Phosphorylation of the Transcription Elongation Factor Spt5 by Yeast Bur1 Kinase Stimulates Recruitment of the PAF Complex

Overview

Journal Mol Cell Biol

Specialty Cell Biology

Date 2009 Jul 8

PMID 19581288

Citations 121

Authors

Ying Liu

Linda Warfield

Chao Zhang

Jie Luo

Jasmina Allen

Walter H Lang

Jeffrey Ranish

Kevan M Shokat

Steven Hahn

Affiliations

Soon will be listed here.

Abstract

The Saccharomyces cerevisiae kinase Bur1 is involved in coupling transcription elongation to chromatin modification, but not all important Bur1 targets in the elongation complex are known. Using a chemical genetics strategy wherein Bur1 kinase was engineered to be regulated by a specific inhibitor, we found that Bur1 phosphorylates the Spt5 C-terminal repeat domain (CTD) both in vivo and in isolated elongation complexes in vitro. Deletion of the Spt5 CTD or mutation of the Spt5 serines targeted by Bur1 reduces recruitment of the PAF complex, which functions to recruit factors involved in chromatin modification and mRNA maturation to elongating polymerase II (Pol II). Deletion of the Spt5 CTD showed the same defect in PAF recruitment as rapid inhibition of Bur1 kinase activity, and this Spt5 mutation led to a decrease in histone H3K4 trimethylation. Brief inhibition of Bur1 kinase activity in vivo also led to a significant decrease in phosphorylation of the Pol II CTD at Ser-2, showing that Bur1 also contributes to Pol II Ser-2 phosphorylation. Genetic results suggest that Bur1 is essential for growth because it targets multiple factors that play distinct roles in transcription.

Citing Articles

DSIF factor Spt5 coordinates transcription, maturation and exoribonucleolysis of RNA polymerase II transcripts.

Kus K, Carrique L, Kecman T, Fournier M, Hassanein S, Aydin E Nat Commun. 2025; 16(1):10.

PMID: 39746995 PMC: 11695829. DOI: 10.1038/s41467-024-55063-7.

A direct interaction between the Chd1 CHCT domain and Rtf1 controls Chd1 distribution and nucleosome positioning on active genes.

Tripplehorn S, Shirra M, Lardo S, Marvil H, Hainer S, Arndt K bioRxiv. 2024; .

PMID: 39677735 PMC: 11643122. DOI: 10.1101/2024.12.06.627179.

The CDK9-SPT5 Axis in Control of Transcription Elongation by RNAPII.

Sun R, Fisher R J Mol Biol. 2024; 437(1):168746.

PMID: 39147127 PMC: 11649480. DOI: 10.1016/j.jmb.2024.168746.

Mechanisms and Functions of the RNA Polymerase II General Transcription Machinery during the Transcription Cycle.

Archuleta S, Goodrich J, Kugel J Biomolecules. 2024; 14(2).

PMID: 38397413 PMC: 10886972. DOI: 10.3390/biom14020176.

Histone H2B ubiquitylation: Connections to transcription and effects on chromatin structure.

Fetian T, Grover A, Arndt K Biochim Biophys Acta Gene Regul Mech. 2024; 1867(2):195018.

PMID: 38331024 PMC: 11098702. DOI: 10.1016/j.bbagrm.2024.195018.

References

Qiu H, Hu C, Hinnebusch A . Phosphorylation of the Pol II CTD by KIN28 enhances BUR1/BUR2 recruitment and Ser2 CTD phosphorylation near promoters. Mol Cell. 2009; 33(6):752-62. PMC: 2683426. DOI: 10.1016/j.molcel.2009.02.018. View

Shah K, Liu Y, Deirmengian C, Shokat K . Engineering unnatural nucleotide specificity for Rous sarcoma virus tyrosine kinase to uniquely label its direct substrates. Proc Natl Acad Sci U S A. 1997; 94(8):3565-70. PMC: 20479. DOI: 10.1073/pnas.94.8.3565. View

Mason P, Struhl K . Distinction and relationship between elongation rate and processivity of RNA polymerase II in vivo. Mol Cell. 2005; 17(6):831-40. DOI: 10.1016/j.molcel.2005.02.017. View

Xiao T, Shibata Y, Rao B, Laribee R, ORourke R, Buck M . The RNA polymerase II kinase Ctk1 regulates positioning of a 5' histone methylation boundary along genes. Mol Cell Biol. 2006; 27(2):721-31. PMC: 1800795. DOI: 10.1128/MCB.01628-06. View

Lindstrom D, Squazzo S, Muster N, Burckin T, Wachter K, Emigh C . Dual roles for Spt5 in pre-mRNA processing and transcription elongation revealed by identification of Spt5-associated proteins. Mol Cell Biol. 2003; 23(4):1368-78. PMC: 141151. DOI: 10.1128/MCB.23.4.1368-1378.2003. View

Biddick R, Law G, Young E . Adr1 and Cat8 mediate coactivator recruitment and chromatin remodeling at glucose-regulated genes. PLoS One. 2008; 3(1):e1436. PMC: 2175534. DOI: 10.1371/journal.pone.0001436. View

Kim J, Sharp P . Positive transcription elongation factor B phosphorylates hSPT5 and RNA polymerase II carboxyl-terminal domain independently of cyclin-dependent kinase-activating kinase. J Biol Chem. 2001; 276(15):12317-23. DOI: 10.1074/jbc.M010908200. View

Chen H, Hahn S . Mapping the location of TFIIB within the RNA polymerase II transcription preinitiation complex: a model for the structure of the PIC. Cell. 2004; 119(2):169-80. DOI: 10.1016/j.cell.2004.09.028. View

Kim T, Buratowski S . Two Saccharomyces cerevisiae JmjC domain proteins demethylate histone H3 Lys36 in transcribed regions to promote elongation. J Biol Chem. 2007; 282(29):20827-35. DOI: 10.1074/jbc.M703034200. View

10.

Li B, Carey M, Workman J . The role of chromatin during transcription. Cell. 2007; 128(4):707-19. DOI: 10.1016/j.cell.2007.01.015. View

11.

Zhou K, Kuo W, Fillingham J, Greenblatt J . Control of transcriptional elongation and cotranscriptional histone modification by the yeast BUR kinase substrate Spt5. Proc Natl Acad Sci U S A. 2009; 106(17):6956-61. PMC: 2678430. DOI: 10.1073/pnas.0806302106. View

12.

Carrozza M, Li B, Florens L, Suganuma T, Swanson S, Lee K . Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription. Cell. 2005; 123(4):581-92. DOI: 10.1016/j.cell.2005.10.023. View

13.

Qiu H, Hu C, Wong C, Hinnebusch A . The Spt4p subunit of yeast DSIF stimulates association of the Paf1 complex with elongating RNA polymerase II. Mol Cell Biol. 2006; 26(8):3135-48. PMC: 1446970. DOI: 10.1128/MCB.26.8.3135-3148.2006. View

14.

Wach A, Brachat A, Pohlmann R, Philippsen P . New heterologous modules for classical or PCR-based gene disruptions in Saccharomyces cerevisiae. Yeast. 1994; 10(13):1793-808. DOI: 10.1002/yea.320101310. View

15.

Keogh M, Podolny V, Buratowski S . Bur1 kinase is required for efficient transcription elongation by RNA polymerase II. Mol Cell Biol. 2003; 23(19):7005-18. PMC: 193923. DOI: 10.1128/MCB.23.19.7005-7018.2003. View

16.

Kanin E, Kipp R, Kung C, Slattery M, Viale A, Hahn S . Chemical inhibition of the TFIIH-associated kinase Cdk7/Kin28 does not impair global mRNA synthesis. Proc Natl Acad Sci U S A. 2007; 104(14):5812-7. PMC: 1851574. DOI: 10.1073/pnas.0611505104. View

17.

Keller A, Nesvizhskii A, Kolker E, Aebersold R . Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal Chem. 2002; 74(20):5383-92. DOI: 10.1021/ac025747h. View

18.

Jones J, Phatnani H, Haystead T, MacDonald J, Alam S, Greenleaf A . C-terminal repeat domain kinase I phosphorylates Ser2 and Ser5 of RNA polymerase II C-terminal domain repeats. J Biol Chem. 2004; 279(24):24957-64. PMC: 2680323. DOI: 10.1074/jbc.M402218200. View

19.

Laribee R, Fuchs S, Strahl B . H2B ubiquitylation in transcriptional control: a FACT-finding mission. Genes Dev. 2007; 21(7):737-43. DOI: 10.1101/gad.1541507. View

20.

Prather D, Larschan E, Winston F . Evidence that the elongation factor TFIIS plays a role in transcription initiation at GAL1 in Saccharomyces cerevisiae. Mol Cell Biol. 2005; 25(7):2650-9. PMC: 1061654. DOI: 10.1128/MCB.25.7.2650-2659.2005. View