Evidence map›Paper›PMID 40473630›Full record

ArticleNature communications2025

An archaeal nucleoid-associated protein binds an essential motif in DNA replication origins.

Rajkumar Dhanaraju, Rachel Y Samson, Xu Feng, Alessandro Costa, Giovanni Gonzalez-Gutierrez, Stephen D Bell

Abstract read
In one paragraph

Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. Review
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

6 authors.

Rajkumar DhanarajuDepartment of Molecular and Cellular Biochemistry, Indiana University, Simon Hall MSB1, 212 S Hawthorne Drive, Bloomington, IN, 47405, USA.
Rachel Y SamsonDepartment of Molecular and Cellular Biochemistry, Indiana University, Simon Hall MSB1, 212 S Hawthorne Drive, Bloomington, IN, 47405, USA.
Xu FengDepartment of Molecular and Cellular Biochemistry, Indiana University, Simon Hall MSB1, 212 S Hawthorne Drive, Bloomington, IN, 47405, USA.ORCID http://orcid.org/0000-0001-5913-9638
Alessandro CostaSir William Dunn School of Pathology, South Parks Road, Oxford, OX1 3RE, UK.ORCID http://orcid.org/0000-0003-1126-2498
Giovanni Gonzalez-GutierrezDepartment of Molecular and Cellular Biochemistry, Indiana University, Simon Hall MSB1, 212 S Hawthorne Drive, Bloomington, IN, 47405, USA.ORCID http://orcid.org/0000-0002-1044-943X
Stephen D BellDepartment of Molecular and Cellular Biochemistry, Indiana University, Simon Hall MSB1, 212 S Hawthorne Drive, Bloomington, IN, 47405, USA. bell.2007@osu.edu.ORCID http://orcid.org/0000-0002-8474-6592

Funding

Archaeal Chromosome DynamicsR35GM152171 · NIGMS · TRUSTEES OF INDIANA UNIVERSITY · PI Stephen David Bell · 2024 to 2026
$1.7M
Chromosome Archae-tecture: Conserved principles of chromosome organizationR01GM135178 · NIGMS · TRUSTEES OF INDIANA UNIVERSITY · PI BELL, STEPHEN DAVID · 2020 to 2023
$1.2M
Initiation of DNA ReplicationR01GM125579 · NIGMS · TRUSTEES OF INDIANA UNIVERSITY · PI BELL, STEPHEN DAVID · 2018 to 2021
$1.2M
NIGMS NIH HHS R01 GM125579NIGMS NIH HHS R01 GM135178NIGMS NIH HHS R35 GM152171U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS) R01GM135178U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS) R35GM152171Wellcome TrustWellcome Trust (Wellcome) 086045/Z/08/Z
6 · The paper itself

Abstract

DNA replication typically has defined start sites, or replication origins, which are designated by their recognition by specific initiator proteins. In addition to initiators, general chromatin or nucleoid-associated proteins have been shown to play roles in modulating origin efficiency in eukaryotes and bacteria. The role of chromatin proteins in origin function in the archaeal domain of life is poorly understood. Here, we describe a dissection of sequences elements required for in vivo function of an archaeal DNA replication origin. Our data reveal a hitherto uncharacterized sequence element, the ucm, is required for origin activity. We identify a protein, UBP, that interacts with the ucm and additionally with hundreds of other sites on the genome. We solve the crystal structure of UBP alone and in complex with ucm DNA, and further show that UBP interacts with the MCM replicative helicase. Taken together, our data provide evidence that UBP functions as a general nucleoid-associated protein that plays a key role in facilitating the egress of the MCM replicative helicase from DNA replication origins.

Indexed as

Archaeal ProteinsDNA, ArchaealDNA-Binding ProteinsDNA ReplicationReplication OriginCrystallography, X-RayModels, MolecularProtein BindingArchaeal ProteinsDNA, ArchaealDNA-Binding Proteins

Identifiers

PMID40473630
PMCPMC12141716

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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.