Evidence map›Paper›PMID 40667222›Full record

ArticlebioRxiv : the preprint server for biology2025

Computation-guided redesign of promoter specificity of a bacterial RNA polymerase.

Xiangyang Liu, Anthony T Meger, Thomas Gillis, Jonah O'Mara Schwartz, Balendra Sah, Robert Landick, Srivatsan Raman

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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

7 authors.

Xiangyang LiuBiophysics Graduate Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.
Anthony T MegerDepartment of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.
Thomas GillisDepartment of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.
Jonah O'Mara SchwartzDepartment of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.
Balendra SahGreat Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.
Robert LandickDepartment of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.
Srivatsan RamanDepartment of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.

Funding

Biotechnology Training ProgramT32GM135066 · NIGMS · UNIVERSITY OF WISCONSIN-MADISON · PI SCOTT M. COYLE, BRIAN G FOX · 2020 to 2026
$7.0M
Understanding molecular rules governing protein allostery by deep mutational scanningDP2GM132682 · NIGMS · UNIVERSITY OF WISCONSIN-MADISON · PI RAMAN, SRIVATSAN · 2018 to 2018
$2.1M
NIGMS NIH HHS DP2 GM132682NIGMS NIH HHS T32 GM135066
6 · The paper itself

Abstract

The ability to regulate genetic circuits and metabolic pathways is central to cellular control. The existing toolkit is predominantly comprised of local transcription regulators that are unsuitable for exerting control at a global genome-wide scale. Bacterial sigma factors are ideal global regulators as together they direct the RNA polymerase to thousands of transcription sites. Here, we redesigned the promoter specificity of the

Indexed as

biological orthogonalizationComputational designhigh-throughput screeningProtein-DNA interactionsspecificity

Identifiers

PMID40667222
PMCPMC12262734

What OpenQuestion holds

Textmetadata
LicenceCC BY-ND
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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.