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International Journal of Biochemistry & Physiology Research Article 8 min read

Sub2: A TFIIB Interacting Protein with Pleiotropic Roles in mRNA Synthesis, Processing and Transport

Fidler E and Ansari A*
* Corresponding author
ISSN: 2577-4360  10.23880/ijbp-16000250  Received: May 20, 2024  Published: June 06, 2024
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Keywords
mRNA Processing and mRNA Trafficking Transcription of Protein Mass Spectrometry
Abstract

The generally accepted view is that different steps of transcription, mRNA processing and mRNA trafficking are performed by dedicated accessory factors. The research during last couple of decades, however, has challenged this dogma. We recently showed that the general transcription factor TFIIB, in addition to its well established role in initiation, is also involved in termination of transcription. Mass spectrometry of purified TFIIB revealed Sub2 as one of its major interacting partners. Sub2 has already been implicated in elongation step of transcription, splicing and mRNA trafficking. Interaction of Sub2 with TFIIB implicates it in initiation and termination steps of transcription. Multiplicity of Sub2 biological roles may be responsible for its link with a number of human pathological conditions making it a potential drug target.

Perspective

TFIIB is a conserved general transcription factor (GTF) required for transcription of protein encoding genes in eukaryotes and archaea [1]. The classical role of TFIIB is to bridge the gap between the promoter binding TFIID and the RNA polymerase II (RNAPII), essentially forming the preinitiation complex (PIC) [2]. However, recent studies have implicated TFIIB in steps beyond initiation of transcription. TFIIB not only occupies the 5’ end of actively transcribed genes, but also their 3’ ends [3, 4, 5, 6, 7]. The 3’ end occupancy of TFIIB is due to a structural conformation of the transcription template called gene looping, where the 5’ and 3’ ends of an actively transcribed gene are juxtaposed, facilitating the hand-off of the RNAPII to the promoter for reinitiation [8].

Perspective

Quantitative proteomic analysis of affinity purified TFIIB from the chromatin fraction revealed that TFIIB associates with two of the three yeast termination complexes, CF1 and Rat1 [9]. Interaction of promoter-linked TFIIB with CF1 and Rat1 complexes occupying the 3’ end of a gene may be responsible for the gene assuming a looped formation.

Mass spectrometry of chromatin-eluted TFIIB revealed a novel interactor, Sub2, which associated with TFIIB at a consistently high level [9]. Sub2 is a splicing factor and a component of the TRanscription EXport (TREX) complex [10]. It has previously been thought to be recruited to the actively transcribed gene during elongation of transcription due to its association with the THO (transcription-dependent hyper recombination complex) complex, an elongation complex in yeast which is a part of the larger TREX complex [11]. The association of Sub2 with TFIIB indicates that it may be recruited to the gene earlier than we thought. Since TFIIB occupies both the promoter and terminator regions of actively transcribing genes, we expected Sub2 to interact with initiation and termination factors like TFIIB. Preliminary results from our laboratory confirmed that Sub2 indeed associates with two termination complexes, the CPF and CF1 complexes (Dwyer and Ansari, 2024, unpublished results). These results strongly suggest that Sub2, in addition to its role in RNA trafficking, splicing and transcription elongation, may also be involved in initiation and termination steps of transcription.

Sub2 may be the factor that links transcription to RNA processing and RNA trafficking. It is an evolutionarily conserved protein with homologs present in humans, flies and worm. The human homolog of Sub2, called UAP56 (U2AF associated protein56; also known as DDX39B), could functionally substitute for Sub2 in budding yeast, thereby affirming the evolutionarily conserved nature of two proteins [12]. Both Sub2 and UAP56 possess RNA-dependent helicase activity. They have been implicated in multiple aspects of mRNA metabolism including mRNA splicing, export, and ribosome biogenesis [13]. Multiple studies have revealed the central role of UAP56 and Sub2 as components of the transcription and export (TREX) complex responsible for guiding mRNA from the nucleus to the cytosol [14, 15, 16]. Cryo- EM studies of yeast TREX complex found THO subunits Tho2 and Hpr1 intertwine to form the binding surface for Mft1, Thp2, and Tex1.The resulting complex homodimerizes with a Sub2 molecule to form the TREX complex [16]. During splicing, Sub2/UAP56 is necessary for proper assembly of the pre-spliceosome complex [17]. Spliceosome assembly is a well-coordinated process involving many proteins and ncRNAs [18]. Loss of Sub2 results in stalling of the pre- spliceosome assembly and therefore improper splicing [17].

Emerging research has indicated that the repertoire of Sub2/UAP56 physiological involvement extends well beyond their established functions in splicing and export. A number of studies have implicated the factor in telomere maintenance and in maintaining genomic integrity through suppression of co-transcriptional R-loop formation [19, 20]. The RNA-DNA helicase activity of Sub2/UAP56 unwinds R-loops around actively transcribed regions of the genome [20]. This function may be responsible for Sub2/UAP56 facilitating transcription elongation by allowing RNAPII to proceed unobstructed through the coding region of the gene [21]. Depletion of Sub2/UAP56 also results in DNA damage at the telomeric regions [22]. Unpublished results from our laboratory suggest that Sub2 may have as yet unidentified roles in transcription cycle than previously thought. The research during the last couple of decades have demonstrated that different steps of transcription are interlinked and occur in a cooperative fashion with RNA processing and transport of mRNA out of the nucleus in cytoplasm [23]. In this context, the study of Sub2 may help us gain insight into how the various steps of gene expression from transcription initiation, splicing, termination to transport of mRNA to the cytoplasm are regulated to coordinate proper expression of a gene in response to external or internal environmental cues.

Probably due to these broadly encompassing roles, Sub2 has been linked to a number of human pathological conditions like cancer, neurodegenerative disorders and viral diseases [24]. Specifically, Sub2/UAP65 depletion affects the expression of the tumor suppressor gene BRCA1 [25]. It has also been implicated in viral RNA transport to the host cytosol for translation [26]. This makes Sub2 a suitable candidate for drug targeting for the above mentioned disorders. Further study of Sub2 is needed to establish the scope of its function in regulation of gene expression and the molecular mechanisms underlying these functions. This will open up the avenues for potential targeting of the protein for drugs to treat linked pathologies.

Author Contribution

AA conceptualized; EF prepared the original draft; AA edited the manuscript. All authors contributed to the article and approve the submitted version.

Funding

This research was supported by the grant from National Institute of Health (Grant # 1R01GM146803-05)

Acknowledgements

We would like to thank Katherine Dwyer for critical reading of the manuscript.

References

  1. Deng W, Roberts SGE (2007) TFIIB and the regulation of transcription by RNA polymerase II. Chromosoma 116(5): 417-429.
  2. Luse DS (2014) The RNA polymerase II preinitiation complex: through what pathway is the complex assembled?. Transcription 5(1): e27050.
  3. Singh BN, Hampsey M (2007) A transcription- independent role for TFIIB in gene looping. Molecular cell, 27(5): 806-816.
  4. Mavrich TN, Ioshikhes IP, Venters BJ, Jiang C, Tomsho LP, et al. (2008) A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome research 18(7): 1073-1083.
  5. El Kaderi B, Medler S, Raghunayakula S, Ansari A (2009) Gene looping is conferred by activator-dependent interaction of transcription initiation and termination machineries. Journal of Biological Chemistry 284(37): 25015-25025.
  6. Medler S, Al Husini N, Raghunayakula S, Mukundan B, Aldea A, et al. (2011) Evidence for a complex of transcription factor IIB (TFIIB) with Poly (A) polymerase and cleavage factor 1 subunits required for gene looping. Journal of Biological Chemistry 286(39): 33709-33718.
  7. Al Husini N, Kudla P, Ansari A (2013) A role for CF1A 3′ end processing complex in promoter-associated transcription. PLoS genetics 9(8): e1003722.
  8. Ansari A, Hampsey M (2005) A role for the CPF 3′-end processing machinery in RNAP II-dependent gene looping. Genes & development 19(24): 2969-2978.
  9. O’Brien MJ, Ansari A (2024) Protein interaction network revealed by quantitative proteomic analysis links TFIIB to multiple aspects of the transcription cycle. Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics 1872(1): 140968.
  10. Sträßer K, Masuda S, Mason P, Pfannstiel J, Oppizzi M, et al. (2002) TREX is a conserved complex coupling transcription with messenger RNA export. Nature 417(6886): 304-308.
  11. Rondón AG, Jimeno S, García-Rubio M, Aguilera A (2003) Molecular evidence that the eukaryotic THO/ TREX complex is required for efficient transcription elongation. Journal of Biological Chemistry 278(40): 39037-39043.
  12. Zhang M Green MR (2001) Identification and characterization of yUAP/Sub2p, a yeast homolog of the essential human pre-mRNA splicing factor hUAP56. Genes & development 15(1): 30-35.
  13. Yellamaty R, Sharma S (2024) Critical Cellular Functions and Mechanisms of Action of the RNA Helicase UAP56. Journal of Molecular Biology 436(12): 168604.
  14. Jimeno S, Rondon AG, Luna R, Aguilera A (2002) The yeast THO complex and mRNA export factors link RNA metabolism with transcription and genome instability. The EMBO journal 21(13): 3526-3535.
  15. Pühringer T, Hohmann U, Fin L, Pacheco-Fiallos B, Schellhaas U, et al. (2020) Structure of the human core transcription-export complex reveals a hub for multivalent interactions. Elife 9: e61503.
  16. Schuller SK, Schuller JM, Prabu JR, Baumgärtner M, Bonneau F, et al. (2020) Structural insights into the nucleic acid remodeling mechanisms of the yeast THO- Sub2 complex. Elife 9: e61467.
  17. Libri D, Graziani N, Saguez C, Boulay J (2001) Multiple roles for the yeast SUB2/yUAP56 gene in splicing. Genes & Development 15(1): 36-41.
  18. Matlin AJ, Moore MJ (2007) Spliceosome assembly and composition. Alternative Splicing in the Postgenomic Era 14-35.
  19. Chen C, Tan M, Wu Z, Zhang Y, He F, et al. (2021) Structural and functional insights into R-loop prevention and mRNA export by budding yeast THO-Sub2 complex. Science Bulletin 66(23): 2347-2352
  20. Pérez-Calero C, Bayona-Feliu A, Xue X, Barroso SI, Muñoz S, et al. (2020) UAP56/DDX39B is a major cotranscriptional RNA–DNA helicase that unwinds harmful R loops genome-wide. Genes & development 34(13-14): 898-912.
  21. Cargill M, Venkataraman R, Lee S (2021) DEAD-box RNA helicases and genome stability. Genes(Basel) 12(10): 1471.
  22. Yoo HH, Chung IK (2011) Requirement of DDX39 DEAD box RNA helicase for genome integrity and telomere protection. Aging cell 10(4): 557-571.
  23. Al-Husini N, Medler S, Ansari A (2020) Crosstalk of promoter and terminator during RNA polymerase II transcription cycle. Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms 1863(12): 194657.
  24. Heath CG, Viphakone N, Wilson SA (2016) The role of TREX in gene expression and disease. Biochemical Journal 473(19): 2911-2935.
  25. Yamazaki T, Fujiwara N, Yukinaga H, Ebisuya M, Shiki T, et al. (2010) The closely related RNA helicases, UAP56 and URH49, preferentially form distinct mRNA export machineries and coordinately regulate mitotic progression. Molecular biology of the cell 21(16): 2953- 2965.
  26. Lischka P, Toth Z, Thomas M, Mueller R, Stamminger T (2006) The UL69 transactivator protein of human cytomegalovirus interacts with DEXD/H-Box RNA helicase UAP56 to promote cytoplasmic accumulation of unspliced RNA. Molecular and cellular biology 26(5): 1631-1643.
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@article{fidler2024,
  title   = {Sub2: A TFIIB Interacting Protein with Pleiotropic Roles in mRNA
Synthesis, Processing and Transport},
  author  = {Fidler E and Ansari A},
  journal = {International Journal of Biochemistry & Physiology},
  year    = {2024},
  volume  = {9},
  number  = {1},
  doi     = {10.23880/ijbp-16000250}
}
Fidler E and Ansari A (2024). Sub2: A TFIIB Interacting Protein with Pleiotropic Roles in mRNA
Synthesis, Processing and Transport. International Journal of Biochemistry & Physiology, 9(1). https://doi.org/10.23880/ijbp-16000250
TY  - JOUR
TI  - Sub2: A TFIIB Interacting Protein with Pleiotropic Roles in mRNA
Synthesis, Processing and Transport
AU  - Fidler E and Ansari A
JO  - International Journal of Biochemistry & Physiology
PY  - 2024
VL  - 9
IS  - 1
DO  - 10.23880/ijbp-16000250
ER  -