The Leishmania major RNA Polymerase II Largest Subunit Lacks a Carboxy-Terminus Heptad Repeat Structure and its Encoding Gene is Linked with the Calreticulin Gene

Protist ◽  
2000 ◽  
Vol 151 (1) ◽  
pp. 57-68 ◽  
Author(s):  
David G. Croan ◽  
John Ellis
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Leishmania Major ◽  
Heptad Repeat ◽  
Carboxy Terminus ◽  
Repeat Structure ◽  
Encoding Gene

scholarly journals Splicing- and cleavage-independent requirement of RNA polymerase II CTD for mRNA release from the transcription site

2007 ◽  
Vol 179 (2) ◽  
pp. 199-207 ◽  
Author(s):  
Noélia Custódio ◽  
Maria Vivo ◽  
Michael Antoniou ◽  
Maria Carmo-Fonseca
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Heptad Repeat ◽  
Exon Junction Complex ◽  
Repeat Structure ◽  
Transcription Site ◽  
Cleavage And Polyadenylation ◽  
Nuclear Exosome ◽  
Heptad Repeats ◽  
Surveillance Mechanism

Eukaryotic cells have a surveillance mechanism that identifies aberrantly processed pre-mRNAs and prevents their flow to the cytoplasm by tethering them near the site of transcription. Here we provide evidence that mRNA release from the transcription site requires the heptad repeat structure of the C-terminal domain (CTD) of RNA polymerase II. The mammalian CTD, which is essential for normal co-transcriptional maturation of mRNA precursors, comprises 52 heptad repeats. We show that a truncated CTD containing 31 repeats (heptads 1–23, 36–38, and 48–52) is sufficient to support transcription, splicing, cleavage, and polyadenylation. Yet, the resulting mRNAs are mostly retained in the vicinity of the gene after transcriptional shutoff. The retained mRNAs maintain the ability to recruit components of the exon junction complex and the nuclear exosome subunit Rrp6p, suggesting that binding of these proteins is not sufficient for RNA release. We propose that the missing heptads in the truncated CTD mutant are required for binding of proteins implicated in a final co-transcriptional maturation of spliced and 3′ end cleaved and polyadenylated mRNAs into export-competent ribonucleoprotein particles.

scholarly journals RNA Polymerase II Accumulation in the Promoter-Proximal Region of the Dihydrofolate Reductase and γ-Actin Genes

2003 ◽  
Vol 23 (6) ◽  
pp. 1961-1967 ◽  
Author(s):  
Chonghui Cheng ◽  
Phillip A. Sharp
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Dihydrofolate Reductase ◽  
Mammalian Cells ◽  
Proximal Region ◽  
Heptad Repeat ◽  
Pol Ii ◽  
Actin Genes ◽  
Carboxyl Terminal ◽  
Promoter Proximal Region

ABSTRACT The carboxyl-terminal domain (CTD) of RNA polymerase II (Pol II) can be phosphorylated at serine 2 (Ser-2) and serine 5 (Ser-5) of the CTD heptad repeat YSPTSPS, and this phosphorylation is important in coupling transcription to RNA processing, including 5′ capping, splicing, and polyadenylation. The mammalian endogenous dihydrofolate reductase and γ-actin genes have been used to study the association of Pol II with different regions of transcribed genes (promoter-proximal compared to distal regions) and the phosphorylation status of its CTD. For both genes, Pol II is more concentrated in the promoter-proximal regions than in the interior regions. Moreover, different phosphorylation forms of Pol II are associated with distinct regions. Ser-5 phosphorylation of Pol II is concentrated near the promoter, while Ser-2 phosphorylation is observed throughout the gene. These results suggest that the accumulation of paused Pol II in promoter-proximal regions may be a common feature of gene regulation in mammalian cells.

scholarly journals Characterization of the RNA polymerase II and III complexes in Leishmania major

2007 ◽  
Vol 37 (5) ◽  
pp. 491-502 ◽  
Author(s):  
Santiago Martínez-Calvillo ◽  
Alka Saxena ◽  
Amanda Green ◽  
Aaron Leland ◽  
Peter J. Myler
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Leishmania Major

DNA-binding studies of XSPTSPSZ, derivatives of the intercalating heptad repeat of RNA polymerase II

Biopolymers ◽  
1997 ◽  
Vol 42 (4) ◽  
pp. 387-398 ◽  
Author(s):  
Margaret M. Harding ◽  
Guy Y. Krippner ◽  
Cathryn J. Shelton ◽  
Alison Rodger ◽  
Karen J. Sanders ◽  
...  
Keyword(s):  
Dna Binding ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Heptad Repeat ◽  
Binding Studies ◽  
Dna Binding Studies ◽  
Derivatives Of

scholarly journals Structure analysis suggests Ess1 isomerizes the carboxy-terminal domain of RNA polymerase II via a bivalent anchoring mechanism

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Kevin E. W. Namitz ◽  
Tongyin Zheng ◽  
Ashley J. Canning ◽  
Nilda L. Alicea-Velazquez ◽  
Carlos A. Castañeda ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Heptad Repeat ◽  
Distance Constraint ◽  
Catalytic Domains ◽  
Terminal Domain ◽  
Carboxy Terminal Domain ◽  
Human Ortholog ◽  
Heptad Repeats ◽  
Carboxy Terminal

AbstractAccurate gene transcription in eukaryotes depends on isomerization of serine-proline bonds within the carboxy-terminal domain (CTD) of RNA polymerase II. Isomerization is part of the “CTD code” that regulates recruitment of proteins required for transcription and co-transcriptional RNA processing.Saccharomyces cerevisiaeEss1 and its human ortholog, Pin1, are prolyl isomerases that engage the long heptad repeat (YSPTSPS)26of the CTD by an unknown mechanism. Here, we used an integrative structural approach to decipher Ess1 interactions with the CTD. Ess1 has a rigid linker between its WW and catalytic domains that enforces a distance constraint for bivalent interaction with the ends of long CTD substrates (≥4–5 heptad repeats). Our binding results suggest that the Ess1 WW domain anchors the proximal end of the CTD substrate during isomerization, and that linker divergence may underlie evolution of substrate specificity.

scholarly journals A novel SH2 recognition mechanism recruits Spt6 to the doubly phosphorylated RNA polymerase II linker at sites of transcription

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Matthew A Sdano ◽  
James M Fulcher ◽  
Sowmiya Palani ◽  
Mahesh B Chandrasekharan ◽  
Timothy J Parnell ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Sh2 Domain ◽  
Heptad Repeat ◽  
Side Chain ◽  
Phosphate Binding ◽  
Recognition Mechanism ◽  
Repressive Chromatin ◽  
Repeat Domain

We determined that the tandem SH2 domain of S. cerevisiae Spt6 binds the linker region of the RNA polymerase II subunit Rpb1 rather than the expected sites in its heptad repeat domain. The 4 nM binding affinity requires phosphorylation at Rpb1 S1493 and either T1471 or Y1473. Crystal structures showed that pT1471 binds the canonical SH2 pY site while pS1493 binds an unanticipated pocket 70 Å distant. Remarkably, the pT1471 phosphate occupies the phosphate-binding site of a canonical pY complex, while Y1473 occupies the position of a canonical pY side chain, with the combination of pT and Y mimicking a pY moiety. Biochemical data and modeling indicate that pY1473 can form an equivalent interaction, and we find that pT1471/pS1493 and pY1473/pS1493 combinations occur in vivo. ChIP-seq and genetic analyses demonstrate the importance of these interactions for recruitment of Spt6 to sites of transcription and for the maintenance of repressive chromatin.

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