T7 RNA Polymerases Backed up by Covalently Trapped Proteins Catalyze Highly Error Prone Transcription

Nakano, Toshiaki; Ouchi, Ryo; Kawazoe, Junya; Pack, Seung Pil; Makino, Keisuke; Ide, Hiroshi

doi:10.1074/jbc.m111.318410

Cited by 56 publications

(46 citation statements)

References 46 publications

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“…It has been shown that DPCs impede the progression of the UvrD helicase involved in nucleotide excision repair only when placed on the translocating strand (14). The progression of T7 RNA polymerase that transiently disrupts dsDNA for transcription is also blocked by DPCs only when DPCs are placed on the transcribed strand (17). It follows that replicative helicases (DnaB, T7gp4, Mcm467, and Tag), UvrD helicase, and T7 RNA polymerase are blocked by DPCs on the translocating or transcribed strand, but not by those on the nontranslocating or nontranscribed strand.…”

Section: Discussionmentioning

confidence: 99%

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Translocation and Stability of Replicative DNA Helicases upon Encountering DNA-Protein Cross-links

Nakano

Miyamoto-Matsubara

Shoulkamy

et al. 2013

Journal of Biological Chemistry

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Background: DNA-protein cross-links (DPCs) are formed by DNA-damaging agents. Results: DPCs on the translocating strand but not on the nontranslocating strand block hexameric replicative helicases in a size-dependent manner. Stalled helicases dissociate from DNA with a half-life of 15-36 min. Conclusion: DPCs on the translocating and nontranslocating strands constitute helicase and polymerase blocks, respectively. Significance: Reversible and irreversible protein roadblocks may have distinct effects on replisomes.

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Section: Discussionmentioning

confidence: 99%

“…Forked DNA substrates containing DPCs for helicase assays (Fig. 1B) were constructed using methods similar to those described previously (13,17,(43)(44)(45). Briefly, a 25-mer oligonucleotide containing oxanine was ligated enzymatically with dT 60 or dT 40 using a scaffold DNA.…”

Section: Methodsmentioning

confidence: 99%

Translocation and Stability of Replicative DNA Helicases upon Encountering DNA-Protein Cross-links

Nakano

Miyamoto-Matsubara

Shoulkamy

et al. 2013

Journal of Biological Chemistry

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“…Owing to their exceptional bulkiness, DPCs are expected to interfere with essential DNA transactions such as transcription and replication (for methods that detect DPCs, see Supplementary information S1 (figure)). Indeed, DPCs form strong blocks for transcription by RNA polymerases when located on the transcribed strand 22 . Furthermore, DPCs (and DPC-mimicking biotin-streptavidin adducts) have been shown to inhibit the unwinding of the DNA duplex during replication in vitro 23,24 and, consequently, to interfere with replicationfork progression in vivo 25 .…”

Section: Toxicity and Effects Of Dpcsmentioning

confidence: 99%

DNA–protein crosslink repair

Stingele

Jentsch

2015

Nat Rev Mol Cell Biol

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DNA-protein crosslinks (DPCs) are highly toxic DNA adducts, but whether dedicated DPC-repair mechanisms exist was until recently unknown. This has changed with discoveries made in yeast and Xenopus laevis that revealed a protease-based DNA-repair pathway specific for DPCs. Importantly, mutations in the gene encoding the putative human homologue of a yeast DPC protease cause a human premature ageing and cancer predisposition syndrome. Thus, DPC repair is a previously overlooked genome-maintenance mechanism that may be essential for tumour suppression.

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“…azadC is incorporated into DNA and covalently traps the reaction intermediate of DNA cytosine methyltransferase, giving rise to DNA-protein cross-links (DPCs) [31]. DPCs block DNA replication and transcription [32,33] and hence constitute the major lethal lesions upon treatment with azadC. cisPt is a bifunctional DNA-damaging The treated cells were further incubated in fresh medium for 6 days, and colonies were scored to calculate the surviving fraction.…”

Section: Discussionmentioning

confidence: 99%

Depletion of RUVBL2 in Human Cells Confers Moderate Sensitivity to Anticancer Agents

Matsubara¹

2014

J Cancer Sci Ther

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IntroductionRuvB-like 1 (RUVBL1, also known as RVB1, TIP49A and Pontin) and RuvB-like 2 (RUVBL2, also known as RVB2, TIP49B and Reptin) belong to the family of ATPases associated with various cell activities (AAA+ ATPase), and are part of large protein complexes that are involved in chromatin remodeling, transcription regulation, DNA damage responses and repair, and the biogenesis of small nucleolar ribonucleoproteins [1,2]. RUVBL1 and RUVBL2 (RUVBLs) share about 45% identity and 60% similarity in the amino acid sequence and are homologous to the prokaryotic RuvB helicase [3,4]. Remarkably, RUVBL1 depletion leads to down regulation of RUVBL2, and vice versa [5]. RUVBLs also interact with oncogenes such as c-Myc and β-catenin and are implicated in cancer [4,6]. Since RUVBLs participate in many aspects of cellular functions, links between these functions are currently being studied extensively.In human cells, RUVBLs serve as the essential components of the TIP60 histone acetyltransferase complex. TIP60 is recruited to DNA damage sites [7,8] and plays multiple roles in DNA damage responses [9]. After treatment with various DNA-damaging agents, RUVBL1 is required for the dephosphorylation of phosphorylated histone H2AX, a marker of DNA double-strand breaks (DSBs), through the histone acetyltransferase activity of TIP60 [8]. Likewise, depletion of RUVBL2 increases the persistence of phosphorylated histone H2AX upon treatment with X-rays [10]. Apart from the pathway involving the TIP60 complex, RUVBLs regulate the abundance and activity of phosphatidylinositol 3-kinases such as ataxia telangiectasia mutated (ATM), ATM-and Rad3-related (ATR) kinase, and DNA-dependent protein kinase (DNA-PK) that sense and activate the DNA damage signal [11]. RUVBLs are also components of the INO80 chromatin remodeling complex that is recruited to the DSB site. A recent study has shown that the mammalian INO80 complex mediates DSB repair through its role in DNA end resection [12]. The ATP-dependent helicase activity of RUVBLs demonstrated in vitro may be involved in the processing of resected DNA ends [13,14]. Depletion of RUVBLs in human cells impairs the recruitment of the RAD51 recombinase to the DSB site following DNA end resection [15]. Consistent with the finding, it has been shown that the functional inactivation or depletion of TIP60 that contains RUVBLs in mouse and human cells impairs the recruitment of RAD51 to the DSB site [16].The aforementioned studies have afforded mechanistic insights into the function of human RUVBLs in DNA damage responses and repair. However, few studies have investigated the role of RUVBLs in

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T7 RNA Polymerases Backed up by Covalently Trapped Proteins Catalyze Highly Error Prone Transcription

Cited by 56 publications

References 46 publications

Translocation and Stability of Replicative DNA Helicases upon Encountering DNA-Protein Cross-links

Translocation and Stability of Replicative DNA Helicases upon Encountering DNA-Protein Cross-links

DNA–protein crosslink repair

Depletion of RUVBL2 in Human Cells Confers Moderate Sensitivity to Anticancer Agents

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