Molecular Cloning and Analysis of Schizosaccharomyces Pombe Reb1p: Sequence-specific Recognition of Two Sites in the Far Upstream RDNA Intergenic Spacer

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 1997 Feb 15

PMID 9016645

Citations 23

Authors

A Zhao

A Guo

Z Liu

L Pape

Affiliations

Soon will be listed here.

Abstract

The coding sequences for a Schizosaccharomyces pombe sequence-specific DNA binding protein, Reb1p, have been cloned. The predicted S. pombe Reb1p is 24-29% identical to mouse TTF-1 (transcription termination factor-1) and Saccharomyces cerevisiae REB1 protein, both of which direct termination of RNA polymerase I catalyzed transcripts. The S.pombe Reb1 cDNA encodes a predicted polypeptide of 504 amino acids with a predicted molecular weight of 58.4 kDa. The S. pombe Reb1p is unusual in that the bipartite DNA binding motif identified originally in S.cerevisiae and Klyveromyces lactis REB1 proteins is uninterrupted and thus S.pombe Reb1p may contain the smallest natural REB1 homologous DNA binding domain. Its genomic coding sequences were shown to be interrupted by two introns. A recombinant histidine-tagged Reb1 protein bearing the rDNA binding domain has two homologous, sequence-specific binding sites in the S. pomber DNA intergenic spacer, located between 289 and 480 nt downstream of the end of the approximately 25S rRNA coding sequences. Each binding site is 13-14 bp downstream of two of the three proposed in vivo termination sites. The core of this 17 bp site, AGGTAAGGGTAATGCAC, is specifically protected by Reb1p in footprinting analysis.

Citing Articles

Defining the Influence of the A12.2 Subunit on Transcription Elongation and Termination by RNA Polymerase I In Vivo.

Clarke A, Huffines A, Edwards Y, Petit C, Schneider D Genes (Basel). 2021; 12(12).

PMID: 34946888 PMC: 8701712. DOI: 10.3390/genes12121939.

Short-Homology-Mediated CRISPR/Cas9-Based Method for Genome Editing in Fission Yeast.

Hayashi A, Tanaka K G3 (Bethesda). 2019; 9(4):1153-1163.

PMID: 30755408 PMC: 6469419. DOI: 10.1534/g3.118.200976.

RNAi drives nonreciprocal translocations at eroding chromosome ends to establish telomere-free linear chromosomes.

Begnis M, Apte M, Masuda H, Jain D, Wheeler D, Cooper J Genes Dev. 2018; 32(7-8):537-554.

PMID: 29654060 PMC: 5959237. DOI: 10.1101/gad.311712.118.

Functional architecture of the Reb1-Ter complex of Schizosaccharomyces pombe.

Jaiswal R, Choudhury M, Zaman S, Singh S, Santosh V, Bastia D Proc Natl Acad Sci U S A. 2016; 113(16):E2267-76.

PMID: 27035982 PMC: 4843429. DOI: 10.1073/pnas.1525465113.

Crystallization and preliminary X-ray characterization of the eukaryotic replication terminator Reb1-Ter DNA complex.

Jaiswal R, Singh S, Bastia D, Escalante C Acta Crystallogr F Struct Biol Commun. 2015; 71(Pt 4):414-8.

PMID: 25849502 PMC: 4388176. DOI: 10.1107/S2053230X15004112.

References

Schagger H, von Jagow G . Tricine-sodium dodecyl sulfate-polyacrylamide gel electrophoresis for the separation of proteins in the range from 1 to 100 kDa. Anal Biochem. 1987; 166(2):368-79. DOI: 10.1016/0003-2697(87)90587-2. View

Bujard H, Gentz R, Lanzer M, Stueber D, Mueller M, Ibrahimi I . A T5 promoter-based transcription-translation system for the analysis of proteins in vitro and in vivo. Methods Enzymol. 1987; 155:416-33. DOI: 10.1016/0076-6879(87)55028-5. View

Bartsch I, Schoneberg C, Grummt I . Purification and characterization of TTFI, a factor that mediates termination of mouse ribosomal DNA transcription. Mol Cell Biol. 1988; 8(9):3891-7. PMC: 365448. DOI: 10.1128/mcb.8.9.3891-3897.1988. View

Kuhn A, Grummt I . 3'-end formation of mouse pre-rRNA involves both transcription termination and a specific processing reaction. Genes Dev. 1989; 3(2):224-31. DOI: 10.1101/gad.3.2.224. View

Wang H, Nicholson P, Stillman D . Identification of a Saccharomyces cerevisiae DNA-binding protein involved in transcriptional regulation. Mol Cell Biol. 1990; 10(4):1743-53. PMC: 362280. DOI: 10.1128/mcb.10.4.1743-1753.1990. View

McStay B, Reeder R . A DNA-binding protein is required for termination of transcription by RNA polymerase I in Xenopus laevis. Mol Cell Biol. 1990; 10(6):2793-800. PMC: 360640. DOI: 10.1128/mcb.10.6.2793-2800.1990. View

Chasman D, Lue N, Buchman A, LaPointe J, Lorch Y, Kornberg R . A yeast protein that influences the chromatin structure of UASG and functions as a powerful auxiliary gene activator. Genes Dev. 1990; 4(4):503-14. DOI: 10.1101/gad.4.4.503. View

Pfleiderer C, Smid A, Bartsch I, Grummt I . An undecamer DNA sequence directs termination of human ribosomal gene transcription. Nucleic Acids Res. 1990; 18(16):4727-36. PMC: 331929. DOI: 10.1093/nar/18.16.4727. View

Ju Q, Morrow B, Warner J . REB1, a yeast DNA-binding protein with many targets, is essential for growth and bears some resemblance to the oncogene myb. Mol Cell Biol. 1990; 10(10):5226-34. PMC: 361205. DOI: 10.1128/mcb.10.10.5226-5234.1990. View

10.

Morrow B, Ju Q, Warner J . Purification and characterization of the yeast rDNA binding protein REB1. J Biol Chem. 1990; 265(34):20778-83. View

11.

Johnson S, Warner J . Termination of transcription of ribosomal RNA in Saccharomyces cerevisiae. Mol Cell Biochem. 1991; 104(1-2):163-8. DOI: 10.1007/BF00229816. View

12.

Kulkens T, van der Sande C, Dekker A, Van Heerikhuizen H, Planta R . A system to study transcription by yeast RNA polymerase I within the chromosomal context: functional analysis of the ribosomal DNA enhancer and the RBP1/REB1 binding sites. EMBO J. 1992; 11(12):4665-74. PMC: 557042. DOI: 10.1002/j.1460-2075.1992.tb05568.x. View

13.

Remacle J, Holmberg S . A REB1-binding site is required for GCN4-independent ILV1 basal level transcription and can be functionally replaced by an ABF1-binding site. Mol Cell Biol. 1992; 12(12):5516-26. PMC: 360489. DOI: 10.1128/mcb.12.12.5516-5526.1992. View

14.

Kang J, Yokoi T, Holland M . Binding sites for abundant nuclear factors modulate RNA polymerase I-dependent enhancer function in Saccharomyces cerevisiae. J Biol Chem. 1995; 270(48):28723-32. DOI: 10.1074/jbc.270.48.28723. View

15.

Huang G, Keil R . Requirements for activity of the yeast mitotic recombination hotspot HOT1: RNA polymerase I and multiple cis-acting sequences. Genetics. 1995; 141(3):845-55. PMC: 1206849. DOI: 10.1093/genetics/141.3.845. View

16.

Liu Z, Zhao A, Chen L, Pape L . Activated levels of rRNA synthesis in fission yeast are driven by an intergenic rDNA region positioned over 2500 nucleotides upstream of the initiation site. Nucleic Acids Res. 1997; 25(3):659-67. PMC: 146475. DOI: 10.1093/nar/25.3.659. View

17.

Scott E, Baker H . Concerted action of the transcriptional activators REB1, RAP1, and GCR1 in the high-level expression of the glycolytic gene TPI. Mol Cell Biol. 1993; 13(1):543-50. PMC: 358933. DOI: 10.1128/mcb.13.1.543-550.1993. View

18.

Lang W, Reeder R . The REB1 site is an essential component of a terminator for RNA polymerase I in Saccharomyces cerevisiae. Mol Cell Biol. 1993; 13(1):649-58. PMC: 358943. DOI: 10.1128/mcb.13.1.649-658.1993. View

19.

Morrow B, Ju Q, Warner J . A bipartite DNA-binding domain in yeast Reb1p. Mol Cell Biol. 1993; 13(2):1173-82. PMC: 359002. DOI: 10.1128/mcb.13.2.1173-1182.1993. View

20.

Morrow B, Johnson S, Warner J . The rRNA enhancer regulates rRNA transcription in Saccharomyces cerevisiae. Mol Cell Biol. 1993; 13(2):1283-9. PMC: 359013. DOI: 10.1128/mcb.13.2.1283-1289.1993. View