10.1038/s41421-018-0044-z. PMC   6066478 . PMID   30083386.
  4. 1 2 Matsuzaki, H.; Kassavetis, G. A.; Geiduschek, E. P. (1994-01-28). "Analysis of RNA chain elongation and termination by Saccharomyces cerevisiae RNA polymerase III". Journal of Molecular Biology. 235 (4): 1173–1192. doi:10.1006/jmbi.1994.1072. ISSN   0022-2836. PMID   8308883.
  5. ↑ Verosloff, M; Corcoran, W; Dolberg, T; Leonard, J; Lucks, J (2020). "RNA sequence and structure determinants of Pol III transcriptional termination in human cells" (PDF). bioRxiv. doi:10.1101/2020.09.11.294140. S2CID   221713150.
  6. ↑ Dieci, Giorgio; Fiorino, Gloria; Castelnuovo, Manuele; Teichmann, Martin; Pagano, Aldo (2007). "The expanding RNA polymerase III transcriptome". Trends in Genetics. 23 (12): 614–622. doi:10.1016/j.tig.2007.09.001. ISSN   0168-9525. PMID   17977614.
  7. ↑ Pagano, Aldo; Castelnuovo, Manuele; Tortelli, Federico; Ferrari, Roberto; Dieci, Giorgio; Cancedda, Ranieri (2007-02-02). "New Small Nuclear RNA Gene-Like Transcriptional Units as Sources of Regulatory Transcripts". PLOS Genetics. 3 (2): e1. doi: 10.1371/journal.pgen.0030001 . ISSN   1553-7404. PMC   1790723 . PMID   17274687.
  8. 1 2 3 Liu, Sijie; Hua, Yu; Wang, Jingna; Li, Lingyan; Yuan, Junjie; Zhang, Bo; Wang, Ziyang; Ji, Jianguo; Kong, Daochun (2021). "RNA polymerase III is required for the repair of DNA double-strand breaks by homologous recombination". Cell. 184 (5): 1314–1329.e10. doi: 10.1016/j.cell.2021.01.048 .
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