CTD phosphatase: Role in RNA polymerase II cycling and the regulation of transcript elongation

Lin, Patrick S.; Marshall, Nicholas F.; Dahmus, Michael E.

doi:10.1016/s0079-6603(02)72074-6

Cited by 47 publications

(32 citation statements)

References 104 publications

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“…After transcript initiation, the CTD is heavily phosphorylated on serine 2 and serine 5 by different protein kinases (pTEFb (yeast Bur1 or Ctdk1)) and TFIIH), respectively (10, 11). Later, during transcript elongation and at transcriptional termination, CTD phosphatases remove the phosphate groups, enabling recycling of RNAPII for a new round of transcription (11,12). A CTD phosphatase was first identified biochemically through its ability to specifically dephosphorylate the RNAPII CTD in vitro (13).…”

Section: During the Rna Polymerase II (Rnapii)mentioning

confidence: 99%

Interaction of Fcp1 Phosphatase with Elongating RNA Polymerase II Holoenzyme, Enzymatic Mechanism of Action, and Genetic Interaction with Elongator

Kong

Kobor

Krogan

et al. 2005

Journal of Biological Chemistry

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Fcp1 de-phosphorylates the RNA polymerase II (RNAPII) C-terminal domain (CTD) in vitro, and mutation of the yeast FCP1 gene results in global transcription defects and increased CTD phosphorylation levels in vivo. Here we show that the Fcp1 protein associates with elongating RNAPII holoenzyme in vitro. Our data suggest that the association of Fcp1 with elongating polymerase results in CTD de-phosphorylation when the native ternary RNAPII0-DNA-RNA complex is disrupted. Surprisingly, highly purified yeast Fcp1 dephosphorylates serine 5 but not serine 2 of the RNAPII CTD repeat. Only free RNAPII0(Ser-5) and not RNA-PII0-DNA-RNA ternary complexes act as a good substrate in the Fcp1 CTD de-phosphorylation reaction. In contrast, TFIIH CTD kinase has a pronounced preference for RNAPII incorporated into a ternary complex. Interestingly, the Fcp1 reaction mechanism appears to entail phosphoryl transfer from RNAPII0 directly to Fcp1. Elongator fails to affect the phosphatase activity of Fcp1 in vitro, but genetic evidence points to a functional overlap between Elongator and Fcp1 in vivo. Genetic interactions between Elongator and a number of other transcription factors are also reported. Together, these results shed new light on mechanisms that drive the transcription cycle and point to a role for Fcp1 in the recycling of RNAPII after dissociation from active genes. During the RNA polymerase II (RNAPII)1 transcription cycle, both the phosphorylation state of the polymerase and the proteins that RNAPII interacts with change dramatically. Throughout promoter recruitment and initiation where RNA-PII exists in a hypo-phosphorylated state, it interacts with general transcription factors, such as TFIID, TFIIB, TFIIF, TFIIE, TFIIH, and Mediator (1). In the process of promoter clearance and early transcript elongation where RNAPII becomes hyper-phosphorylated, interactions with initiation-specific factors are severed, and interactions with other proteins are established. Factors that have been shown to preferentially associate with hyper-phosphorylated elongating RNAPII include RNA processing factors (2) and factors thought to play a role in transcript elongation, such as Elongator, Set1, and Set2 (3-8).The C-terminal repeat domain (CTD) of RNAPII is the specific target for kinases that phosphorylates the polymerase at the transition from initiation to elongation. The CTD consists of the conserved heptapeptide, Tyr-Ser-Pro-Thr-Ser-Pro-Ser, repeated 26 times in yeast and up to 52 times in metazoans (9). After transcript initiation, the CTD is heavily phosphorylated on serine 2 and serine 5 by different protein kinases (pTEFb (yeast Bur1 or Ctdk1)) and TFIIH), respectively (10, 11). Later, during transcript elongation and at transcriptional termination, CTD phosphatases remove the phosphate groups, enabling recycling of RNAPII for a new round of transcription (11,12). A CTD phosphatase was first identified biochemically through its ability to specifically dephosphorylate the RNAPII CTD in vitro (13). The gene encoding a TFIIF-inter...

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Section: During the Rna Polymerase II (Rnapii)mentioning

confidence: 99%

Interaction of Fcp1 Phosphatase with Elongating RNA Polymerase II Holoenzyme, Enzymatic Mechanism of Action, and Genetic Interaction with Elongator

Kong

Kobor

Krogan

et al. 2005

Journal of Biological Chemistry

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“…Analysis of Arabidopsis mutants that display hyperinduction of RD29a expression under stress conditions have identified a family of C-terminal domain (CTD) phosphatase-like (CPL) genes that negatively regulate stressresponsive transcription (5,6). The CPL1 and CPL3 genes discovered in the screen for hyperinduction are so named because they encode large polypeptides (967 and 1,241 aa, respectively) with local primary structure similarity to the Fcp1 family of fungal and metazoan protein serine phosphatases, which regulate transcription by dephosphorylating the CTD of the largest subunit of RNA Pol II (10).…”

mentioning

confidence: 99%

“…Studies of CTD function in fungi and metazoans have illuminated its role as a structurally plastic ''landing pad'' for proteins that regulate transcription and cotranscriptional mRNA processing (11). The CTD undergoes waves of phosphorylation and dephosphorylation at positions Ser-5 and Ser-2 during the transcription cycle and in response to environmental stress (10). Remodeling of the CTD phosphorylation array accompanies the transition from initiation to elongation modes and controls the recruitment, activity, and egress of the various mRNA processing machines that act on the nascent transcript (12)(13)(14)(15).…”

mentioning

confidence: 99%

Arabidopsis C-terminal domain phosphatase-like 1 and 2 are essential Ser-5-specific C-terminal domain phosphatases

Koiwa

Hausmann

Bang

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

108

164

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Transcription and mRNA processing are regulated by phosphorylation and dephosphorylation of the C-terminal domain (CTD) of RNA polymerase II, which consists of tandem repeats of a Y 1 S 2 P 3 T 4 S 5 P 6 S 7 heptapeptide. Previous studies showed that members of the plant CTD phosphatase-like (CPL) protein family differentially regulate osmotic stress-responsive and abscisic acidresponsive transcription in Arabidopsis thaliana. Here we report that AtCPL1 and AtCPL2 specifically dephosphorylate Ser-5 of the CTD heptad in Arabidopsis RNA polymerase II, but not Ser-2. An N-terminal catalytic domain of CPL1, which suffices for CTD Ser-5 phosphatase activity in vitro, includes a signature DXDXT acylphosphatase motif, but lacks a breast cancer 1 CTD, which is an essential component of the fungal and metazoan Fcp1 CTD phosphatase enzymes. The CTD of CPL1, which contains two putative doublestranded RNA binding motifs, is essential for the in vivo function of CPL1 and includes a C-terminal 23-aa signal responsible for its nuclear targeting. CPL2 has a similar domain structure but contains only one double-stranded RNA binding motif. Combining mutant alleles of CPL1 and CPL2 causes synthetic lethality of the male but not the female gametes. These results indicate that CPL1 and CPL2 exemplify a unique family of CTD Ser-5-specific phosphatases with an essential role in plant growth and development.T ranscriptional induction of genes that encode stress tolerance determinants is an integral part of the survival strategy of plants in adverse environments. The Arabidopsis thaliana responsive to dehydration (RD) genes are prototypal outputs of stress signal integration activated by low temperature, hyperosmolarity, and the plant hormone abscisic acid (ABA). The stress-inducible promoter of the RD29a gene contains dehydration͞cold-responsive elements and ABA-responsive elements that are the targets of distinct families of DNA binding transcription factors (1, 2). The plant stress response is also regulated by proteins that impact the core RNA polymerase II (Pol II) transcriptional machinery, the mRNA maturation process, and chromatin structure (3-9). Analysis of Arabidopsis mutants that display hyperinduction of RD29a expression under stress conditions have identified a family of C-terminal domain (CTD) phosphatase-like (CPL) genes that negatively regulate stressresponsive transcription (5, 6). The CPL1 and CPL3 genes discovered in the screen for hyperinduction are so named because they encode large polypeptides (967 and 1,241 aa, respectively) with local primary structure similarity to the Fcp1 family of fungal and metazoan protein serine phosphatases, which regulate transcription by dephosphorylating the CTD of the largest subunit of RNA Pol II (10).The Pol II CTD is composed of a tandemly repeated heptapeptide of consensus sequence Y . The number of CTD heptad repeats varies widely among species and correlates roughly with evolutionary complexity; e.g., mammals have 52 repeats, Drosophila has 42 repeats, fission yeast Schizosacc...

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“…Analysis of Arabidopsis (Arabidopsis thaliana) mutants that are hyperresponsive to osmotic stresses and ABA has identified a family of CTD phosphatase-like (CPL) genes that negatively regulate stress-responsive gene expression Xiong et al, 2002). CPL1 and CPL3 were so named because the encoded polypeptides (967 and 1,241 amino acids, respectively) are homologous to the FCP1 family of fungal and metazoan protein Ser phosphatases, which regulate transcription by dephosphorylating the carboxylterminal domain (CTD) of the largest subunit of Pol II (Lin et al, 2002b (Nawrath et al, 1990). Dynamic changes in the CTD phosphoarray are controlled by CTD kinases and phosphatases that have Ser-2 and Ser-5 target specificity (Palancade and Bensaude, 2003).…”

mentioning

confidence: 99%

“…CPL3 and CPL4 belong to the FCP1 (TFIIF-interacting CTD phosphatase 1) family of phosphatases that are established to be transcriptional regulators in fungi and metazoa (Archambault et al, 1997(Archambault et al, , 1998Hausmann and Shuman, 2002;Lin et al, 2002b). Genetic evidence indicated that CPL3 is a negative regulator of ABA signaling .…”

mentioning

confidence: 99%

Arabidopsis Carboxyl-Terminal Domain Phosphatase-Like Isoforms Share Common Catalytic and Interaction Domains But Have Distinct in Planta Functions

et al. 2006

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An Arabidopsis (Arabidopsis thaliana) multigene family (predicted to be more than 20 members) encodes plant C-terminal domain (CTD) phosphatases that dephosphorylate Ser residues in tandem heptad repeat sequences of the RNA polymerase II C terminus. CTD phosphatase-like (CPL) isoforms 1 and 3 are regulators of osmotic stress and abscisic acid (ABA) signaling. Evidence presented herein indicates that CPL3 and CPL4 are homologs of a prototype CTD phosphatase, FCP1 (TFIIFinteracting CTD-phosphatase). CPL3 and CPL4 contain catalytic FCP1 homology and breast cancer 1 C terminus (BRCT) domains. Recombinant CPL3 and CPL4 interact with AtRAP74, an Arabidopsis ortholog of a FCP1-interacting TFIIF subunit. A CPL3 or CPL4 C-terminal fragment that contains the BRCT domain mediates molecular interaction with AtRAP74. Consistent with their predicted roles in transcriptional regulation, green fluorescent protein fusion proteins of CPL3, CPL4, and RAP74 all localize to the nucleus. cpl3 mutations that eliminate the BRCT or FCP1 homology domain cause ABA hyperactivation of the stress-inducible RD29a promoter, whereas RNAi suppression of CPL4 results in dwarfism and reduced seedling growth. These results indicate CPL3 and CPL4 are a paralogous pair of general transcription regulators with similar biochemical properties, but are required for the distinct developmental and environmental responses. CPL4 is necessary for normal plant growth and thus most orthologous to fungal and metazoan FCP1, whereas CPL3 is an isoform that specifically facilitates ABA signaling.

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CTD phosphatase: Role in RNA polymerase II cycling and the regulation of transcript elongation

Cited by 47 publications

References 104 publications

Interaction of Fcp1 Phosphatase with Elongating RNA Polymerase II Holoenzyme, Enzymatic Mechanism of Action, and Genetic Interaction with Elongator

Interaction of Fcp1 Phosphatase with Elongating RNA Polymerase II Holoenzyme, Enzymatic Mechanism of Action, and Genetic Interaction with Elongator

Arabidopsis C-terminal domain phosphatase-like 1 and 2 are essential Ser-5-specific C-terminal domain phosphatases

Arabidopsis Carboxyl-Terminal Domain Phosphatase-Like Isoforms Share Common Catalytic and Interaction Domains But Have Distinct in Planta Functions

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