Multiple Protein-Protein Interactions by RNA Polymerase I-Associated Factor PAF49 and Role of PAF49 in rRNA Transcription

Yamamoto, Kazuo; Yamamoto, Mika; Hanada, Ken-ichi; Nogi, Yasuhisa; Matsuyama, Tomohiro; Muramatsu, Masami

doi:10.1128/mcb.24.14.6338-6349.2004

Cited by 40 publications

(70 citation statements)

References 56 publications

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“…Heterodimerization of A49 and A34.5 explains why the two subunits dissociate together from Pol I upon urea treatment (Huet et al, 1975), why Pol I purified from a yeast strain lacking the gene for A34.5 also lacks A49 (Gadal et al, 1997), and why two distantly related mammalian Pol I subunits bind each other (Yamamoto et al, 2004). It is also consistent with the observed continuous EM (Armache et al, 2005) (gray) into the EM density (blue).…”

Section: A49 and A345 Form A Tfiif-like Heterodimer Near The Funnelsupporting

confidence: 75%

Functional architecture of RNA polymerase I

Geiger¹,

Kuhn²,

Baumli³

et al. 2009

Acta Cryst Sect A

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SUMMARYSynthesis of ribosomal RNA (rRNA) by RNA polymerase (Pol) I is the first step in ribosome biogenesis and a regulatory switch in eukaryotic cell growth. Here we report the 12 Å cryoelectron microscopic structure for the complete 14-subunit yeast Pol I, a homology model for the core enzyme, and the crystal structure of the subcomplex A14/43. In the resulting hybrid structure of Pol I, A14/43, the clamp, and the dock domain contribute to a unique surface interacting with promoter-specific initiation factors. The Pol I-specific subunits A49 and A34.5 form a heterodimer near the enzyme funnel that acts as a built-in elongation factor and is related to the Pol II-associated factor TFIIF. In contrast to Pol II, Pol I has a strong intrinsic 3 0 -RNA cleavage activity, which requires the C-terminal domain of subunit A12.2 and, apparently, enables ribosomal RNA proofreading and 3 0 -end trimming.

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Section: A49 and A345 Form A Tfiif-like Heterodimer Near The Funnelsupporting

confidence: 75%

Functional architecture of RNA polymerase I

Geiger¹,

Kuhn²,

Baumli³

et al. 2009

Acta Cryst Sect A

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“…We believe that the primary sequence of the A34.5 homolog, if any such protein exists, may be poorly conserved in S. pombe. Mouse pol I has been found to contain distinct subunits from lower eukaryotes, such as PAF67 and PAF49 (33,34,50). These results tempt us to speculate that lower eukaryotes such as yeast might conserve the 14 subunits found in S. cerevisiae and that higher eukaryotes might have more specific subunits such as PAF67 and PAF49, in addition to the 14 conserved subunits.…”

Section: Ker1p Heterodimerizes With Rpa21 11472mentioning

confidence: 68%

“…However, it is not clear whether all 14 subunits identified in S. cerevisiae pol I are conserved in other eukaryotes (33,34). To gain further insight into the structure and function of pol I, we have been studying pol I of Schizosaccharomyces pombe, which is only distantly related to S. cerevisiae, but is amenable to genetic analysis (35).…”

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confidence: 99%

The Fission Yeast Protein Ker1p Is an Ortholog of RNA Polymerase I Subunit A14 in Saccharomyces cerevisiae and Is Required for Stable Association of Rrn3p and RPA21 in RNA Polymerase I

Imazawa

Hisatake

Mitsuzawa

et al. 2005

Journal of Biological Chemistry

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A heterodimer formed by the A14 and A43 subunits of RNA polymerase (pol) I in Saccharomyces cerevisiae is proposed to correspond to the Rpb4/Rpb7 and C17/C25 heterodimers in pol II and pol III, respectively, and to play a role(s) in the recruitment of pol I to the promoter. However, the question of whether the A14/A43 heterodimer is conserved in eukaryotes other than S. cerevisiae remains unanswered, although both Rpb4/Rpb7 and C17/C25 are conserved from yeast to human. To address this question, we have isolated a Schizosaccharomyces pombe gene named ker1 ؉ using a yeast twohybrid system, including rpa21 ؉ , which encodes an ortholog of A43, as bait. Although no homolog of A14 has previously been found in the S. pombe genome, functional characterization of Ker1p and alignment of Ker1p and A14 showed that Ker1p is an ortholog of A14. Disruption of ker1 ؉ resulted in temperature-sensitive growth, and the temperature-sensitive deficit of ker1⌬ was suppressed by overexpression of either rpa21 ؉ or rrn3 ؉ , which encodes the rDNA transcription factor Rrn3p, suggesting that Ker1p is involved in stabilizing the association of RPA21 and Rrn3p in pol I. We also found that Ker1p dissociated from pol I in post-logphase cells, suggesting that Ker1p is involved in growthdependent regulation of rDNA transcription.There are three distinct types of eukaryotic nuclear RNA polymerases: RNA polymerase (pol) 1 I, pol II, and pol III. Among eukaryotic organisms, the structure and function of RNA polymerases in Saccharomyces cerevisiae have been studied fairly extensively (1-4). S. cerevisiae pol I consists of 14 subunits. The core structure contains 10 subunits (A190, A135, AC40, AC19, Rpb5, Rpb6, Rpb8, Rpb10, Rpb12, and A12.2) and is believed to be sufficient for nonspecific transcription, but not for accurate initiation of transcription (5). In fact, pol I requires four specific subunits (A49, A43, A34.5, and A14) for specific transcription of rDNA. A43 is also essential for cell growth (6), whereas A49 (7), A34.5 (8), and A14 (9) are dispensable.Much attention has recently been focused on the A14 and A43 subunits in view of the structural and functional conservation of these two subunits in eukaryotes. A43 is conserved in a variety of eukaryotes (10) and shows amino acid sequence similarity to Rpb7 (a specific subunit of pol II), C25 (a specific subunit of pol III), and RpoE (a subunit of archaeal RNA polymerases) across multiple RNA polymerases (11). Furthermore, A43 forms a heterodimer with A14 that is similar to the Rpb4/Rpb7 (11, 12), C17/C25 (13), and RpoF/RpoE (14) heterodimers in pol II, pol III, and archaeal RNA polymerases, respectively. It should be noted that Rpb4, C17, and RpoF have mutual sequence similarity and are grouped into a gene family, but no obvious homolog of A14 has been found in available data bases. A14 and Rpb4 are required for the stable assembly of A43 and Rpb7, respectively, in their respective RNA polymerases, suggesting a functional similarity of A14 to Rpb4 (5,11,15,16). The position of A14/A43 in...

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“…Cytotoxicity from cisplatin and other platinum containing drugs is attributed to the formation of platinum-DNA (Plt-DNA) adducts which is mainly repaired by the NER pathway, one of the DNA repair mechanisms (27). Clinical outcome measured as either tumor regression or survival, is better in patients with higher levels of Plt-DNA adducts (28,29).…”

Section: Discussionmentioning

confidence: 99%

Predictive Effect of XPA and XPD Polymorphisms on Survival of Advanced NSCLC Patients Treated with Platinum-Based Chemotherapy: A Three-Dimensional (3-D), Polyacrylamide Gel-Based DNA Microarray Method

Cheng

Qin

Sun

et al. 2013

Technol Cancer Res Treat

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Platinum-based chemotherapy is a primary treatment for patients with advanced non-small cell lung cancer (NSCLC). Considering individual differences, an effective and convenient method is urgently needed to identify the sensitivity of individual patient to platinum based regimen. Genetic variants in DNA repair genes are presumed to represent important determinants of drug efficacy. Our previous studies have demonstrated the involvement of xeroderma pigmentosum group A (XPA) codon23 and xeroderma pigmentosum group D (XPD) codon751 single-nucleotide polymorphisms (SNPs) in clinical response to platinum based chemotherapy in advanced NSCLC patients. Thus, a follow-up study was carried out to investigate the relevance of these genotypes and survival of the cohort (n 5 115). The threedimensional (3-D), polyacrylamide gel-based DNA microarray method was used to assess the genotypes of XPA and XPD in peripheral lymphocytes. Log-rank test revealed that the variant genotypes of XPA23 (A/G1G/G) were associated with significantly longer progression-free survival (PFS) (6.0 m vs. 10.6 m, log-rank P 5 0.001) and overall survival (OS) (11.2 m vs. 20.8 m, log-rank P 5 0.001). In Cox proportional hazards model, the hazard ratio (HR) for death in patients with G allele was 0.65 (P 5 0.049). While no significant differences were observed in PFS or OS according to XPD Lys751Gln genotypes (log-rank P  0.05).In combination with our previous short-term clinical results, this study further confirmed that by detecting the SNPs in blood cells, XPA A23G polymorphic variants might be a promising biomarker in predicting a favor prognosis of NSCLC patients and be helpful towards designing individualized treatments.

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Multiple Protein-Protein Interactions by RNA Polymerase I-Associated Factor PAF49 and Role of PAF49 in rRNA Transcription

Cited by 40 publications

References 56 publications

Functional architecture of RNA polymerase I

Functional architecture of RNA polymerase I

The Fission Yeast Protein Ker1p Is an Ortholog of RNA Polymerase I Subunit A14 in Saccharomyces cerevisiae and Is Required for Stable Association of Rrn3p and RPA21 in RNA Polymerase I

Predictive Effect of XPA and XPD Polymorphisms on Survival of Advanced NSCLC Patients Treated with Platinum-Based Chemotherapy: A Three-Dimensional (3-D), Polyacrylamide Gel-Based DNA Microarray Method

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