1
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Fidler E, Dwyer K, Ansari A. Ssu72: a versatile protein with functions in transcription and beyond. Front Mol Biosci 2024; 11:1332878. [PMID: 38304578 PMCID: PMC10830811 DOI: 10.3389/fmolb.2024.1332878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 01/08/2024] [Indexed: 02/03/2024] Open
Abstract
Eukaryotic transcription is a complex process involving a vast network of protein and RNA factors that influence gene expression. The main player in transcription is the RNA polymerase that synthesizes the RNA from the DNA template. RNA polymerase II (RNAPII) transcribes all protein coding genes and some noncoding RNAs in eukaryotic cells. The polymerase is aided by interacting partners that shuttle it along the gene for initiation, elongation and termination of transcription. One of the many factors that assist RNAPII in transcription of genes is Ssu72. It is a carboxy-terminal-domain (CTD)-phosphatase that plays pleiotropic roles in the transcription cycle. It is essential for cell viability in Saccharomyces cerevisiae, the organism in which it was discovered. The homologues of Ssu72 have been identified in humans, mice, plants, flies, and fungi thereby suggesting the evolutionarily conserved nature of the protein. Recent studies have implicated the factor beyond the confines of transcription in homeostasis and diseases.
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Affiliation(s)
| | | | - Athar Ansari
- Department of Biological Sciences, Wayne State University, Detroit, MI, United States
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2
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Zhao T, Vvedenskaya IO, Lai WKM, Basu S, Pugh BF, Nickels BE, Kaplan CD. Ssl2/TFIIH function in transcription start site scanning by RNA polymerase II in Saccharomyces cerevisiae. eLife 2021; 10:e71013. [PMID: 34652274 PMCID: PMC8589449 DOI: 10.7554/elife.71013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 10/14/2021] [Indexed: 12/31/2022] Open
Abstract
In Saccharomyces cerevisiae, RNA polymerase II (Pol II) selects transcription start sites (TSSs) by a unidirectional scanning process. During scanning, a preinitiation complex (PIC) assembled at an upstream core promoter initiates at select positions within a window ~40-120 bp downstream. Several lines of evidence indicate that Ssl2, the yeast homolog of XPB and an essential and conserved subunit of the general transcription factor (GTF) TFIIH, drives scanning through its DNA-dependent ATPase activity, therefore potentially controlling both scanning rate and scanning extent (processivity). To address questions of how Ssl2 functions in promoter scanning and interacts with other initiation activities, we leveraged distinct initiation-sensitive reporters to identify novel ssl2 alleles. These ssl2 alleles, many of which alter residues conserved from yeast to human, confer either upstream or downstream TSS shifts at the model promoter ADH1 and genome-wide. Specifically, tested ssl2 alleles alter TSS selection by increasing or narrowing the distribution of TSSs used at individual promoters. Genetic interactions of ssl2 alleles with other initiation factors are consistent with ssl2 allele classes functioning through increasing or decreasing scanning processivity but not necessarily scanning rate. These alleles underpin a residue interaction network that likely modulates Ssl2 activity and TFIIH function in promoter scanning. We propose that the outcome of promoter scanning is determined by two functional networks, the first being Pol II activity and factors that modulate it to determine initiation efficiency within a scanning window, and the second being Ssl2/TFIIH and factors that modulate scanning processivity to determine the width of the scanning widow.
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Affiliation(s)
- Tingting Zhao
- Department of Biological Sciences, University of PittsburghPittsburghUnited States
| | - Irina O Vvedenskaya
- Department of Genetics and Waksman Institute, Rutgers UniversityPiscatawayUnited States
| | - William KM Lai
- Department of Molecular Biology and Genetics, Cornell UniversityIthacaUnited States
| | - Shrabani Basu
- Department of Biological Sciences, University of PittsburghPittsburghUnited States
| | - B Franklin Pugh
- Department of Molecular Biology and Genetics, Cornell UniversityIthacaUnited States
| | - Bryce E Nickels
- Department of Genetics and Waksman Institute, Rutgers UniversityPiscatawayUnited States
| | - Craig D Kaplan
- Department of Biological Sciences, University of PittsburghPittsburghUnited States
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3
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Transcription and chromatin-based surveillance mechanism controls suppression of cryptic antisense transcription. Cell Rep 2021; 36:109671. [PMID: 34496258 PMCID: PMC8441049 DOI: 10.1016/j.celrep.2021.109671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 08/26/2020] [Accepted: 08/13/2021] [Indexed: 12/25/2022] Open
Abstract
Phosphorylation of the RNA polymerase II C-terminal domain Y1S2P3T4S5P6S7 consensus sequence coordinates key events during transcription, and its deregulation leads to defects in transcription and RNA processing. Here, we report that the histone deacetylase activity of the fission yeast Hos2/Set3 complex plays an important role in suppressing cryptic initiation of antisense transcription when RNA polymerase II phosphorylation is dysregulated due to the loss of Ssu72 phosphatase. Interestingly, although single Hos2 and Set3 mutants have little effect, loss of Hos2 or Set3 combined with ssu72Δ results in a synergistic increase in antisense transcription globally and correlates with elevated sensitivity to genotoxic agents. We demonstrate a key role for the Ssu72/Hos2/Set3 mechanism in the suppression of cryptic antisense transcription at the 3' end of convergent genes that are most susceptible to these defects, ensuring the fidelity of gene expression within dense genomes of simple eukaryotes.
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4
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Turner RE, Harrison PF, Swaminathan A, Kraupner-Taylor CA, Goldie BJ, See M, Peterson AL, Schittenhelm RB, Powell DR, Creek DJ, Dichtl B, Beilharz TH. Genetic and pharmacological evidence for kinetic competition between alternative poly(A) sites in yeast. eLife 2021; 10:65331. [PMID: 34232857 PMCID: PMC8263057 DOI: 10.7554/elife.65331] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 06/22/2021] [Indexed: 01/23/2023] Open
Abstract
Most eukaryotic mRNAs accommodate alternative sites of poly(A) addition in the 3’ untranslated region in order to regulate mRNA function. Here, we present a systematic analysis of 3’ end formation factors, which revealed 3’UTR lengthening in response to a loss of the core machinery, whereas a loss of the Sen1 helicase resulted in shorter 3’UTRs. We show that the anti-cancer drug cordycepin, 3’ deoxyadenosine, caused nucleotide accumulation and the usage of distal poly(A) sites. Mycophenolic acid, a drug which reduces GTP levels and impairs RNA polymerase II (RNAP II) transcription elongation, promoted the usage of proximal sites and reversed the effects of cordycepin on alternative polyadenylation. Moreover, cordycepin-mediated usage of distal sites was associated with a permissive chromatin template and was suppressed in the presence of an rpb1 mutation, which slows RNAP II elongation rate. We propose that alternative polyadenylation is governed by temporal coordination of RNAP II transcription and 3’ end processing and controlled by the availability of 3’ end factors, nucleotide levels and chromatin landscape.
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Affiliation(s)
- Rachael Emily Turner
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Paul F Harrison
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia.,Monash Bioinformatics Platform, Monash University, Melbourne, Australia
| | - Angavai Swaminathan
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Calvin A Kraupner-Taylor
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Belinda J Goldie
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Michael See
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia.,Monash Bioinformatics Platform, Monash University, Melbourne, Australia
| | - Amanda L Peterson
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Ralf B Schittenhelm
- Monash Proteomics & Metabolomics Facility, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - David R Powell
- Monash Bioinformatics Platform, Monash University, Melbourne, Australia
| | - Darren J Creek
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Bernhard Dichtl
- School of Life and Environmental Sciences, Deakin University, Geelong, Australia
| | - Traude H Beilharz
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
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5
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González-Jiménez A, Campos A, Navarro F, Clemente-Blanco A, Calvo O. Regulation of Eukaryotic RNAPs Activities by Phosphorylation. Front Mol Biosci 2021; 8:681865. [PMID: 34250017 PMCID: PMC8268151 DOI: 10.3389/fmolb.2021.681865] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 06/07/2021] [Indexed: 01/11/2023] Open
Abstract
Evolutionarily conserved kinases and phosphatases regulate RNA polymerase II (RNAPII) transcript synthesis by modifying the phosphorylation status of the carboxyl-terminal domain (CTD) of Rpb1, the largest subunit of RNAPII. Proper levels of Rpb1-CTD phosphorylation are required for RNA co-transcriptional processing and to coordinate transcription with other nuclear processes, such as chromatin remodeling and histone modification. Whether other RNAPII subunits are phosphorylated and influences their role in gene expression is still an unanswered question. Much less is known about RNAPI and RNAPIII phosphorylation, whose subunits do not contain functional CTDs. However, diverse studies have reported that several RNAPI and RNAPIII subunits are susceptible to phosphorylation. Some of these phosphorylation sites are distributed within subunits common to all three RNAPs whereas others are only shared between RNAPI and RNAPIII. This suggests that the activities of all RNAPs might be finely modulated by phosphorylation events and raises the idea of a tight coordination between the three RNAPs. Supporting this view, the transcription by all RNAPs is regulated by signaling pathways that sense different environmental cues to adapt a global RNA transcriptional response. This review focuses on how the phosphorylation of RNAPs might regulate their function and we comment on the regulation by phosphorylation of some key transcription factors in the case of RNAPI and RNAPIII. Finally, we discuss the existence of possible common mechanisms that could coordinate their activities.
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Affiliation(s)
- Araceli González-Jiménez
- Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas, Universidad de Salamanca, Salamanca, Spain
| | - Adrián Campos
- Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas, Universidad de Salamanca, Salamanca, Spain
| | - Francisco Navarro
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Jaén, Spain.,Centro de Estudios Avanzados en Aceite de Oliva y Olivar, Universidad de Jaén, Jaén, Spain
| | - Andrés Clemente-Blanco
- Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas, Universidad de Salamanca, Salamanca, Spain
| | - Olga Calvo
- Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas, Universidad de Salamanca, Salamanca, Spain
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6
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Peck Justice SA, McCracken NA, Victorino JF, Qi GD, Wijeratne AB, Mosley AL. Boosting Detection of Low-Abundance Proteins in Thermal Proteome Profiling Experiments by Addition of an Isobaric Trigger Channel to TMT Multiplexes. Anal Chem 2021; 93:7000-7010. [PMID: 33908254 PMCID: PMC8153406 DOI: 10.1021/acs.analchem.1c00012] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
![]()
The study of low-abundance
proteins is a challenge to discovery-based
proteomics. Mass spectrometry (MS) applications, such as thermal proteome
profiling (TPP), face specific challenges in the detection of the
whole proteome as a consequence of the use of nondenaturing extraction
buffers. TPP is a powerful method for the study of protein thermal
stability, but quantitative accuracy is highly dependent on consistent
detection. Therefore, TPP can be limited in its amenability to study
low-abundance proteins that tend to have stochastic or poor detection
by MS. To address this challenge, we incorporated an affinity-purified
protein complex sample at submolar concentrations as an isobaric trigger
channel into a mutant TPP (mTPP) workflow to provide reproducible
detection and quantitation of the low-abundance subunits of the cleavage
and polyadenylation factor (CPF) complex. The inclusion of an isobaric
protein complex trigger channel increased detection an average of
40× for previously detected subunits and facilitated detection
of CPF subunits that were previously below the limit of detection.
Importantly, these gains in CPF detection did not cause large changes
in melt temperature (Tm) calculations
for other unrelated proteins in the samples, with a high positive
correlation between Tm estimates in samples
with and without isobaric trigger channel addition. Overall, the incorporation
of an affinity-purified protein complex as an isobaric trigger channel
within a tandem mass tag (TMT) multiplex for mTPP experiments is an
effective and reproducible way to gather thermal profiling data on
proteins that are not readily detected using the original TPP or mTPP
protocols.
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Affiliation(s)
- Sarah A Peck Justice
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Neil A McCracken
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - José F Victorino
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Guihong D Qi
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Aruna B Wijeratne
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Amber L Mosley
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
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7
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Hwang S, Kim MH, Lee CW. Ssu72 Dual-Specific Protein Phosphatase: From Gene to Diseases. Int J Mol Sci 2021; 22:3791. [PMID: 33917542 PMCID: PMC8038829 DOI: 10.3390/ijms22073791] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/02/2021] [Accepted: 04/05/2021] [Indexed: 12/22/2022] Open
Abstract
More than 70% of eukaryotic proteins are regulated by phosphorylation. However, the mechanism of dephosphorylation that counteracts phosphorylation is less studied. Phosphatases are classified into 104 distinct groups based on substrate-specific features and the sequence homologies in their catalytic domains. Among them, dual-specificity phosphatases (DUSPs) that dephosphorylate both phosphoserine/threonine and phosphotyrosine are important for cellular homeostasis. Ssu72 is a newly studied phosphatase with dual specificity that can dephosphorylate both phosphoserine/threonine and phosphotyrosine. It is important for cell-growth signaling, metabolism, and immune activation. Ssu72 was initially identified as a phosphatase for the Ser5 and Ser7 residues of the C-terminal domain of RNA polymerase II. It prefers the cis configuration of the serine-proline motif within its substrate and regulates Pin1, different from other phosphatases. It has recently been reported that Ssu72 can regulate sister chromatid cohesion and the separation of duplicated chromosomes during the cell cycle. Furthermore, Ssu72 appears to be involved in the regulation of T cell receptor signaling, telomere regulation, and even hepatocyte homeostasis in response to a variety of stress and damage signals. In this review, we aim to summarize various functions of the Ssu72 phosphatase, their implications in diseases, and potential therapeutic indications.
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Affiliation(s)
- Soeun Hwang
- Department of Molecular Cell Biology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon 16419, Korea; (S.H.); (M.-H.K.)
| | - Min-Hee Kim
- Department of Molecular Cell Biology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon 16419, Korea; (S.H.); (M.-H.K.)
| | - Chang-Woo Lee
- Department of Molecular Cell Biology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon 16419, Korea; (S.H.); (M.-H.K.)
- SKKU Institute for Convergence, Sungkyunkwan University, Suwon 16419, Korea
- Curogen Technology, Suwon 16419, Korea
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8
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Lim S, Ahn H, Duan R, Liu Y, Ryu HY, Ahn SH. The Spt7 subunit of the SAGA complex is required for the regulation of lifespan in both dividing and nondividing yeast cells. Mech Ageing Dev 2021; 196:111480. [PMID: 33831401 DOI: 10.1016/j.mad.2021.111480] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 03/23/2021] [Accepted: 03/31/2021] [Indexed: 11/30/2022]
Abstract
Spt7 belongs to the suppressor of Ty (SPT) module of the Spt-Ada-Gcn5-acetyltransferase (SAGA) complex and is known as the yeast ortholog of human STAF65γ. Spt7 lacks intrinsic enzymatic activity but is responsible for the integrity and proper assembly of the SAGA complex. Here, we determined the role of the SAGA Spt7 subunit in cellular aging. We found that Spt7 was indispensable for a normal lifespan in both dividing and nondividing yeast cells. In the quiescent state of cells, Spt7 was required for the control of overall mRNA levels. In mitotically active cells, deletion of the SPT module had little effect on the recombination rate within heterochromatic ribosomal DNA (rDNA) loci, but loss of Spt7 profoundly elevated the plasmid-based DNA recombination frequency. Consistently, loss of Spt7 increased spontaneous Rad52 foci by approximately two-fold upon entry into S phase. These results provide evidence that Spt7 contributes to the regulation of the normal replicative lifespan (RLS) and chronological lifespan (CLS), possibly by controlling the DNA recombination rate and overall mRNA expression. We propose that the regulation of SAGA complex integrity by Spt7 might be involved in the conserved regulatory pathway for lifespan regulation in eukaryotes.
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Affiliation(s)
- Suji Lim
- Department of Molecular and Life Science, College of Science and Convergence Technology, Hanyang University ERICA Campus, Ansan 15588, Republic of Korea
| | - Hyojeong Ahn
- Department of Molecular and Life Science, College of Science and Convergence Technology, Hanyang University ERICA Campus, Ansan 15588, Republic of Korea
| | - Ruxin Duan
- Department of Molecular and Life Science, College of Science and Convergence Technology, Hanyang University ERICA Campus, Ansan 15588, Republic of Korea
| | - Yan Liu
- Department of Molecular and Life Science, College of Science and Convergence Technology, Hanyang University ERICA Campus, Ansan 15588, Republic of Korea
| | - Hong-Yeoul Ryu
- School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, College of National Sciences, Kyungpook National University, Daegu 41566, Republic of Korea.
| | - Seong Hoon Ahn
- Department of Molecular and Life Science, College of Science and Convergence Technology, Hanyang University ERICA Campus, Ansan 15588, Republic of Korea.
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9
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Wang YT, Hsiao WY, Wang SW. The fission yeast Pin1 peptidyl-prolyl isomerase promotes dissociation of Sty1 MAPK from RNA polymerase II and recruits Ssu72 phosphatase to facilitate oxidative stress induced transcription. Nucleic Acids Res 2021; 49:805-817. [PMID: 33410907 PMCID: PMC7826279 DOI: 10.1093/nar/gkaa1243] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 12/10/2020] [Accepted: 12/11/2020] [Indexed: 01/07/2023] Open
Abstract
Pin1 is a peptidyl-prolyl isomerase that regulates the structure and function of eukaryotic RNA polymerase II (Pol II) through interaction with the C-terminal domain (CTD) of Rpb1, the largest subunit of Pol II. We demonstrated that this function is important for cellular response to oxidative stress in the fission yeast Schizosaccharomyces pombe. In response to oxidative stress, the Atf1 transcription factor targets Sty1, the mitogen-activated protein kinase (MAPK), to specific stress-responsive promoters. Anchored Sty1 recruits Pol II through direct association with Rpb1-CTD and phosphorylates the reiterated heptad sequence at Serine 5. Pin1 binds phosphorylated CTD to promote dissociation of Sty1 from it, and directly recruits Ssu72 phosphatase to facilitate dephosphorylation of CTD for transcription elongation. In the absence of Pin1, the association of Sty1-Atf1 with Rpb1 persists on stress-responsive promoters failed to generate transcripts of the corresponding genes effectively. The identified characteristic features of the fission yeast Pin1 are conserved in humans. We demonstrated that elevated Pin1 level in cancer cells might help to sustain survival under oxidative stress generated from their altered metabolic pathways. Together, these results suggest a conserved function of Pin1 in cellular response to oxidative stress among eukaryotic cells that might have clinical implication.
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Affiliation(s)
- Yi-Ting Wang
- Institute of Molecular & Genomic Medicine, National Health Research Institutes, 35 Keyan Road, Zhunan Town, Miaoli County 350, Taiwan
| | - Wan-Yi Hsiao
- Institute of Molecular & Genomic Medicine, National Health Research Institutes, 35 Keyan Road, Zhunan Town, Miaoli County 350, Taiwan
| | - Shao-Win Wang
- Institute of Molecular & Genomic Medicine, National Health Research Institutes, 35 Keyan Road, Zhunan Town, Miaoli County 350, Taiwan
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10
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Liu C, Zhang W, Xing W. Diverse and conserved roles of the protein Ssu72 in eukaryotes: from yeast to higher organisms. Curr Genet 2020; 67:195-206. [PMID: 33244642 DOI: 10.1007/s00294-020-01132-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 11/04/2020] [Accepted: 11/06/2020] [Indexed: 01/21/2023]
Abstract
Gene transcription is a complex biological process that involves a set of factors, enzymes and nucleotides. Ssu72 plays a crucial role in every step of gene transcription. RNA polymerase II (RNAPII) occupies an important position in the synthesis of mRNAs. The largest subunit of RNAPII, Rpb1, harbors its C-terminal domain (CTD), which participates in the initiation, elongation and termination of transcription. The CTD consists of heptad repeats of the consensus motif Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7 and is highly conserved among different species. The CTD is flexible in structure and undergoes conformational changes in response to serine phosphorylation and proline isomerization, which are regulated by specific kinases/phosphatases and isomerases, respectively. Ssu72 is a CTD phosphatase with catalytic activity against phosphorylated Ser5 and Ser7. The isomerization of Pro6 affects the binding of Ssu72 to its substrate. Ssu72 can also indirectly change the phosphorylation status of Ser2. In addition, Ssu72 is a member of the 3'-end cleavage and polyadenylation factor (CPF) complex. Together with other CPF components, Ssu72 regulates the 3'-end processing of premature mRNA. Recent studies have revealed other roles of Ssu72, including its roles in balancing phosphate homeostasis and controlling chromosome behaviors, which should be further explored. In conclusion, the protein Ssu72 is an enzyme worthy of attention, not confined to its role in gene transcription.
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Affiliation(s)
- Changfu Liu
- Department of Interventional Treatment, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Weihao Zhang
- Department of Interventional Treatment, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Wenge Xing
- Department of Interventional Treatment, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China.
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11
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Qiu C, Jin H, Vvedenskaya I, Llenas JA, Zhao T, Malik I, Visbisky AM, Schwartz SL, Cui P, Čabart P, Han KH, Lai WKM, Metz RP, Johnson CD, Sze SH, Pugh BF, Nickels BE, Kaplan CD. Universal promoter scanning by Pol II during transcription initiation in Saccharomyces cerevisiae. Genome Biol 2020; 21:132. [PMID: 32487207 PMCID: PMC7265651 DOI: 10.1186/s13059-020-02040-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 05/08/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The majority of eukaryotic promoters utilize multiple transcription start sites (TSSs). How multiple TSSs are specified at individual promoters across eukaryotes is not understood for most species. In Saccharomyces cerevisiae, a pre-initiation complex (PIC) comprised of Pol II and conserved general transcription factors (GTFs) assembles and opens DNA upstream of TSSs. Evidence from model promoters indicates that the PIC scans from upstream to downstream to identify TSSs. Prior results suggest that TSS distributions at promoters where scanning occurs shift in a polar fashion upon alteration in Pol II catalytic activity or GTF function. RESULTS To determine the extent of promoter scanning across promoter classes in S. cerevisiae, we perturb Pol II catalytic activity and GTF function and analyze their effects on TSS usage genome-wide. We find that alterations to Pol II, TFIIB, or TFIIF function widely alter the initiation landscape consistent with promoter scanning operating at all yeast promoters, regardless of promoter class. Promoter architecture, however, can determine the extent of promoter sensitivity to altered Pol II activity in ways that are predicted by a scanning model. CONCLUSIONS Our observations coupled with previous data validate key predictions of the scanning model for Pol II initiation in yeast, which we term the shooting gallery. In this model, Pol II catalytic activity and the rate and processivity of Pol II scanning together with promoter sequence determine the distribution of TSSs and their usage.
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Affiliation(s)
- Chenxi Qiu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843-2128, USA
- Present Address: Department of Medicine, Division of Translational Therapeutics, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Huiyan Jin
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843-2128, USA
| | - Irina Vvedenskaya
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854, USA
- Department of Genetics, Rutgers University, Piscataway, NJ, 08854, USA
| | - Jordi Abante Llenas
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, 77843-3128, USA
- Present Address: Whitaker Biomedical Engineering Institute, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Tingting Zhao
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Indranil Malik
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843-2128, USA
- Present Address: Department of Neurology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Alex M Visbisky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Scott L Schwartz
- Genomics and Bioinformatics Service, Texas A&M AgriLife, College Station, TX, 77845, USA
| | - Ping Cui
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843-2128, USA
| | - Pavel Čabart
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843-2128, USA
- Present Address: First Faculty of Medicine, Charles University, BIOCEV, 252 42, Vestec, Czech Republic
| | - Kang Hoo Han
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA, 16802, USA
| | - William K M Lai
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA, 16802, USA
- Present Address: Department of Molecular Biology and Genetics, 458 Biotechnology, Cornell University, New York, 14853, USA
| | - Richard P Metz
- Genomics and Bioinformatics Service, Texas A&M AgriLife, College Station, TX, 77845, USA
| | - Charles D Johnson
- Genomics and Bioinformatics Service, Texas A&M AgriLife, College Station, TX, 77845, USA
| | - Sing-Hoi Sze
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843-2128, USA
- Department of Computer Science and Engineering, Texas A&M University, College Station, TX, 77843-3127, USA
| | - B Franklin Pugh
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA, 16802, USA
- Present Address: Department of Molecular Biology and Genetics, 458 Biotechnology, Cornell University, New York, 14853, USA
| | - Bryce E Nickels
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854, USA
- Department of Genetics, Rutgers University, Piscataway, NJ, 08854, USA
| | - Craig D Kaplan
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA.
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12
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Allepuz-Fuster P, O'Brien MJ, González-Polo N, Pereira B, Dhoondia Z, Ansari A, Calvo O. RNA polymerase II plays an active role in the formation of gene loops through the Rpb4 subunit. Nucleic Acids Res 2019; 47:8975-8987. [PMID: 31304538 PMCID: PMC6753479 DOI: 10.1093/nar/gkz597] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/27/2019] [Accepted: 06/29/2019] [Indexed: 01/19/2023] Open
Abstract
Gene loops are formed by the interaction of initiation and termination factors occupying the distal ends of a gene during transcription. RNAPII is believed to affect gene looping indirectly owing to its essential role in transcription. The results presented here, however, demonstrate a direct role of RNAPII in gene looping through the Rpb4 subunit. 3C analysis revealed that gene looping is abolished in the rpb4Δ mutant. In contrast to the other looping-defective mutants, rpb4Δ cells do not exhibit a transcription termination defect. RPB4 overexpression, however, rescued the transcription termination and gene looping defect of sua7-1, a mutant of TFIIB. Furthermore, RPB4 overexpression rescued the ssu72-2 gene looping defect, while SSU72 overexpression restored the formation of gene loops in rpb4Δ cells. Interestingly, the interaction of TFIIB with Ssu72 is compromised in rpb4Δ cells. These results suggest that the TFIIB-Ssu72 interaction, which is critical for gene loop formation, is facilitated by Rpb4. We propose that Rpb4 is promoting the transfer of RNAPII from the terminator to the promoter for reinitiation of transcription through TFIIB-Ssu72 mediated gene looping.
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Affiliation(s)
| | - Michael J O'Brien
- Department of Biological Science. Wayne State University. Detroit, MI 48202, USA
| | | | - Bianca Pereira
- Department of Biological Science. Wayne State University. Detroit, MI 48202, USA
| | - Zuzer Dhoondia
- Department of Biological Science. Wayne State University. Detroit, MI 48202, USA
| | - Athar Ansari
- Department of Biological Science. Wayne State University. Detroit, MI 48202, USA
| | - Olga Calvo
- Instituto de Biología Funcional y Genómica, CSIC-USAL, Salamanca, Spain
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13
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Functional interaction of human Ssu72 with RNA polymerase II complexes. PLoS One 2019; 14:e0213598. [PMID: 30901332 PMCID: PMC6430399 DOI: 10.1371/journal.pone.0213598] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 02/25/2019] [Indexed: 11/19/2022] Open
Abstract
Phosphorylation of the C-terminal domain (CTD) of the large subunit of human RNA polymerase II (Pol II) is regulated during the transcription cycle by the combined action of specific kinases and phosphatases. Pol II enters into the preinitiation complex (PIC) unphosphorylated, but is quickly phosphorylated by Cdk7 during initiation. How phosphatases alter the pattern and extent of CTD phosphorylation at this early stage of transcription is not clear. We previously demonstrated the functional association of an early-acting, magnesium-independent phosphatase with early elongation complexes. Here we show that Ssu72 is responsible for that activity. We found that the phosphatase enters the transcription cycle during the formation of PICs and that Ssu72 is physically associated with very early elongation complexes. The association of Ssu72 with elongation complexes was stable to extensive washing with up to 200 mM KCl. Interestingly, Ssu72 ceased to function on complexes that contained RNA longer than 28 nt. However, when PICs were washed before initiation, the strict cutoff at 28 nt was lost. This suggests that factor(s) are important for the specific regulation of Ssu72 function during the transition between initiation and pausing. Overall, our results demonstrate when Ssu72 can act on early transcription complexes and suggest that Ssu72 may also function in the PIC prior to initiation.
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14
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Offley SR, Schmidt MC. Protein phosphatases of Saccharomyces cerevisiae. Curr Genet 2018; 65:41-55. [PMID: 30225534 DOI: 10.1007/s00294-018-0884-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 08/27/2018] [Accepted: 09/08/2018] [Indexed: 10/28/2022]
Abstract
The phosphorylation status of a protein is highly regulated and is determined by the opposing activities of protein kinases and protein phosphatases within the cell. While much is known about the protein kinases found in Saccharomyces cerevisiae, the protein phosphatases are much less characterized. Of the 127 protein kinases in yeast, over 90% are in the same evolutionary lineage. In contrast, protein phosphatases are fewer in number (only 43 have been identified in yeast) and comprise multiple, distinct evolutionary lineages. Here we review the protein phosphatase families of yeast with regard to structure, catalytic mechanism, regulation, and signal transduction participation.
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Affiliation(s)
- Sarah R Offley
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 450 Technology Drive, Pittsburgh, PA, 15219, USA
| | - Martin C Schmidt
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 450 Technology Drive, Pittsburgh, PA, 15219, USA.
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15
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Mischo HE, Chun Y, Harlen KM, Smalec BM, Dhir S, Churchman LS, Buratowski S. Cell-Cycle Modulation of Transcription Termination Factor Sen1. Mol Cell 2018; 70:312-326.e7. [PMID: 29656924 PMCID: PMC5919780 DOI: 10.1016/j.molcel.2018.03.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 06/26/2017] [Accepted: 03/08/2018] [Indexed: 01/14/2023]
Abstract
Many non-coding transcripts (ncRNA) generated by RNA polymerase II in S. cerevisiae are terminated by the Nrd1-Nab3-Sen1 complex. However, Sen1 helicase levels are surprisingly low compared with Nrd1 and Nab3, raising questions regarding how ncRNA can be terminated in an efficient and timely manner. We show that Sen1 levels increase during the S and G2 phases of the cell cycle, leading to increased termination activity of NNS. Overexpression of Sen1 or failure to modulate its abundance by ubiquitin-proteasome-mediated degradation greatly decreases cell fitness. Sen1 toxicity is suppressed by mutations in other termination factors, and NET-seq analysis shows that its overexpression leads to a decrease in ncRNA production and altered mRNA termination. We conclude that Sen1 levels are carefully regulated to prevent aberrant termination. We suggest that ncRNA levels and coding gene transcription termination are modulated by Sen1 to fulfill critical cell cycle-specific functions. Transcription termination factor Sen1 levels fluctuate throughout the cell cycle APC targets Sen1 for degradation during G1 Reduced Sen1 levels lower efficiency of Sen1-mediated termination Sen1 overexpression reduces cell viability because of excessive termination
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Affiliation(s)
- Hannah E Mischo
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Sir William Dunn School of Pathology, Oxford University, South Parks Road, Oxford OX1 3RE, UK; Mechanisms of Transcription Laboratory, Clare Hall Laboratories, Cancer Research UK London Research Institute, South Mimms EN6 3LD, UK.
| | - Yujin Chun
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Kevin M Harlen
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Brendan M Smalec
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Somdutta Dhir
- Sir William Dunn School of Pathology, Oxford University, South Parks Road, Oxford OX1 3RE, UK
| | | | - Stephen Buratowski
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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16
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Chereji RV, Bharatula V, Elfving N, Blomberg J, Larsson M, Morozov AV, Broach JR, Björklund S. Mediator binds to boundaries of chromosomal interaction domains and to proteins involved in DNA looping, RNA metabolism, chromatin remodeling, and actin assembly. Nucleic Acids Res 2017; 45:8806-8821. [PMID: 28575439 PMCID: PMC5587782 DOI: 10.1093/nar/gkx491] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 05/23/2017] [Indexed: 01/24/2023] Open
Abstract
Mediator is a multi-unit molecular complex that plays a key role in transferring signals from transcriptional regulators to RNA polymerase II in eukaryotes. We have combined biochemical purification of the Saccharomyces cerevisiae Mediator from chromatin with chromatin immunoprecipitation in order to reveal Mediator occupancy on DNA genome-wide, and to identify proteins interacting specifically with Mediator on the chromatin template. Tandem mass spectrometry of proteins in immunoprecipitates of mediator complexes revealed specific interactions between Mediator and the RSC, Arp2/Arp3, CPF, CF 1A and Lsm complexes in chromatin. These factors are primarily involved in chromatin remodeling, actin assembly, mRNA 3′-end processing, gene looping and mRNA decay, but they have also been shown to enter the nucleus and participate in Pol II transcription. Moreover, we have found that Mediator, in addition to binding Pol II promoters, occupies chromosomal interacting domain (CID) boundaries and that Mediator in chromatin associates with proteins that have been shown to interact with CID boundaries, such as Sth1, Ssu72 and histone H4. This suggests that Mediator plays a significant role in higher-order genome organization.
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Affiliation(s)
- Razvan V Chereji
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Vasudha Bharatula
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA
| | - Nils Elfving
- Department of Medical Biochemistry and Biophysics Umeå University, 901 87 Umeå, Sweden
| | - Jeanette Blomberg
- Department of Medical Biochemistry and Biophysics Umeå University, 901 87 Umeå, Sweden
| | - Miriam Larsson
- Department of Medical Biochemistry and Biophysics Umeå University, 901 87 Umeå, Sweden
| | - Alexandre V Morozov
- Department of Physics and Astronomy, Rutgers University, Piscataway, NJ 08854, USA.,Center for Quantitative Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - James R Broach
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA
| | - Stefan Björklund
- Department of Medical Biochemistry and Biophysics Umeå University, 901 87 Umeå, Sweden
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17
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Lee SH, Kim EK, Kwon JE, Lee JK, Lee D, Kim SY, Seo HB, Na HS, Jung K, Kwok SK, Lee CW, Park SH, Cho ML. Ssu72 attenuates autoimmune arthritis via targeting of STAT3 signaling and Th17 activation. Sci Rep 2017; 7:5506. [PMID: 28710354 PMCID: PMC5511296 DOI: 10.1038/s41598-017-05421-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 05/30/2017] [Indexed: 02/06/2023] Open
Abstract
Signal transducer and activator of transcription 3 (STAT3) orchestrates the differentiation of several cell types, including interleukin-17 (IL-17)-releasing Th17 cells. Dysregulation of Th17 cells results in chronic inflammatory responses. Ssu72 is a C-terminal domain phosphatase required for transcriptional regulation. However, the mechanism by which Ssu72 affects STAT3 activation and Th17 cell differentiation is unclear. Here, we found that Ssu72 overexpression suppresses STAT3 activation and Th17 cell responses in vitro. A systemic infusion of Ssu72 attenuates experimental autoimmune arthritis by reducing STAT3 activity and the differentiation of Th17 cells. It also reduces joint destruction, serum immunoglobulin concentrations and osteoclastogenesis but increases the number of marginal zone B cells and B10 cells. These effects are associated with reduced p-STAT3 levels and the suppression of Th17 cell formation in vivo. Based on these data, Ssu72 is related to STAT3 activation and the inflammatory response; and Ssu72 overexpression in T-cell-mediated immunity has potential utility for the treatment of autoimmune arthritis.
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Affiliation(s)
- Seung Hoon Lee
- The Rheumatism Research Center, Catholic Research Institute of Medical Science, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Eun-Kyung Kim
- The Rheumatism Research Center, Catholic Research Institute of Medical Science, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Jeong-Eun Kwon
- The Rheumatism Research Center, Catholic Research Institute of Medical Science, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Jin-Kwan Lee
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, 06351, Korea
| | - DoHyeong Lee
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, 16419, Korea
| | - Se-Young Kim
- The Rheumatism Research Center, Catholic Research Institute of Medical Science, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Hyeon-Beom Seo
- The Rheumatism Research Center, Catholic Research Institute of Medical Science, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Hyun Sik Na
- The Rheumatism Research Center, Catholic Research Institute of Medical Science, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | | | - Seung-Ki Kwok
- Division of Rheumatology, Department of Internal Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, 137-701, South Korea
| | - Chang-Woo Lee
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, 06351, Korea.,Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, 16419, Korea
| | - Sung-Hwan Park
- The Rheumatism Research Center, Catholic Research Institute of Medical Science, College of Medicine, The Catholic University of Korea, Seoul, South Korea. .,Division of Rheumatology, Department of Internal Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, 137-701, South Korea.
| | - Mi-La Cho
- The Rheumatism Research Center, Catholic Research Institute of Medical Science, College of Medicine, The Catholic University of Korea, Seoul, South Korea. .,Laboratory of Immune Network, Conversant Research Consortium in Immunologic Disease, College of Medicine, The Catholic University of Korea, Seoul, South Korea. .,The Institute for Aging and Metabolic Diseases, College of Medicine, The Catholic University of Korea, Seoul, 06591, South Korea.
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18
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Mayfield JE, Burkholder NT, Zhang YJ. Dephosphorylating eukaryotic RNA polymerase II. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:372-87. [PMID: 26779935 DOI: 10.1016/j.bbapap.2016.01.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 01/11/2016] [Accepted: 01/14/2016] [Indexed: 12/20/2022]
Abstract
The phosphorylation state of the C-terminal domain of RNA polymerase II is required for the temporal and spatial recruitment of various factors that mediate transcription and RNA processing throughout the transcriptional cycle. Therefore, changes in CTD phosphorylation by site-specific kinases/phosphatases are critical for the accurate transmission of information during transcription. Unlike kinases, CTD phosphatases have been traditionally neglected as they are thought to act as passive negative regulators that remove all phosphate marks at the conclusion of transcription. This over-simplified view has been disputed in recent years and new data assert the active and regulatory role phosphatases play in transcription. We now know that CTD phosphatases ensure the proper transition between different stages of transcription, balance the distribution of phosphorylation for accurate termination and re-initiation, and prevent inappropriate expression of certain genes. In this review, we focus on the specific roles of CTD phosphatases in regulating transcription. In particular, we emphasize how specificity and timing of dephosphorylation are achieved for these phosphatases and consider the various regulatory factors that affect these dynamics.
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Affiliation(s)
- Joshua E Mayfield
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Nathaniel T Burkholder
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Yan Jessie Zhang
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.
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19
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Rege M, Subramanian V, Zhu C, Hsieh THS, Weiner A, Friedman N, Clauder-Münster S, Steinmetz LM, Rando OJ, Boyer LA, Peterson CL. Chromatin Dynamics and the RNA Exosome Function in Concert to Regulate Transcriptional Homeostasis. Cell Rep 2015; 13:1610-22. [PMID: 26586442 PMCID: PMC4662874 DOI: 10.1016/j.celrep.2015.10.030] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 09/02/2015] [Accepted: 10/09/2015] [Indexed: 12/12/2022] Open
Abstract
The histone variant H2A.Z is a hallmark of nucleosomes flanking promoters of protein-coding genes and is often found in nucleosomes that carry lysine 56-acetylated histone H3 (H3-K56Ac), a mark that promotes replication-independent nucleosome turnover. Here, we find that H3-K56Ac promotes RNA polymerase II occupancy at many protein-coding and noncoding loci, yet neither H3-K56Ac nor H2A.Z has a significant impact on steady-state mRNA levels in yeast. Instead, broad effects of H3-K56Ac or H2A.Z on RNA levels are revealed only in the absence of the nuclear RNA exosome. H2A.Z is also necessary for the expression of divergent, promoter-proximal non-coding RNAs (ncRNAs) in mouse embryonic stem cells. Finally, we show that H2A.Z functions with H3-K56Ac to facilitate formation of chromosome interaction domains (CIDs). Our study suggests that H2A.Z and H3-K56Ac work in concert with the RNA exosome to control mRNA and ncRNA expression, perhaps in part by regulating higher-order chromatin structures.
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Affiliation(s)
- Mayuri Rege
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Vidya Subramanian
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Chenchen Zhu
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Tsung-Han S Hsieh
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Assaf Weiner
- School of Computer Science and Engineering, The Hebrew University, Jerusalem 91904, Israel; Alexander Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
| | - Nir Friedman
- School of Computer Science and Engineering, The Hebrew University, Jerusalem 91904, Israel; Alexander Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
| | | | - Lars M Steinmetz
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Oliver J Rando
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Laurie A Boyer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Craig L Peterson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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20
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Allepuz-Fuster P, Martínez-Fernández V, Garrido-Godino AI, Alonso-Aguado S, Hanes SD, Navarro F, Calvo O. Rpb4/7 facilitates RNA polymerase II CTD dephosphorylation. Nucleic Acids Res 2014; 42:13674-88. [PMID: 25416796 PMCID: PMC4267648 DOI: 10.1093/nar/gku1227] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 11/04/2014] [Accepted: 11/10/2014] [Indexed: 12/11/2022] Open
Abstract
The Rpb4 and Rpb7 subunits of eukaryotic RNA polymerase II (RNAPII) participate in a variety of processes from transcription, DNA repair, mRNA export and decay, to translation regulation and stress response. However, their mechanism(s) of action remains unclear. Here, we show that the Rpb4/7 heterodimer in Saccharomyces cerevisiae plays a key role in controlling phosphorylation of the carboxy terminal domain (CTD) of the Rpb1 subunit of RNAPII. Proper phosphorylation of the CTD is critical for the synthesis and processing of RNAPII transcripts. Deletion of RPB4, and mutations that disrupt the integrity of Rpb4/7 or its recruitment to the RNAPII complex, increased phosphorylation of Ser2, Ser5, Ser7 and Thr4 within the CTD. RPB4 interacted genetically with genes encoding CTD phosphatases (SSU72, FCP1), CTD kinases (KIN28, CTK1, SRB10) and a prolyl isomerase that targets the CTD (ESS1). We show that Rpb4 is important for Ssu72 and Fcp1 phosphatases association, recruitment and/or accessibility to the CTD, and that this correlates strongly with Ser5P and Ser2P levels, respectively. Our data also suggest that Fcp1 is the Thr4P phosphatase in yeast. Based on these and other results, we suggest a model in which Rpb4/7 helps recruit and potentially stimulate the activity of CTD-modifying enzymes, a role that is central to RNAPII function.
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Affiliation(s)
- Paula Allepuz-Fuster
- Instituto de Biología Funcional y Genómica, CSIC/Universidad de Salamanca, Salamanca 37007, Spain
| | - Verónica Martínez-Fernández
- Departamento de Biología Experimental, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén 23071, Spain
| | - Ana I. Garrido-Godino
- Departamento de Biología Experimental, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén 23071, Spain
| | - Sergio Alonso-Aguado
- Instituto de Biología Funcional y Genómica, CSIC/Universidad de Salamanca, Salamanca 37007, Spain
| | - Steven D. Hanes
- Department of Biochemistry and Molecular Biology, Upstate Medical University, Syracuse, NY 13210, USA
| | - Francisco Navarro
- Departamento de Biología Experimental, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén 23071, Spain
| | - Olga Calvo
- Instituto de Biología Funcional y Genómica, CSIC/Universidad de Salamanca, Salamanca 37007, Spain
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21
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Rosado-Lugo JD, Hampsey M. The Ssu72 phosphatase mediates the RNA polymerase II initiation-elongation transition. J Biol Chem 2014; 289:33916-26. [PMID: 25339178 DOI: 10.1074/jbc.m114.608695] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Transitions between the different stages of the RNAPII transcription cycle involve the recruitment and exchange of factors, including mRNA capping enzymes, elongation factors, splicing factors, 3'-end-processing complexes, and termination factors. These transitions are coordinated by the dynamic phosphorylation of the C-terminal domain (CTD) of the largest subunit of RNAPII (Rpb1). The CTD is composed of reiterated heptapeptide repeats (Y(1)S(2)P(3)T(4)S(5)P(6)S(7)) that undergo phosphorylation and dephosphorylation as RNAPII transitions through the transcription cycle. An essential phosphatase in this process is Ssu72, which exhibits catalytic specificity for Ser(P)(5) and Ser(P)(7). Ssu72 is unique in that it is specific for Ser(P)(5) in one orientation of the CTD and for Ser(P)(7) when bound in the opposite orientation. Moreover, Ssu72 interacts with components of the initiation machinery and affects start site selection yet is an integral component of the CPF 3'-end-processing complex. Here we provide a comprehensive view of the effects of Ssu72 with respect to its Ser(P)(5) phosphatase activity. We demonstrate that Ssu72 dephosphorylates Ser(P)(5) at the initiation-elongation transition. Furthermore, Ssu72 indirectly affects the levels of Ser(P)(2) during the elongation stage of transcription but does so independent of its catalytic activity.
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Affiliation(s)
- Jesús D Rosado-Lugo
- From the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey 08854
| | - Michael Hampsey
- From the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey 08854
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22
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Corden JL. RNA polymerase II C-terminal domain: Tethering transcription to transcript and template. Chem Rev 2013; 113:8423-55. [PMID: 24040939 PMCID: PMC3988834 DOI: 10.1021/cr400158h] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Jeffry L Corden
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine , 725 North Wolfe Street, Baltimore Maryland 21205, United States
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23
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Abstract
Gene looping, defined as the physical interaction between the promoter and terminator regions of a RNA polymerase II-transcribed gene, is widespread in yeast and mammalian cells. Gene looping has been shown to play important roles in transcription. Gene-loop formation is dependent on regulatory proteins localized at the 5' and 3' ends of genes, such as TFIIB. However, whether other factors contribute to gene looping remains to be elucidated. Here, we investigated the contribution of intrinsic DNA and chromatin structures to gene looping. We found that Saccharomyces cerevisiae looped genes show high DNA bendability around middle and 3/4 regions in open reading frames (ORFs). This bendability pattern is conserved between yeast species, whereas the position of bendability peak varies substantially among species. Looped genes in human cells also show high DNA bendability. Nucleosome positioning around looped ORF middle regions is unstable. We also present evidence indicating that this unstable nucleosome positioning is involved in gene looping. These results suggest a mechanism by which DNA bendability and unstable nucleosome positioning could assist in the formation of gene loops.
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Affiliation(s)
- Zhiming Dai
- Department of Electronics and Communication Engineering, School of Information Science and Technology, Sun Yat-Sen University, Guangzhou, China
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24
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Jeronimo C, Bataille AR, Robert F. The Writers, Readers, and Functions of the RNA Polymerase II C-Terminal Domain Code. Chem Rev 2013; 113:8491-522. [DOI: 10.1021/cr4001397] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Célia Jeronimo
- Institut de recherches cliniques de Montréal, Montréal, Québec,
Canada H2W 1R7
| | - Alain R. Bataille
- Institut de recherches cliniques de Montréal, Montréal, Québec,
Canada H2W 1R7
| | - François Robert
- Institut de recherches cliniques de Montréal, Montréal, Québec,
Canada H2W 1R7
- Département
de Médecine,
Faculté de Médecine, Université de Montréal, Montréal, Québec,
Canada H3T 1J4
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25
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Rodríguez-Torres AM, Lamas-Maceiras M, García-Díaz R, Freire-Picos MA. Structurally conserved and functionally divergent yeast Ssu72 phosphatases. FEBS Lett 2013; 587:2617-22. [PMID: 23831060 DOI: 10.1016/j.febslet.2013.06.044] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 06/18/2013] [Accepted: 06/25/2013] [Indexed: 12/25/2022]
Abstract
The eukaryotic Ssu72 factor is involved in several RNA biogenesis processes. It has phosphatase activity on the carboxy-terminal domain (CTD) of the major subunit of RNA polymerase II. The Kluyveromyces lactis Ssu72 (KlSsu72) shows in vitro phosphatase activity for the pNPP substrate, and this activity is inhibited by ortho-vanadate. The expression of KlSsu72 in Saccharomyces cerevisiae shows defective CTD serine5-P phosphatase activity and reveals the importance of Ssu72 for the normal CTD serine5-P levels at two growth states. The divergence is emphasised by the remarkable changes in RNA14 alternative 3'-end RNA processing, which are independent of the CTD serine5-P levels.
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Tan-Wong SM, Zaugg JB, Camblong J, Xu Z, Zhang DW, Mischo HE, Ansari AZ, Luscombe NM, Steinmetz LM, Proudfoot NJ. Gene loops enhance transcriptional directionality. Science 2012; 338:671-5. [PMID: 23019609 PMCID: PMC3563069 DOI: 10.1126/science.1224350] [Citation(s) in RCA: 179] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Eukaryotic genomes are extensively transcribed, forming both messenger RNAs (mRNAs) and noncoding RNAs (ncRNAs). ncRNAs made by RNA polymerase II often initiate from bidirectional promoters (nucleosome-depleted chromatin) that synthesize mRNA and ncRNA in opposite directions. We demonstrate that, by adopting a gene-loop conformation, actively transcribed mRNA encoding genes restrict divergent transcription of ncRNAs. Because gene-loop formation depends on a protein factor (Ssu72) that coassociates with both the promoter and the terminator, the inactivation of Ssu72 leads to increased synthesis of promoter-associated divergent ncRNAs, referred to as Ssu72-restricted transcripts (SRTs). Similarly, inactivation of individual gene loops by gene mutation enhances SRT synthesis. We demonstrate that gene-loop conformation enforces transcriptional directionality on otherwise bidirectional promoters.
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MESH Headings
- Exosome Multienzyme Ribonuclease Complex/metabolism
- Genes, Fungal
- Genome, Fungal
- Mutation
- Nucleic Acid Conformation
- Phosphoprotein Phosphatases/metabolism
- Promoter Regions, Genetic
- RNA Polymerase II/metabolism
- RNA Stability
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Untranslated/genetics
- RNA, Untranslated/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Saccharomyces cerevisiae Proteins/metabolism
- Transcription, Genetic
- mRNA Cleavage and Polyadenylation Factors/metabolism
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Affiliation(s)
- Sue Mei Tan-Wong
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
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27
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Kaplan CD, Jin H, Zhang IL, Belyanin A. Dissection of Pol II trigger loop function and Pol II activity-dependent control of start site selection in vivo. PLoS Genet 2012; 8:e1002627. [PMID: 22511879 PMCID: PMC3325174 DOI: 10.1371/journal.pgen.1002627] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2011] [Accepted: 02/15/2012] [Indexed: 12/27/2022] Open
Abstract
Structural and biochemical studies have revealed the importance of a conserved, mobile domain of RNA Polymerase II (Pol II), the Trigger Loop (TL), in substrate selection and catalysis. The relative contributions of different residues within the TL to Pol II function and how Pol II activity defects correlate with gene expression alteration in vivo are unknown. Using Saccharomyces cerevisiae Pol II as a model, we uncover complex genetic relationships between mutated TL residues by combinatorial analysis of multiply substituted TL variants. We show that in vitro biochemical activity is highly predictive of in vivo transcription phenotypes, suggesting direct relationships between phenotypes and Pol II activity. Interestingly, while multiple TL residues function together to promote proper transcription, individual residues can be separated into distinct functional classes likely relevant to the TL mechanism. In vivo, Pol II activity defects disrupt regulation of the GTP-sensitive IMD2 gene, explaining sensitivities to GTP-production inhibitors, but contrasting with commonly cited models for this sensitivity in the literature. Our data provide support for an existing model whereby Pol II transcriptional activity provides a proxy for direct sensing of NTP levels in vivo leading to IMD2 activation. Finally, we connect Pol II activity to transcription start site selection in vivo, implicating the Pol II active site and transcription itself as a driver for start site scanning, contravening current models for this process. Transcription by multisubunit RNA polymerases (msRNAPs) is essential for all kingdoms of life. A conserved region within msRNAPs called the trigger loop (TL) is critical for selection of nucleotide substrates and activity. We present analysis of the RNA Polymerase II (Pol II) TL from the model eukaryote Saccharomyces cerevisiae. Our experiments reveal how TL residues differentially contribute to viability and transcriptional activity. We find that in vivo growth phenotypes correlate with severity of transcriptional defects and that changing Pol II activity to either faster or slower than wild type causes specific transcription defects. We identify transcription start site selection as sensitive to Pol II catalytic activity, proposing that RNA synthesis (an event downstream of many steps in the initiation process) contributes to where productive transcription occurs. Pol II transcription activity was excluded from previous models for selection of productive Pol II start sites. Finally, drug sensitivity data have been widely interpreted to indicate that Pol II mutants defective in elongation properties are sensitized to reduction in GTP levels (a Pol II substrate). Our data suggest an alternate explanation, that sensitivity to decreased GTP levels may be explained in light of Pol II mutant transcriptional start site defects.
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Affiliation(s)
- Craig D Kaplan
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America.
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28
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Kireeva ML, Domecq C, Coulombe B, Burton ZF, Kashlev M. Interaction of RNA polymerase II fork loop 2 with downstream non-template DNA regulates transcription elongation. J Biol Chem 2011; 286:30898-30910. [PMID: 21730074 DOI: 10.1074/jbc.m111.260844] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Fork loop 2 is a small semiconservative segment of the larger fork domain in the second largest Rpb2 subunit of RNA polymerase II (Pol II). This flexible loop, juxtaposed at the leading edge of transcription bubble, has been proposed to participate in DNA strand separation, translocation along DNA, and NTP loading to Pol II during elongation. Here we show that the Rpb2 mutant carrying a deletion of the flexible part of the loop is not lethal in yeast. The mutation exhibits no defects in DNA melting and translocation in vitro but confers a moderate decrease of the catalytic activity of the enzyme caused by the impaired sequestration of the NTP substrate in the active center prior to catalysis. In the structural model of the Pol II elongation complex, fork loop 2 directly interacts with an unpaired DNA residue in the non-template DNA strand one nucleotide ahead from the active center (the i+2 position). We showed that elimination of this putative interaction by replacement of the i+2 residue with an abasic site inhibits Pol II activity to the same degree as the deletion of fork loop 2. This replacement has no detectable effect on the activity of the mutant enzyme. We provide direct evidence that interaction of fork loop 2 with the non-template DNA strand facilitates NTP sequestration through interaction with the adjacent segment of the fork domain involved in the active center of Pol II.
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Affiliation(s)
- Maria L Kireeva
- NCI-Frederick, National Institutes of Health, Center for Cancer Research, Frederick, Maryland 21702-1201
| | - Céline Domecq
- Gene Transcription and Proteomics Laboratory, Institut de Recherches Cliniques de Montréal and Department of Biochemistry, Université de Montréal, Montréal, Québec, H2W 1R7 Canada
| | - Benoit Coulombe
- Gene Transcription and Proteomics Laboratory, Institut de Recherches Cliniques de Montréal and Department of Biochemistry, Université de Montréal, Montréal, Québec, H2W 1R7 Canada
| | - Zachary F Burton
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319
| | - Mikhail Kashlev
- NCI-Frederick, National Institutes of Health, Center for Cancer Research, Frederick, Maryland 21702-1201.
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Hampsey M, Singh BN, Ansari A, Lainé JP, Krishnamurthy S. Control of eukaryotic gene expression: gene loops and transcriptional memory. ACTA ACUST UNITED AC 2010; 51:118-25. [PMID: 21036187 DOI: 10.1016/j.advenzreg.2010.10.001] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2010] [Accepted: 10/19/2010] [Indexed: 01/08/2023]
Abstract
Gene loops are dynamic structures that juxtapose promoter–terminator regions of Pol II-transcribed genes. Although first described in yeast, gene loops have now been identified in yeast and mammalian cells. Looping requires components of the transcription preinitiation complex, the pre-mRNA 30-end processing machinery, and subunits of the nuclear pore complex. Loop formation is transcription-dependent, but neither basal nor activated transcription requires looping. Rather, looping appears to affect cellular memory of recent transcriptional activity, enabling a more rapid response to subsequent stimuli. The nuclear pore has been implicated in both memory and looping. Our working model is that loops are formed and/or maintained at the nuclear pore to facilitate hand-off of Pol II form the terminator to the promoter, thereby bypassing Pol II recruitment as the rate-limiting step in reactivation of transcription. Involvement of the nuclear pore also suggests that looping might facilitate mRNA export to the cytoplasm. The technology now exists to test these ideas.
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Affiliation(s)
- Michael Hampsey
- Department of Biochemistry, Robert Wood Johnson Medical School, Piscataway, NJ 08854-0009, United States.
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30
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Kim HS, Baek KH, Ha GH, Lee JC, Kim YN, Lee J, Park HY, Lee NR, Lee H, Cho Y, Lee CW. The hsSsu72 phosphatase is a cohesin-binding protein that regulates the resolution of sister chromatid arm cohesion. EMBO J 2010; 29:3544-57. [PMID: 20818333 PMCID: PMC2964166 DOI: 10.1038/emboj.2010.217] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2010] [Accepted: 08/12/2010] [Indexed: 11/08/2022] Open
Abstract
Cohesin is a multiprotein complex that establishes sister chromatid cohesion from S phase until mitosis or meiosis. In vertebrates, sister chromatid cohesion is dissolved in a stepwise manner: most cohesins are removed from the chromosome arms via a process that requires polo-like kinase 1 (Plk1), aurora B and Wapl, whereas a minor amount of cohesin, found preferentially at the centromere, is cleaved by separase following its activation by the anaphase-promoting complex/cyclosome. Here, we report that our budding yeast two-hybrid assay identified hsSsu72 phosphatase as a Rad21-binding protein. Additional experiments revealed that Ssu72 directly interacts with Rad21 and SA2 in vitro and in vivo, and associates with sister chromatids in human cells. Interestingly, depletion or mutational inactivation of Ssu72 phosphatase activity caused the premature resolution of sister chromatid arm cohesion, whereas the overexpression of Ssu72 yielded high resistance to this resolution. Interestingly, it appears that Ssu72 regulates the cohesion of chromosome arms but not centromeres, and acts by counteracting the phosphorylation of SA2. Thus, our study provides important new evidence, suggesting that Ssu72 is a novel cohesin-binding protein capable of regulating cohesion between sister chromatid arms.
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Affiliation(s)
- Hyun-Soo Kim
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea
- Center for Molecular Medicine, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Kwan-Hyuck Baek
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Geun-Hyoung Ha
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea
- Center for Molecular Medicine, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Jae-Chul Lee
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Yu-Na Kim
- Department of Microbiology, College of Medicine, Gyeonsang National University, Jinju, Korea
| | - Janet Lee
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Hye-Young Park
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Noo Ri Lee
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Ho Lee
- Division of Cancer Biology, Research Institute, National Cancer Center, Goyang, Korea
| | - Yunje Cho
- Department of Life Science, Pohang University of Science and Technology, Pohang, Korea
| | - Chang-Woo Lee
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea
- Center for Molecular Medicine, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, Korea
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31
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Seibold SA, Singh BN, Zhang C, Kireeva M, Domecq C, Bouchard A, Nazione AM, Feig M, Cukier RI, Coulombe B, Kashlev M, Hampsey M, Burton ZF. Conformational coupling, bridge helix dynamics and active site dehydration in catalysis by RNA polymerase. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2010; 1799:575-87. [PMID: 20478425 DOI: 10.1016/j.bbagrm.2010.05.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2010] [Revised: 04/21/2010] [Accepted: 05/07/2010] [Indexed: 01/22/2023]
Abstract
Molecular dynamics simulation of Thermus thermophilus (Tt) RNA polymerase (RNAP) in a catalytic conformation demonstrates that the active site dNMP-NTP base pair must be substantially dehydrated to support full active site closing and optimum conditions for phosphodiester bond synthesis. In silico mutant beta R428A RNAP, which was designed based on substitutions at the homologous position (Rpb2 R512) of Saccharomyces cerevisiae (Sc) RNAP II, was used as a reference structure to compare to Tt RNAP in simulations. Long range conformational coupling linking a dynamic segment of the bridge alpha-helix, the extended fork loop, the active site, and the trigger loop-trigger helix is apparent and adversely affected in beta R428A RNAP. Furthermore, bridge helix bending is detected in the catalytic structure, indicating that bridge helix dynamics may regulate phosphodiester bond synthesis as well as translocation. An active site "latch" assembly that includes a key trigger helix residue Tt beta' H1242 and highly conserved active site residues beta E445 and R557 appears to help regulate active site hydration/dehydration. The potential relevance of these observations in understanding RNAP and DNAP induced fit and fidelity is discussed.
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Affiliation(s)
- Steve A Seibold
- Department of Biochemistry and Molecular Biology, Michigan State University, E. Lansing, MI 48824-1319, USA
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32
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Kireeva M, Kashlev M, Burton ZF. Translocation by multi-subunit RNA polymerases. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2010; 1799:389-401. [PMID: 20097318 DOI: 10.1016/j.bbagrm.2010.01.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2009] [Revised: 01/14/2010] [Accepted: 01/14/2010] [Indexed: 11/30/2022]
Abstract
DNA template and RNA/DNA hybrid movement through RNA polymerase (RNAP) is referred to as "translocation". Because nucleic acid movement is coupled to NTP loading, pyrophosphate release, and conformational changes, the precise ordering of events during bond addition is consequential. Moreover, based on several lines of experimental evidence, translocation, pyrophosphate release or an associated conformational change may determine the transcription elongation rate. In this review we discuss various models of translocation, the data supporting the hypothesis that translocation rate determines transcription elongation rate and also data that may be inconsistent with this point of view. A model of the nucleotide addition cycle accommodating available experimental data is proposed. On the basis of this model, the molecular mechanisms regulating translocation and potential routes for NTP entry are discussed.
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Affiliation(s)
- Maria Kireeva
- National Cancer Institute-Frederick, Frederick, MD 21702-1201, USA
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33
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The shuttling protein Npl3 promotes translation termination accuracy in Saccharomyces cerevisiae. J Mol Biol 2009; 394:410-22. [PMID: 19733178 DOI: 10.1016/j.jmb.2009.08.067] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2009] [Revised: 08/24/2009] [Accepted: 08/29/2009] [Indexed: 01/20/2023]
Abstract
Heterogeneous nuclear ribonucleoproteins are multifunctional proteins that bind to newly synthesized mRNAs in the nucleus and participate in many subsequent steps of gene expression. A well-studied Saccharomyces cerevisiae heterogeneous nuclear ribonucleoprotein that has several nuclear functions is Npl3p. Here, we provide evidence that Npl3p also has a cytoplasmic role: it functions in translation termination fidelity. Yeast harboring the npl3-95 mutant allele have an impaired ability to translate lacZ, enhanced sensitivity to cycloheximide and paromomycin, and increased ability to read through translation termination codons. Most of these defects are enhanced in yeast that also lack Upf1p, an RNA surveillance factor crucial for translation termination. We show that the npl3-95 mutant allele encodes a form of Npl3p that is part of high molecular-weight complexes that cofractionate with the poly(A)-binding protein Pab1p. Together, these results lead us to propose a model in which Npl3p engenders translational fidelity by promoting the remodeling of mRNPs during translation termination.
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34
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Domecq C, Kireeva M, Archambault J, Kashlev M, Coulombe B, Burton ZF. Site-directed mutagenesis, purification and assay of Saccharomyces cerevisiae RNA polymerase II. Protein Expr Purif 2009; 69:83-90. [PMID: 19567268 DOI: 10.1016/j.pep.2009.06.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2009] [Accepted: 06/17/2009] [Indexed: 10/20/2022]
Abstract
In order to analyze the structure-function of multi-subunit RNA polymerases (RNAPs), it is necessary to make site-directed mutations in key residues. Because Saccharomyces cerevisiae RNAP II is isolated as a 12 subunit enzyme that has not been amenable to in vitro reconstitution, making site-directed mutations in a particular subunit presents technical issues. In this work, we demonstrate a method to generate and purify site-directed mutants in the second largest (Rpb2) RNAP II subunit from yeast, using a tandem affinity purification tag. Mutants are analyzed for growth defects in vivo and for defects in transcriptional elongation in vitro. We show that Rpb2 R512A/C located just C-terminal to fork loop 2 (Rpb2 500-511) has transcriptional defects that are distinct from surrounding fork loop 2 region mutants. Rpb2 E529A/D replacements are faster and E529Q is slower than wild type RNAP II in elongation. E529 appears to form an ion pair with K987, an essential active site residue. Mutations are also analyzed within the active site region indicating key residues for catalysis and the importance of a Rpb2 R983-E1028 ion pair. Rpb2 R983Q and E1028Q are defective in escape from a transcriptional stall.
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Affiliation(s)
- Céline Domecq
- Institut de Recherches Cliniques de Montréal, 110, Montréal, Que., Canada H2W 1R7
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35
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Functional interaction of the Ess1 prolyl isomerase with components of the RNA polymerase II initiation and termination machineries. Mol Cell Biol 2009; 29:2925-34. [PMID: 19332564 DOI: 10.1128/mcb.01655-08] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The C-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II) is a reiterated heptad sequence (Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7) that plays a key role in the transcription cycle, coordinating the exchange of transcription and RNA processing factors. The structure of the CTD is flexible and undergoes conformational changes in response to serine phosphorylation and proline isomerization. Here we report that the Ess1 peptidyl prolyl isomerase functionally interacts with the transcription initiation factor TFIIB and with the Ssu72 CTD phosphatase and Pta1 components of the CPF 3'-end processing complex. The ess1(A144T) and ess1(H164R) mutants, initially described by Hanes and coworkers (Yeast 5:55-72, 1989), accumulate the pSer5 phosphorylated form of Pol II; confer phosphate, galactose, and inositol auxotrophies; and fail to activate PHO5, GAL10, and INO1 reporter genes. These mutants are also defective for transcription termination, but in vitro experiments indicate that this defect is not caused by altering the processing efficiency of the cleavage/polyadenylation machinery. Consistent with a role in initiation and termination, Ess1 associates with the promoter and terminator regions of the PMA1 and PHO5 genes. We propose that Ess1 facilitates pSer5-Pro6 dephosphorylation by generating the CTD structural conformation recognized by the Ssu72 phosphatase and that pSer5 dephosphorylation affects both early and late stages of the transcription cycle.
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36
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A reduction in RNA polymerase II initiation rate suppresses hyper-recombination and transcription-elongation impairment of THO mutants. Mol Genet Genomics 2008; 280:327-36. [PMID: 18682986 DOI: 10.1007/s00438-008-0368-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2007] [Accepted: 07/19/2008] [Indexed: 10/21/2022]
Abstract
Hrs1/Med3, a component of the Mediator involved in transcription initiation, was previously isolated as a suppressor of hpr1Delta hyper-recombination linked to transcription elongation. Here we show that hrs1Delta-mediated suppression is specific of transcription-associated hyper-recombination (TAR). The decrease in recombination associated with hrs1Delta, either in wild-type or hpr1Delta cells is only observed in DNA repeats constructs in which transcription is Hrs1-dependent. We propose that the suppression of THO mutants by hrs1Delta is due to the specific effect of hrs1Delta on transcription initiation of the recombination system. In parallel we show that the higher the transcription of a gene the more important becomes the THO complex for its expression, implying that the in vivo relevance of this complex is dependent on the frequency of RNAPII transcription initiation. This study furthers the understanding of the importance of THO in transcription and the maintenance of genome stability.
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37
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Abstract
Most eukaryotic mRNA precursors (premRNAs) must undergo extensive processing, including cleavage and polyadenylation at the 3'-end. Processing at the 3'-end is controlled by sequence elements in the pre-mRNA (cis elements) as well as protein factors. Despite the seeming biochemical simplicity of the processing reactions, more than 14 proteins have been identified for the mammalian complex, and more than 20 proteins have been identified for the yeast complex. The 3'-end processing machinery also has important roles in transcription and splicing. The mammalian machinery contains several sub-complexes, including cleavage and polyadenylation specificity factor, cleavage stimulation factor, cleavage factor I, and cleavage factor II. Additional protein factors include poly(A) polymerase, poly(A)-binding protein, symplekin, and the C-terminal domain of RNA polymerase II largest subunit. The yeast machinery includes cleavage factor IA, cleavage factor IB, and cleavage and polyadenylation factor.
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Affiliation(s)
- C. R. Mandel
- Department of Biological Sciences, Columbia University, New York, NY 10027 USA
| | - Y. Bai
- Department of Biological Sciences, Columbia University, New York, NY 10027 USA
| | - L. Tong
- Department of Biological Sciences, Columbia University, New York, NY 10027 USA
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38
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Deng W, Roberts SGE. TFIIB and the regulation of transcription by RNA polymerase II. Chromosoma 2007; 116:417-29. [PMID: 17593382 DOI: 10.1007/s00412-007-0113-9] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2007] [Revised: 05/21/2007] [Accepted: 05/21/2007] [Indexed: 02/01/2023]
Abstract
Accurate transcription of a gene by RNA polymerase II requires the assembly of a group of general transcription factors at the promoter. The general transcription factor TFIIB plays a central role in preinitiation complex assembly, providing a bridge between promoter-bound TFIID and RNA polymerase II. TFIIB makes extensive contact with the core promoter via two independent DNA-recognition modules. In addition to interacting with other general transcription factors, TFIIB directly modulates the catalytic center of RNA polymerase II in the transcription complex. Moreover, TFIIB has been proposed as a target of transcriptional activator proteins that act to stimulate preinitiation complex assembly. In this review, we will discuss our current understanding of these activities of TFIIB.
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Affiliation(s)
- Wensheng Deng
- Faculty of Life Sciences, University of Manchester, The Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
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39
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Reyes-Reyes M, Hampsey M. Role for the Ssu72 C-terminal domain phosphatase in RNA polymerase II transcription elongation. Mol Cell Biol 2007; 27:926-36. [PMID: 17101794 PMCID: PMC1800697 DOI: 10.1128/mcb.01361-06] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2006] [Revised: 08/18/2006] [Accepted: 11/01/2006] [Indexed: 12/31/2022] Open
Abstract
The RNA polymerase II (RNAP II) transcription cycle is accompanied by changes in the phosphorylation status of the C-terminal domain (CTD), a reiterated heptapeptide sequence (Y(1)S(2)P(3)T(4)S(5)P(6)S(7)) present at the C terminus of the largest RNAP II subunit. One of the enzymes involved in this process is Ssu72, a CTD phosphatase with specificity for serine-5-P. Here we report that the ssu72-2-encoded Ssu72-R129A protein is catalytically impaired in vitro and that the ssu72-2 mutant accumulates the serine-5-P form of RNAP II in vivo. An in vitro transcription system derived from the ssu72-2 mutant exhibits impaired elongation efficiency. Mutations in RPB1 and RPB2, the genes encoding the two largest subunits of RNAP II, were identified as suppressors of ssu72-2. The rpb1-1001 suppressor encodes an R1281A replacement, whereas rpb2-1001 encodes an R983G replacement. This information led us to identify the previously defined rpb2-4 and rpb2-10 alleles, which encode catalytically slow forms of RNAP II, as additional suppressors of ssu72-2. Furthermore, deletion of SPT4, which encodes a subunit of the Spt4-Spt5 early elongation complex, also suppresses ssu72-2, whereas the spt5-242 allele is suppressed by rpb2-1001. These results define Ssu72 as a transcription elongation factor. We propose a model in which Ssu72 catalyzes serine-5-P dephosphorylation subsequent to addition of the 7-methylguanosine cap on pre-mRNA in a manner that facilitates the RNAP II transition into the elongation stage of the transcription cycle.
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Affiliation(s)
- Mariela Reyes-Reyes
- Department of Biochemistry, Robert Wood Johnson Medical School, 683 Hoes Lane West, Piscataway, NJ 08854, USA
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40
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Trinh V, Langelier MF, Archambault J, Coulombe B. Structural perspective on mutations affecting the function of multisubunit RNA polymerases. Microbiol Mol Biol Rev 2006; 70:12-36. [PMID: 16524917 PMCID: PMC1393249 DOI: 10.1128/mmbr.70.1.12-36.2006] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
High-resolution crystallographic structures of multisubunit RNA polymerases (RNAPs) have increased our understanding of transcriptional mechanisms. Based on a thorough review of the literature, we have compiled the mutations affecting the function of multisubunit RNA polymerases, many of which having been generated and studied prior to the publication of the first high-resolution structure, and highlighted the positions of the altered amino acids in the structures of both the prokaryotic and eukaryotic enzymes. The observations support many previous hypotheses on the transcriptional process, including the implication of the bridge helix and the trigger loop in the processivity of RNAP, the importance of contacts between the RNAP jaw-lobe module and the downstream DNA in the establishment of a transcription bubble and selection of the transcription start site, the destabilizing effects of ppGpp on the open promoter complex, and the link between RNAP processivity and termination. This study also revealed novel, remarkable features of the RNA polymerase catalytic mechanisms that will require additional investigation, including the putative roles of fork loop 2 in the establishment of a transcription bubble, the trigger loop in start site selection, and the uncharacterized funnel domain in RNAP processivity.
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Affiliation(s)
- Vincent Trinh
- Gene Transcription Laboratory, Institut de Recherches Cliniques de Montréal, 110 Ave. des Pins Ouest, Montréal, Québec, Canada
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41
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Affiliation(s)
- Lilia R Nunez
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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42
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Ganem C, Miled C, Facca C, Valay JG, Labesse G, Ben Hassine S, Mann C, Faye G. Kinase Cak1 functionally interacts with the PAF1 complex and phosphatase Ssu72 via kinases Ctk1 and Bur1. Mol Genet Genomics 2005; 275:136-47. [PMID: 16362371 DOI: 10.1007/s00438-005-0071-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2005] [Accepted: 10/24/2005] [Indexed: 11/25/2022]
Abstract
Protein kinases orthologous with Cak1 of Saccharomyces cerevisiae (ScCak1) appear specific to ascomycetes. ScCak1 phosphorylates Cdc28, the cyclin-dependent kinase (CDK) governing the cell cycle, as well as Kin28, Bur1 and Ctk1, CDKs required for the transcription process performed by RNA polymerase II (RNA Pol II). Using genetic methods, we found that Cak1 genetically interacts with Paf1 and Ctr9, two components belonging to the PAF1 elongation complex needed for histone modifications, and with Ssu72, a protein phosphatase that dephosphorylates serine-5 phosphate in the RNA Pol II C-terminal domain. We present evidence suggesting that the interactions linking Cak1 with the PAF1 complex and with Ssu72 are not direct but mediated via Ctk1 and Bur1. We discuss the possibility that Ssu72 intervenes at the capping checkpoint step of the transcription cycle.
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Affiliation(s)
- Carine Ganem
- Institut Curie, UMR2027 CNRS, Centre Universitaire, Orsay, France
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43
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Meinhart A, Kamenski T, Hoeppner S, Baumli S, Cramer P. A structural perspective of CTD function. Genes Dev 2005; 19:1401-15. [PMID: 15964991 DOI: 10.1101/gad.1318105] [Citation(s) in RCA: 255] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The C-terminal domain (CTD) of RNA polymerase II (Pol II) integrates nuclear events by binding proteins involved in mRNA biogenesis. CTD-binding proteins recognize a specific CTD phosphorylation pattern, which changes during the transcription cycle, due to the action of CTD-modifying enzymes. Structural and functional studies of CTD-binding and -modifying proteins now reveal some of the mechanisms underlying CTD function. Proteins recognize CTD phosphorylation patterns either directly, by contacting phosphorylated residues, or indirectly, without contact to the phosphate. The catalytic mechanisms of CTD kinases and phosphatases are known, but the basis for CTD specificity of these enzymes remains to be understood.
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Affiliation(s)
- Anton Meinhart
- Department of Chemistry and Biochemistry, Gene Center, University of Munich (LMU), 81377 Munich, Germany
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St-Pierre B, Liu X, Kha LCT, Zhu X, Ryan O, Jiang Z, Zacksenhaus E. Conserved and specific functions of mammalian ssu72. Nucleic Acids Res 2005; 33:464-77. [PMID: 15659578 PMCID: PMC548335 DOI: 10.1093/nar/gki171] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
We describe the cloning and characterization of a human homolog of the yeast transcription/RNA-processing factor Ssu72, following a yeast two-hybrid screen for pRb-binding factors in the prostate gland. Interaction between hSsu72 and pRb was observed in transfected mammalian cells and involved multiple domains in pRb; however, so far, mutual effects of these two factors could not be demonstrated. Like the yeast counterpart, mammalian Ssu72 associates with TFIIB and the yeast cleavage/polyadenylation factor Pta1, and exhibits intrinsic phosphatase activity. Mammals contain a single ssu72 gene and a few pseudogenes. During mouse embryogenesis, ssu72 was highly expressed in the nervous system and intestine; high expression in the nervous system persisted in adult mice and was also readily observed in multiple human tumor cell lines. Both endogenous and ectopically expressed mammalian Ssu72 proteins resided primarily in the cytoplasm and only partly in the nucleus. Interestingly, fusion to a strong nuclear localization signal conferred nuclear localization only in a fraction of transfected cells, suggesting active tethering in the cytoplasm. Suppression of ssu72 expression in mammalian cells by siRNA did not reduce proliferation/survival, and its over-expression did not affect transcription of candidate genes in transient reporter assays. Despite high conservation, hssu72 was unable to rescue an ssu72 lethal mutation in yeast. Together, our results highlight conserved and mammalian specific characteristics of mammalian ssu72.
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Affiliation(s)
- Benoit St-Pierre
- Division of Cell and Molecular Biology, Toronto General Research Institute, University Health Network67 College Street, Room 407, Toronto, Ontario, Canada M5G 2m1
| | - Xudong Liu
- Division of Cell and Molecular Biology, Toronto General Research Institute, University Health Network67 College Street, Room 407, Toronto, Ontario, Canada M5G 2m1
| | - Lan-Chau T. Kha
- Division of Cell and Molecular Biology, Toronto General Research Institute, University Health Network67 College Street, Room 407, Toronto, Ontario, Canada M5G 2m1
- Department of Medical Biophysics, University of TorontoToronto, Ontario, Canada M5G 2M1
| | - Xudong Zhu
- Division of Cell and Molecular Biology, Toronto General Research Institute, University Health Network67 College Street, Room 407, Toronto, Ontario, Canada M5G 2m1
| | - Owen Ryan
- Banting and Best Department of Medical ResearchToronto, Ontario, Canada M5G 1L6
| | - Zhe Jiang
- Division of Cell and Molecular Biology, Toronto General Research Institute, University Health Network67 College Street, Room 407, Toronto, Ontario, Canada M5G 2m1
| | - Eldad Zacksenhaus
- Division of Cell and Molecular Biology, Toronto General Research Institute, University Health Network67 College Street, Room 407, Toronto, Ontario, Canada M5G 2m1
- Department of Medicine, University of TorontoToronto, Ontario, Canada M5G 2M1
- Department of Laboratory Medicine and Pathobiology, University of TorontoToronto, Ontario, Canada M5G 2M1
- Department of Medical Biophysics, University of TorontoToronto, Ontario, Canada M5G 2M1
- To whom correspondence should be addressed. Tel: +1 416 340 4800 ext. 5106; Fax: +1 416 340 3453;
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Krishnamurthy S, He X, Reyes-Reyes M, Moore C, Hampsey M. Ssu72 Is an RNA polymerase II CTD phosphatase. Mol Cell 2004; 14:387-94. [PMID: 15125841 DOI: 10.1016/s1097-2765(04)00235-7] [Citation(s) in RCA: 181] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2003] [Revised: 03/08/2004] [Accepted: 03/24/2004] [Indexed: 11/20/2022]
Abstract
Phosphorylation of serine-2 (S2) and serine-5 (S5) of the C-terminal domain (CTD) of RNA polymerase II (RNAP II) is a dynamic process that regulates the transcription cycle and coordinates recruitment of RNA processing factors. The Fcp1 CTD phosphatase catalyzes dephosphorylation of S2-P. Here, we report that Ssu72, a component of the yeast cleavage/polyadenylation factor (CPF) complex, is a CTD phosphatase with specificity for S5-P. Ssu72 catalyzes CTD S5-P dephosphorylation in association with the Pta1 component of the CPF complex, although its essential role in 3' end processing is independent of catalytic activity. Depletion of Ssu72 impairs transcription in vitro, and this defect can be rescued by recombinant, catalytically active Ssu72. We propose that Ssu72 has a dual role in transcription, one as a CTD S5-P phosphatase that regenerates the initiation-competent, hypophosphorylated form of RNAP II and the other as a factor necessary for cleavage of pre-mRNA and efficient transcription termination.
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Affiliation(s)
- Shankarling Krishnamurthy
- Department of Biochemistry, Division of Nucleic Acids Enzymology, Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
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Chen BS, Hampsey M. Functional interaction between TFIIB and the Rpb2 subunit of RNA polymerase II: implications for the mechanism of transcription initiation. Mol Cell Biol 2004; 24:3983-91. [PMID: 15082791 PMCID: PMC387735 DOI: 10.1128/mcb.24.9.3983-3991.2004] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2003] [Revised: 10/31/2003] [Accepted: 02/02/2004] [Indexed: 11/20/2022] Open
Abstract
The general transcription factor TFIIB is required for accurate initiation, although the mechanism by which RNA polymerase II (RNAP II) identifies initiation sites is not well understood. Here we describe results from genetic and biochemical analyses of an altered form of yeast TFIIB containing an arginine-78 --> cysteine (R78C) replacement in the "B-finger" domain. TFIIB R78C shifts start site selection downstream of normal and confers a cold-sensitive growth defect (Csm(-)). Suppression of the R78C Csm(-) phenotype identified a functional interaction between TFIIB and the Rpb2 subunit of RNAP II and defined a novel role for Rpb2 in start site selection. The rpb2 suppressor encodes a glycine-369 --> serine (G369S) replacement, located in the "lobe" domain of Rpb2 and near the Rpb9 subunit, which was identified previously as an effector of start site selection. The Rpb2-Rpb9 "lobe-jaw" region of RNAP II is downstream of the catalytic center and distal to the site of RNAP II-TFIIB interaction. A TFIIB R78C mutant extract was defective for promoter-specific run-on transcription but yielded an altered pattern of abortive initiation products, indicating that the R78C defect does not preclude initiation. The sua7-3 rpb2-101 double mutant was sensitive to 6-azauracil in vivo and to nucleoside triphosphate substrate depletion in vitro. In the context of the recent X-ray structure of the yeast RNAP II-TFIIB complex, these results define a functional interaction between the B-finger domain of TFIIB and the distal lobe-jaw region of RNAP II and provide insight into the mechanism of start site selection.
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Affiliation(s)
- Bo-Shiun Chen
- Division of Nucleic Acids Enzymology, Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, New Jersey 08854, USA
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Steinmetz EJ, Brow DA. Ssu72 protein mediates both poly(A)-coupled and poly(A)-independent termination of RNA polymerase II transcription. Mol Cell Biol 2003; 23:6339-49. [PMID: 12944462 PMCID: PMC193702 DOI: 10.1128/mcb.23.18.6339-6349.2003] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2003] [Revised: 05/06/2003] [Accepted: 06/04/2003] [Indexed: 11/20/2022] Open
Abstract
Termination of transcription by RNA polymerase II (Pol II) is a poorly understood yet essential step in eukaryotic gene expression. Termination of pre-mRNA synthesis is coupled to recognition of RNA signals that direct cleavage and polyadenylation of the nascent transcript. Termination of nonpolyadenylated transcripts made by Pol II in the yeast Saccharomyces cerevisiae, including the small nuclear and small nucleolar RNAs, requires distinct RNA elements recognized by the Nrd1 protein and other factors. We have used genetic selection to characterize the terminator of the SNR13 snoRNA gene, revealing a bipartite structure consisting of an upstream element closely matching a Nrd1-binding sequence and a downstream element similar to a cleavage/polyadenylation signal. Genome-wide selection for factors influencing recogniton of the SNR13 terminator yielded mutations in the gene coding for the essential Pol II-binding protein Ssu72. Ssu72 has recently been found to associate with the pre-mRNA cleavage/polyadenylation machinery, and we find that an ssu72 mutation that disrupts Nrd1-dependent termination also results in deficient poly(A)-dependent termination. These findings extend the parallels between the two termination pathways and suggest that they share a common mechanism to signal Pol II termination.
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Affiliation(s)
- Eric J Steinmetz
- Department of Biomolecular Chemistry, University of Wisconsin Medical School, 1300 University Avenue, Madison, WI 53706-1532, USA
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Nedea E, He X, Kim M, Pootoolal J, Zhong G, Canadien V, Hughes T, Buratowski S, Moore CL, Greenblatt J. Organization and function of APT, a subcomplex of the yeast cleavage and polyadenylation factor involved in the formation of mRNA and small nucleolar RNA 3'-ends. J Biol Chem 2003; 278:33000-10. [PMID: 12819204 DOI: 10.1074/jbc.m304454200] [Citation(s) in RCA: 145] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Messenger RNA 3'-end formation is functionally coupled to transcription by RNA polymerase II. By tagging and purifying Ref2, a non-essential protein previously implicated in mRNA cleavage and termination, we isolated a multiprotein complex, holo-CPF, containing the yeast cleavage and polyadenylation factor (CPF) and six additional polypeptides. The latter can form a distinct complex, APT, in which Pti1, Swd2, a type I protein phosphatase (Glc7), Ssu72 (a TFIIB and RNA polymerase II-associated factor), Ref2, and Syc1 are associated with the Pta1 subunit of CPF. Systematic tagging and purification of holo-CPF subunits revealed that yeast extracts contain similar amounts of CPF and holo-CPF. By purifying holo-CPF from strains lacking Ref2 or containing truncated subunits, subcomplexes were isolated that revealed additional aspects of the architecture of APT and holo-CPF. Chromatin immunoprecipitation was used to localize Ref2, Ssu72, Pta1, and other APT subunits on small nucleolar RNA (snoRNA) genes and primarily near the polyadenylation signals of the constitutively expressed PYK1 and PMA1 genes. Use of mutant components of APT revealed that Ssu72 is important for preventing readthrough-dependent expression of downstream genes for both snoRNAs and polyadenylated transcripts. Ref2 and Pta1 similarly affect at least one snoRNA transcript.
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Affiliation(s)
- Eduard Nedea
- Banting and Best Department of Medical Research and Department of Molecular and Medical Genetics, University of Toronto, Toronto, Ontario M5G 1L6, Canada
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Meinhart A, Silberzahn T, Cramer P. The mRNA transcription/processing factor Ssu72 is a potential tyrosine phosphatase. J Biol Chem 2003; 278:15917-21. [PMID: 12606538 DOI: 10.1074/jbc.m301643200] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Ssu72 is an essential and highly conserved protein involved in mRNA transcription and 3'-end processing. The biochemical function of Ssu72 was so far unknown. We report here evidence that Ssu72 is a phosphatase that resembles protein tyrosine phosphatases (PTPases). First, recombinant Ssu72 cleaves the phosphotyrosine analogue p-nitrophenylphosphate, and this catalytic activity is impaired by PTPase-inhibiting agents. Second, the Ssu72 sequence contains the CX(5)R signature motif of PTPases; mutation of the catalytic cysteine in this motif abolishes Ssu72 activity in vitro and has been shown to confer lethality in vivo. Third, secondary structure prediction and site-directed mutagenesis predict that Ssu72 adopts the fold of PTPases of the low molecular weight family. Distinguishing features, such as a short "aspartate loop" at the active site, suggest however that Ssu72 is the founding member of a new phosphatase subfamily. The novel Ssu72 activity may regulate coupling events during mRNA biogenesis.
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Affiliation(s)
- Anton Meinhart
- Institute of Biochemistry, Gene Center, University of Munich, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
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50
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He X, Khan AU, Cheng H, Pappas DL, Hampsey M, Moore CL. Functional interactions between the transcription and mRNA 3' end processing machineries mediated by Ssu72 and Sub1. Genes Dev 2003; 17:1030-42. [PMID: 12704082 PMCID: PMC196040 DOI: 10.1101/gad.1075203] [Citation(s) in RCA: 116] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Transcription and processing of pre-mRNA are coupled events. By using a combination of biochemical, molecular, and genetic methods, we have found that the phylogenetically conserved transcription factor Ssu72 is a component of the cleavage/polyadenylation factor (CPF) of Saccharomyces cerevisiae. Our results demonstrate that Ssu72 is required for 3' end cleavage of pre-mRNA but is dispensable for poly(A) addition and RNAP II termination. The in vitro cleavage defect caused by depletion of Ssu72 from cells can be rescued by addition of recombinant Ssu72. Ssu72 interacts physically and genetically with the Pta1 subunit of CPF. Overexpression of PTA1 causes synthetic lethality in an ssu72-3 mutant. Moreover, Sub1, which has been implicated in transcription initiation and termination, also interacts with Pta1, and overexpression of SUB1 suppresses the growth and processing defect of a pta1 mutation. Physical interactions of Ssu72 and Sub1 with Pta1 are mutually exclusive. Based on the interactions of Ssu72 and Sub1 with both the Pta1 of CPF and the TFIIB component of the initiation complex, we present a model describing how these novel connections between the transcription and 3' end processing machineries might facilitate transitions in the RNAP II transcription cycle.
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Affiliation(s)
- Xiaoyuan He
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts 02111, USA
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