Archaeal transcription factor B

Last updated
Transcription factor II B
1D3U.png
Crystallographic structure of transcription factor II B (top; rainbow colored, N-terminus = blue, C-terminus = red) complexed with double stranded DNA (bottom).
Identifiers
Organism Pyrococcus woesei
Symboltfb
PDB 1d3u
UniProt P61999

Archaeal transcription factor B (ATFB or TFB) is a protein family of extrinsic transcription factors that guide the initiation of RNA transcription in organisms that fall under the domain of Archaea. [1] It is homologous to eukaryotic TFIIB and, more distantly, to bacterial sigma factor. [2] Like these proteins, it is involved in forming transcription preinitiation complexes. [3] 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. [1]

Contents

History

In bacteria and eukaryotes, proteins TFIIB and sigma factor are involved in the initiation of transcription, where they facilitate preinitiation complex formation and specific RNA Polymerase-DNA binding. The archaeal counterpart to these two proteins is TFB, which was first identified in the species Pyrococcus woesei in 1992. [4] [5] Since then, research has found that archaeal species must contain at least one copy of TFB to function, although some species may have multiple isoforms in their genome. [6]

Structure

TFB is a single polypeptide, around 280 to 300 amino acids in length and 34 kDa in mass, [3] that is required for the recruitment of RNA polymerase (RNAP) to begin transcription, and it may also affect the transcription complex's structure during changes that occur before transcription, though specific mechanisms are unknown. TFB's structure consists of an amino-terminal region (TFBN) with conserved sequences and complex structures, linked to a larger, globular carboxyl-terminal region (TFBC). [1] While the N-terminal domain mediates the RNAP interactions, the C-terminal domain mediates interactions with complex formed of the TATA box and TBP, a DNA sequence and polypeptide involved with translation initiation. [7] The degree of conservation of TFB's sequence throughout Archaea ranges from 50% to 60%. [3] In respect to its eukaryotic equivalent, TFB shows "high levels of structural and functional conservation." [1] The interactions between TBP and a sequence upstream of the TATA box governs transcription polarity, "yields an archaeal preinitiation complex," and orients the complex in the direction in which the target gene should be transcribed. The TBP shows an inverted orientation compared to the eukaryotic TFIIB. [8]

TFBN makes up approximately one third of the protein and contains both a B-finger motif (homologous to the TFIIB B-finger) and a zinc-finger motif, [9] the latter of which is located at amino acids 2-34. [10] The N-terminal domain size varies from 100 to 120 amino acids in length. [3] Crosslinking experiments have shown this domain is located close to the transcription start site. The zinc-finger interacts with the RNAP dock domain, and the B-finger may affect RNAP-promoter interactions. TFBC contains motifs which interact with the TATA binding protein (TBP), the TFB-recognition elements (BRE) upstream of the TATA box, and sequences of DNA downstream of the TATA. [1] Its size is approximately 180 amino acids, which is made up of two repeats of a 90-amino acid sequence. The C-terminal domain specifically may be what influences the direction of the preinitiation complex. [3] Since TFBN binds the RNAP and TFBC binds the TBP-TATA complex, TBP connects the two. [7]

Mechanism

TFB is recruited by another translation factor, TBP, after it recognizes the TATA box and bends the DNA so transcription can initiate. TFB stabilizes the TBP-DNA complex so that the proteins can recruit RNA Polymerase and melt the DNA via a yet-unknown mechanism. This opening of the DNA is not an energy-dependent process in Archaea; since TFB, TBP, and RNAP are located more closely to each other than in Eukarya, the tightness of the proteins and their interactions may provide more areas of contact to open the DNA as well as physically strain the DNA, which leads to an open transcription complex. [6]

TFB uses a zinc ion (Zn2+) as a cofactor and accepts one ion per subunit. [10]

Related Research Articles

<span class="mw-page-title-main">Transcription (biology)</span> 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). mRNA comprises only 1-3% of total RNA samples. 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.

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

In molecular biology, RNA polymerase, or more specifically DNA-directed/dependent RNA polymerase (DdRP), is an enzyme that synthesizes RNA from a DNA template.

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 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.

<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">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.

<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">Intrinsic termination</span>

Intrinsic, or rho-independent termination, is a process in prokaryotes to signal the end of transcription and release the newly constructed RNA molecule. In prokaryotes 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 and adenine 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">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.

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">Selective factor 1</span>

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 archeaeal 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. 1 2 3 4 5 Micorescu M, Grünberg S, Franke A, Cramer P, Thomm M, Bartlett M (January 2008). "Archaeal transcription: function of an alternative transcription factor B from Pyrococcus furiosus". Journal of Bacteriology. 190 (1): 157–67. doi:10.1128/JB.01498-07. PMC   2223750 . PMID   17965161.
  2. ↑ Burton SP, Burton ZF (6 November 2014). "The σ enigma: bacterial σ factors, archaeal TFB and eukaryotic TFIIB are homologs". Transcription. 5 (4): e967599. doi:10.4161/21541264.2014.967599. PMC   4581349 . PMID   25483602.
  3. 1 2 3 4 5 Soppa J (March 1999). "Transcription initiation in Archaea: facts, factors and future aspects". Molecular Microbiology. 31 (5): 1295–305. doi: 10.1046/j.1365-2958.1999.01273.x . PMID   10200952.
  4. ↑ Kyrpides NC, Ouzounis CA (July 1999). "Transcription in archaea". Proceedings of the National Academy of Sciences of the United States of America. 96 (15): 8545–50. Bibcode:1999PNAS...96.8545K. doi: 10.1073/pnas.96.15.8545 . PMC   17553 . PMID   10411912.
  5. ↑ Ouzounis C, Sander C (October 1992). "TFIIB, an evolutionary link between the transcription machineries of archaebacteria and eukaryotes". Cell. 71 (2): 189–90. doi:10.1016/0092-8674(92)90347-F. PMID   1423586. S2CID   11141214.
  6. 1 2 Gehring AM, Walker JE, Santangelo TJ (July 2016). "Transcription Regulation in Archaea". Journal of Bacteriology. 198 (14): 1906–1917. doi:10.1128/JB.00255-16. PMC   4936096 . PMID   27137495.
  7. 1 2 Renfrow MB, Naryshkin N, Lewis LM, Chen HT, Ebright RH, Scott RA (January 2004). "Transcription factor B contacts promoter DNA near the transcription start site of the archaeal transcription initiation complex". The Journal of Biological Chemistry. 279 (4): 2825–31. doi: 10.1074/jbc.M311433200 . PMID   14597623.
  8. ↑ Bell SD, Kosa PL, Sigler PB, Jackson SP (November 1999). "Orientation of the transcription preinitiation complex in archaea". Proceedings of the National Academy of Sciences of the United States of America. 96 (24): 13662–7. Bibcode:1999PNAS...9613662B. doi: 10.1073/pnas.96.24.13662 . PMC   24121 . PMID   10570129.
  9. ↑ Paytubi S, White MF (June 2009). "The crenarchaeal DNA damage-inducible transcription factor B paralogue TFB3 is a general activator of transcription". Molecular Microbiology. 72 (6): 1487–99. doi:10.1111/j.1365-2958.2009.06737.x. PMID   19460096. S2CID   37733296.
  10. 1 2 "tfb - Transcription initiation factor IIB - Pyrococcus woesei - tfb gene & protein". www.uniprot.org. Retrieved 2018-07-15.
This page is based on this Wikipedia article
Text is available under the CC BY-SA 4.0 license; additional terms may apply.
Images, videos and audio are available under their respective licenses.