Evidence map›Paper›PMID 35042867›Full record

ArticleNature communications2022

Deciphering the mechanism of processive ssDNA digestion by the Dna2-RPA ensemble.

Jiangchuan Shen, Yiling Zhao, Nhung Tuyet Pham, Yuxi Li, Yixiang Zhang, Jonathan Trinidad, Grzegorz Ira, Zhi Qi, Hengyao Niu

Abstract read
In one paragraph

Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.

0numbers the graph read from it
0cells of the map it votes in
12citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

12 citing papers in PubMed.

  1. Review
  2. Article
  3. Review
  4. The canonical RPA complex interacts with Est3 to regulate yeast telomerase activity.Proceedings of the National Academy of Sciences of the United States of America · 2025
    Article
  5. Article
  6. Article
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

9 authors.

Jiangchuan Shen *Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, 47405, USA.ORCID 0000-0003-1699-564X
Yiling Zhao *Center for Quantitative Biology, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China.
Nhung Tuyet Pham *Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.ORCID 0000-0003-4792-3761
Yuxi LiDepartment of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, 47405, USA.
Yixiang ZhangDepartment of Chemistry, Biological Mass Spectrometry Facility, Indiana University, Bloomington, IN, 47405, USA.ORCID 0000-0003-3422-8436
Jonathan TrinidadDepartment of Chemistry, Biological Mass Spectrometry Facility, Indiana University, Bloomington, IN, 47405, USA.ORCID 0000-0002-8279-1509
Grzegorz IraDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
Zhi QiCenter for Quantitative Biology, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China. zhiqi7@pku.edu.cn.ORCID 0000-0002-1572-9721
Hengyao NiuDepartment of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, 47405, USA. hniu@indiana.edu.ORCID 0000-0003-1768-0674

Funding

Regulation of DNA recombination in Saccharomyces cerevisiaeR01GM080600 · NIGMS · BAYLOR COLLEGE OF MEDICINE · PI IRA, GRZEGORZ A · 2007 to 2024
$5.5M
Regulation of Initial Steps of Chromosomal Breaks RepairR01GM125650 · NIGMS · BAYLOR COLLEGE OF MEDICINE · PI IRA, GRZEGORZ A · 2018 to 2025
$2.9M
Mechanisms of DNA helicases and nucleases in genome maintenanceR35GM124765 · NIGMS · TRUSTEES OF INDIANA UNIVERSITY · PI NIU, HENGYAO · 2017 to 2021
$2.0M
NIGMS NIH HHS R01 GM080600NIGMS NIH HHS R01 GM125650NIGMS NIH HHS R35 GM124765
6 · The paper itself

Abstract

Single-stranded DNA (ssDNA) commonly occurs as intermediates in DNA metabolic pathways. The ssDNA binding protein, RPA, not only protects the integrity of ssDNA, but also directs the downstream factor that signals or repairs the ssDNA intermediate. However, it remains unclear how these enzymes/factors outcompete RPA to access ssDNA. Using the budding yeast Saccharomyces cerevisiae as a model system, we find that Dna2 - a key nuclease in DNA replication and repair - employs a bimodal interface to act with RPA both in cis and in trans. The cis-activity makes RPA a processive unit for Dna2-catalyzed ssDNA digestion, where RPA delivers its bound ssDNA to Dna2. On the other hand, activity in trans is mediated by an acidic patch on Dna2, which enables it to function with a sub-optimal amount of RPA, or to overcome DNA secondary structures. The trans-activity mode is not required for cell viability, but is necessary for effective double strand break (DSB) repair.

Indexed as

BiocatalysisCell SurvivalDNA Breaks, Double-StrandedDNA, FungalDNA HelicasesDNA RepairDNA, Single-StrandedModels, BiologicalMutationPeptidesPhleomycinsProtein BindingProtein DomainsReplication Protein ASaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsDNA2 protein, S cerevisiaeDNA, FungalDNA HelicasesDNA, Single-StrandedPeptidesPhleomycinsReplication Protein ASaccharomyces cerevisiae ProteinsTyrosine

Identifiers

PMID35042867
PMCPMC8766458

What OpenQuestion holds

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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.