UBTF ( English upstream binding transcription factor, RNA polymerase I , other names UBF; UBF1; UBF2; UBF-1; NOR-90) is a nucleolar transcription factor that regulates the transcription of rRNA genes by and a number of other processes. In humans, it is encoded by the UBTF gene located on the 17th chromosome [1] . UBTF is represented by a single polypeptide chain, and the special domain of the HGM box is responsible for binding to DNA . The protein is localized in the nucleolus , more precisely, in the fibrillar centers and the dense fibrillar component. Disorders of UBTF lead to various diseases, including cancer .
UBTF | |||||||||||||
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Symbol | ; NOR-90; UBF; UBF-1; UBF1; UBF2 | ||||||||||||
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Classification
According to , the UBTF protein belongs to the group “4.7. Class HMG "," 4.7.4 family of UBF " [2] . Other authors distinguish the HMGB-proteins superfamily, in which the UBTF protein belongs to the HMG / UBF family [3] [4] .
Gene and Isoforms
The human UBTF gene is located on chromosome 17 at locus 17q21.31 and contains 25 exons . In mammals , 2 UBTF protein isoforms are known, which are formed due to the alternative splicing of the primary transcripts of the UBTF gene: UBTF1 and UBTF2 [5] . Pseudogenes of this gene are located on the short arms of chromosomes 3 , 11 and X , as well as the long arm of chromosome 11 [1] [6] .
Structure
UBTF protein is represented by a single chain of 764 amino acid residues . The secondary structure contains alpha-helixes , beta-layers, and . DNA binding is provided by six motifs . The protein is also characterized by the presence of an N-terminal dimerization domain and a C-terminal sour tail. The UBTF2 isoform lacks 37 amino acids from the second HGM box [5] .
In a solution, UBTF forms dimers, dimerization is carried out at the expense of the N-terminal domain with a length of more than 80 amino acid residues. This domain is extremely conservative , therefore, it may also be involved in the regulation of transcription and / or the binding of UBTF with functional nucleolar organizers . Among the UGTF HGM boxes, only the first is absolutely necessary for DNA binding, while other HGM boxes enhance this interaction. UBTF HGM boxes have a characteristic curved L-shape and consist of three alpha helices that can make conformational changes in DNA. In vitro, the UBTF dimer of the Xenopus frog can bend a loop-free rDNA nucleosome up to 180 base pairs into a loop. In addition, UBTF can simultaneously bind to two DNA molecules [5] .
The C-terminal UBTF domain consists of 57 acidic amino acid residues ( glutamic and aspartic acid ), as well as 23 serine residues . The acid domain plays a key role in the participation of UBTF in transcription activation. It is this negatively charged domain that causes the active nucleolar organizers to stain with silver salts [5] .
UBTF can undergo post-translational modifications such as acetylation and phosphorylation (on a threonine Thr201 residue and 12 serine residues) [6] . For the functional meaning of posttranslational modifications, see the Regulation section.
Intracellular localization
UBTF is an extremely numerous transcription factor; thus, up to 10 6 molecules per cell are found in primary human fibroblasts [7] . UBTF is a nucleolar protein that is found in two nucleolar components - a dense fibrillar component and fibrillar centers. In addition, it can be found in the nucleoplasm [6] . UBTF is characterized by very high affinity for rDNA and, under in vivo conditions, can bind to it in the absence of promoters and transcription [8] . On HeLa cells , it was shown that the nucleolus localization of UBTF is associated with the intensity of transcription of rRNA genes (rDNA). In nucleoli having a single large fibrillar center (such nucleoli are characterized by a low level of rDNA transcription), UBTF is located mainly there. However, in the nucleoli characterized by intense transcription of rDNA and having many small fibrillar centers, UBTF is localized mainly at the border of the fibrillar centers and the dense fibrillar component [9] .
Functions
For a long time, it was believed that the only function of UBTF is to participate in the formation of the on the rDNA promoters . According to one of the models, UBTF binds upstream and core promoter elements, resulting in a DNA loop, on which a protein complex similar to the nucleosome is assembled. Due to this, UBTF can interact with the transcription factor TIF-1B (SL1). The resulting complex attracts RNA polymerase I. However, the present mechanism of the formation of the pre-initiation complex and the role of UBTF in initiating transcription of rDNA are less clear: it has been shown that in vitro UBTF is not absolutely necessary for transcription initiation [10] .
In the course of experiments on the integration of a long number of UBTF binding sites from the rDNA of the Xenopus laevis frog into the genome of human cells, it was shown that UBTF is necessary for the formation of the nucleolus. The formation of nucleolus-like structures was observed in these rows, therefore, UBTF acted as a platform for the assembly of nucleoli even in the absence of transcription mediated by RNA polymerase I [11] . UBTF together with the RNA polymerase I machine, nucleolin , nucleophosmin and fibrillarin are among the first factors that begin the assembly of the nucleolus and the attraction of other protein components of the nucleoli [12] . UBTF is involved in the regulation of ribosome biogenesis [13] .
There is some evidence that UBTF is involved in chromatin remodeling ( chromatin remodeling ). It is shown that UBTF is necessary to maintain the structure of euchromatin in the region of active nucleolar organizers (the nucleolar organizer region, NOR ). It is possible that this is due to the competitive displacement of the UBTF linker , which is involved in heterochromatinization . UBTF is absolutely necessary for the formation of active nucleolar organizers, in the conditions of knockout in mice of the corresponding gene, the formation of NOR is impaired [14] . Thus, UBTF prevents the formation of heterochromatin in the rDNA region and contributes to maintaining the active chromatin conformation [10] .
In mice, methylation of the CpG dinucleotide at position –133 relative to the core part of the rDNA promoter in the NoRC nucleolacid remodeling complex was shown to provide transcriptional silencing of rRNA genes and reduce the binding of UBTF to rDNA promoters. In the final stages of the differentiation of mouse promyelocytes , the silencing of rDNA is increased, and the binding of UBTF to repeat rDNA is also reduced. Since the expression of UBTF is gradually reduced at the final stages of differentiation of many cell lines, it is possible that the regulation of UBTF is a key mechanism for the silencing of rDNA during development [10] . Indeed, by deleting the UBTF gene, it was shown that the UBTF protein is necessary for the development of the embryo to the morula stage . Interestingly, the loss of UBTF induced the formation of large intranuclear structures in oocytes and early embryos , similar to nucleoli progenitor nuclei (NPB) [15] . In the absence of UBTF in mice, it has been shown that nucleoli are disassembled in somatic cells and accumulate key transcription factors of rRNA genes in dense intranuclear bodies similar to NPB. In the embryos, NPBs themselves and the surrounding heterochromatin are destroyed [16] .
In 2015, it was shown that UBTF is involved in maintaining the stability of the genome by regulating genes that are actively transcribed by RNA polymerase II [17] .
Regulation
UBTF activity can be regulated through post-translational modifications. For example, phosphorylation of UBTF enhances the transcription of rDNA genes [18] . Thus, the mTOR protein (a key regulator of cell growth) regulates the transcription of rRNA genes through the S6K 1 protein and phosphorylation of the C-terminal domain of UBTF [19] . Phosphoinositide-3-kinase phosphorylates UBTF during the signaling pathway of . UBTF can also be phosphorylated by kinases / . Thus, activation of the MAPK / ERK pathway by epidermal growth factor (EGF) causes mediated phosphorylation of UBTF in the first two HGM boxes, which leads to a positive regulation of rDNA transcription by enhancing the elongation of transcription by RNA polymerase I. HGM-phosphorylation boxes 1 and 2 via ERK increase their affinity for linear DNA, which facilitates the elongation of transcription performed by RNA polymerase I [13] . UBTF can be activated as a result of phosphorylation by complexes of cyclins and cyclin-dependent kinases specific for the G1 phase of the cell cycle [20] . The human tumor suppressor suppresses the phosphorylation of UBTF and, consequently, the transcription of rDNA [21] .
It was shown that the state of acetylation of UBTF changes during the cell cycle and the acetylation of UBTF affects its interaction with RNA polymerase I [22] . The protein complex and histone deacetylase 1 (HDAC1) regulates the expression of rRNA, deacetylating UBTF [23] . The hALP protein can activate transcription mediated by RNA polymerase I, binding to UBTF and acetylating it [24] .
The interaction of UBTF with DNA can be directly regulated by binding to [25] .
Interaction with other proteins
The table below lists the key proteins with which UBTF interacts [26] :
Protein | Function | Experimental confirmation |
---|---|---|
PAF53 | RNA polymerase I subunit | In vitro and immunoprecipitation interaction |
PAF49 | RNA polymerase I subunit | In vitro interaction |
TAF I 48 | Subunit SL1 | In vitro interaction |
Subunit SL1 | In vitro interaction | |
Interacts with boxing C / D small nucleolar RNA | Yeast two-hybrid system and coimmunoprecipitation | |
SIRT7 | Potential and deacetylase | In vitro interaction |
CTCF | Chromatin organization | Interaction in vitro and |
Conservatism
For a long time, it was believed that UBTF is present only in vertebrates . This view was reinforced by the absence of UBTF-like proteins in such model organisms as the Drosophila fly , the roundworm Caenorhabditis elegans , the yeast Saccharomyces cerevisiae and the flowering plant Arabidopsis . However, with increasing data on the DNA sequences of various organisms, UBTF was found in non-vertebrate animals . For example, UBTF was found in a chordate animal, the ascidian Ciona intestinalis . The amino acid sequences of the N-terminal dimerization domain and the first HGM-box in Ciona and humans coincide by 40 and 54%, respectively. Moreover, in Ciona , as in humans, the UBTF contains several (at least five) HGM boxes [27] .
It turned out, further, that UBTF is present in a variety of arthropods (for example, in the tick Ixodes scapularis , the beetle Tribolium castaneum , aphids Acyrthosiphon pisum ). Even in the genome of the primitive animal Trichoplax adhaerens an open reading frame was found, very similar to UBTF. A comparison of UBTF Trichoplax and Ciona revealed 27% similarity in the sequence of dimerization domains. The UBTF Trichoplax homolog also has several HGM boxes, with the box adjacent to the dimerization domain having a 30% similarity to the similar Ciona domain, but the Trichoplax UBTF does not have a sour N-terminal domain. Apparently, in model invertebrates , there was a strong loss of genes, including those encoding UBTF. Mushrooms and plants seem to have no UBTF. HGM-containing protein HMO1 was found in the yeast Saccharomyces cerevisiae , which can play roles similar to the functions of UBTF Metazoa [28] .
Clinical value
The first type of herpes simplex virus causes the UBTF to move from the nucleolus of the host cell to the viral replication compartments. However, it was shown that UBTF does not contribute to the replication of the virus, but, on the contrary, suppresses it [29] .
It has been demonstrated that oncoprotein E7 of the human papillomavirus stimulates the transcription of rDNA genes, increasing the amount of the phosphorylated form of UBTF [30] .
An increased level of UBTF expression, corresponding to a positive regulation of rDNA transcription, is associated with cardiac hypertrophy [31] . On the contrary, during differentiation, the level of transcription of rDNA is reduced, which corresponds to a significant decrease in the expression of UBTF [32] .
It was established that violations of the acetylation of UBTF at the lysine residue 352 are associated with impaired rDNA transcription in Huntington's disease [33] .
It has been shown that in patients with hepatocellular carcinoma , an increase in the level of UBTF expression is observed, leading to an oncogenic effect. It turned out that the HBx protein of the hepatitis B virus activates the malignant transformation of cells through c- Myc- dependent enhancement of UBTF expression [34] .
The relationship between human hair loss and the expression level of UBTF has been shown [35] .
Notes
- ↑ 1 2 UBTF upstream binding transcription factor, RNA polymerase I [Homo sapiens (human) ] .
- ↑ Classification according to TRANSFAC Unc .
- ↑ Soullier S. , Jay P. , Poulat F. , Vanacker JM , Berta P. , Laudet V. Diversification pattern of the HMG and SOX family members during evolution. (English) // Journal of molecular evolution. - 1999. - Vol. 48, no. 5 - P. 517—527. - PMID 10198118 .
- ↑ Ait Benkhali J. , Coppin E. , Brun S. , Peraza-Reyes L. , Martin T. , Dixelius C. , Lazar N. , van Tilbeurgh H. , Debuchy R. A network of HMG-box transcription factors regulated sexual cycle in the fungus Podospora anserina. (English) // PLoS genetics. - 2013. - Vol. 9, no. 7 - P. e1003642. - DOI : 10.1371 / journal.pgen.1003642 . - PMID 23935511 .
- ↑ 1 2 3 4 The Nucleolus, 2011 , p. 88
- ↑ 1 2 3 UniProtKB - P17480 (UBF1_HUMAN) .
- ↑ The Nucleolus, 2011 , p. 89
- ↑ The Nucleolus, 2011 , p. 90.
- J. He J. , Wu X. , Tao W. Nucleolar localization of upstream binding factors in HeLa cells depends on rRNA synthesis activities. (English) // Folia biologica. - 2008. - Vol. 54, no. 6 - P. 202-206. - PMID 19393134 .
- 2 1 2 3 Sanij E. , Hannan RDNA chromatin. (English) // Epigenetics. - 2009. - Vol. 4, no. 6 - P. 374-382. - PMID 19717978 .
- ↑ Proteins of the Nucleolus, 2013 , p. 125
- ↑ Proteins of the Nucleolus, 2013 , p. 213.
- ↑ 1 2 The Nucleolus, 2011 , p. 94.
- ↑ The Nucleolus, 2011 , p. 83
- ↑ Hamdane N. , Stefanovsky VY , Tremblay MG , Nemeth A. , Paquet E. , Lessard F. , Sanij E. , Hannan R. , Moss T. Conditional inactivation of the so-called Binding Factors nucleolar precursor body. (English) // PLoS genetics. - 2014. - Vol. 10, no. 8 - P. e1004505. - DOI : 10.1371 / journal.pgen.1004505 . - PMID 25121932 .
- ↑ Hamdane N. , Tremblay MG , Dillinger S. , Stefanovsky VY , Németh A. , Moss T. Disruption of the UBF gene induces aberrant somatic nucleic bodies and disrupts embryo nucleolar precursor bodies // Gene. - 2016. - DOI : 10.1016 / j.gene.2016.09.013 . - PMID 27614293 .
- ↑ Sanij E. , Diesch J. , Lesmana A. , Poortinga G. , Hein N. , Lidgerwood G. , Cameron DP , Ellul J. , Goodall GJ , Wong LH , Dhillon AS , Hamdane N. , Rothblum LI , Pearson RB , Haviv I. , Moss T. , Hannan RD transcription factor, Pol II genes. (English) // Genome research. - 2015. - Vol. 25, no. 2 - P. 201-212. - DOI : 10.1101 / gr.176115.114 . - PMID 25452314 .
- CH Lin CH , Platt MD , Ficarro SB , Hoofnagle MH , Shabanowitz J. , Comai L. , Hunt DF , Owens GK transcription factor and transcription factor upstream binding factor. (English) // American journal of physiology. Cell physiology. - 2007. - Vol. 292, no. 5 - P. 1617-1624. - DOI : 10.1152 / ajpcell.00176.2006 . - PMID 17182730 .
- ↑ Hannan KM , Brandenburger Y. , Jenkins A. , Sharkey K. , Cavanaugh A. , Rothblum L. , Moss T. , Poortinga G. , McArthur GA , Pearson RB , Hannan RD mTOR-dependent regulation of ribosomal gene S6K1 and it is mediated by the phosphorylation of the carboxy-terminal UBF. (English) // Molecular and cellular biology. - 2003. - Vol. 23, no. 23 . - P. 8862-8877. - PMID 14612424 .
- ↑ Voit R. , Hoffmann M. , Grummt I. Phosphorylation by G1-specific cdk-cyclin complex activates the nucleolar transcription factor UBF. (English) // The EMBO journal. - 1999. - Vol. 18, no. 7 - P. 1891-1899. - DOI : 10.1093 / emboj / 18.7.1891 . - PMID 10202152 .
- ↑ Ayrault O. , Andrique L. , Fauvin D. , Eymin B. , Gazzeri S. , Séité P. Human tumor suppressor p14ARF negatively regulates rRNA transcription and inhibits UBF1 transcription factor phosphorylation. (English) // Oncogene. - 2006. - Vol. 25, no. 58 . - P. 7577-7586. - DOI : 10.1038 / sj.onc.1209743 . - PMID 16924243 .
- ↑ Meraner J. , Lechner M. , Loidl A. , Goralik-Schramel M. , Voit R. , Grummt I. , Loidl P. Acetylation of UBF with RNA polymerase I. ( English) // Nucleic acids research. - 2006. - Vol. 34, no. 6 - P. 1798-1806. - DOI : 10.1093 / nar / gkl101 . - PMID 16582105 .
- SA Ali SA , Dobson JR , Lian JB , Stein JL , van Wijnen AJ , Zaidi SK , Stein GS A RUNX2-HDAC1 co-repressor complex regulates the rRNA gene expression by modulating UBF acetylation. (English) // Journal of cell science. - 2012. - Vol. 125, no. Pt 11 . - P. 2732-2739. - DOI : 10.1242 / jcs.100909 . - PMID 22393235 .
- R. Kong R. , Zhang L. , Hu L. , Peng Q. , Han W. , Du X. , Ke Y. hALP, a three-protein novel transcriptional U (t-UTP), activates RNA polymerase I transcription by binding and acetylating the upstream binding factor (UBF). (Eng.) // The Journal of biological chemistry. - 2011. - Vol. 286, no. 9 - P. 7139-7148. - DOI : 10.1074 / jbc.M110.173393 . - PMID 21177859 .
- ↑ Yildirim S. , Castano E. , Sobol M. , Philimonenko VV , Dzijak R. , Venit T. , Hozák P. Involvement of phosphatidylinositol 4,5-bisphosphate in RNA polymerase I transcription. (English) // Journal of cell science. - 2013. - Vol. 126, no. Pt 12 . - P. 2730-2739. - DOI : 10.1242 / jcs.123661 . - PMID 23591814 .
- ↑ The Nucleolus, 2011 , p. 92
- ↑ The Nucleolus, 2011 , p. 95-96.
- ↑ The Nucleolus, 2011 , p. 96-97.
- ↑ Ouellet Lavall G. , Pearson A. Upstream binding factor inhibits herpes simplex virus replication. (English) // Virology. - 2015. - Vol. 483. - p. 108-1116. - DOI : 10.1016 / j.virol.2015.04.003 . - PMID 25965800 .
- ↑ Dichamp I. , Séité P. , Agius G. , Barbarin A. , Beby-Defaux A. Human papillomavirus 16 oncoprotein E7 stimulates the transcription, inhibiting a p53-independent activity of p14ARF. (eng.) // Public Library of Science ONE. - 2014. - Vol. 9, no. 5 - P. e96136. - DOI : 10.1371 / journal.pone.0096136 . - PMID 24798431 .
- ↑ Brandenburger Y. , Arthur JF , Woodcock EA , Du XJ , Gao XM , Autelitano DJ , Rothblum LI , Hannan RD Cardiac hypertrophy in vivo is associated with UBF. (English) // FEBS letters. - 2003. - Vol. 548, no. 1-3 . - P. 79-84. - PMID 12885411 .
- ↑ The Nucleolus, 2011 , p. 95
- J. Lee J. , Hwang YJ , Boo JH , Han D. , Kwon OK , Todorova K. , Kowall NW , Kim Y. , Ryu H. Dysregulation of upstream binding factor-1; Huntington's disease. (English) // Cell death and differentiation. - 2011. - Vol. 18, no. 11 - P. 1726-1735. - DOI : 10.1038 / cdd.2011.38 . - PMID 21546905 .
- J Rajput P. , Shukla SK , Kumar V. The RB polymerase I transcription factor UBF. (Eng.) // Virology journal. - 2015. - Vol. 12. - P. 62. - DOI : 10.1186 / s12985-015-0293-5 . - PMID 25890091 .
- De Tasdemir S. , Eroz R. , Dogan H. , Erdem HB , Sahin I. , Kara M. , Engin RI , Turkez H. Association of Nucleolin, Nucleophosmin and UBTF Genes. (English) // Genetic testing and molecular biomarkers. - 2016. - Vol. 20, no. 4 - P. 197-202. - DOI : 10.1089 / gtmb.2015.0246 . - PMID 26866305 .
Literature
- The Nucleolus / Ed. by Mark O. J. Olson. - New York: Springer Science + Business Media , 2011. - xxvi + 414 p. - (Protein Reviews, vol. 15). - ISBN 978-1-4614-0514-6 . - DOI : 10.1007 / 978-1-4614-0514-6 .
- Proteins of the Nucleolus / O'Day, Danton H, Catalano, Andrew. - Netherlands: Springer, 2013. - ISBN 978-94-007-5818-6 . - DOI : 10.1007 / 978-94-007-5818-6 .