Genetic Approaches to Study the Interplay Between Transcription and Nucleoid-Associated Proteins in Escherichia coli.

Aathmaja Anandhi Rangarajan, Cihan Yilmaz, Karin Schnetz

Abstract read

In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2024. 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

3 authors.

Aathmaja Anandhi RangarajanInstitute for Genetics, University of Cologne, Cologne, Germany.ORCID 0000-0003-3471-0257

Cihan YilmazInstitute for Genetics, University of Cologne, Cologne, Germany.

Karin SchnetzInstitute for Genetics, University of Cologne, Cologne, Germany. schnetz@uni-koeln.de.ORCID 0000-0003-4693-6202

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Bacterial nucleoid-associated proteins are important factors in regulation of transcription, in nucleoid structuring, and in homeostasis of DNA supercoiling. Vice versa, transcription influences DNA supercoiling and can affect DNA binding of nucleoid-associated proteins (NAPs) such as H-NS in Escherichia coli. Here we describe genetic tools to study the interplay between transcription and nucleoid-associated proteins in E. coli. These methods include construction of genomic and plasmidic transcriptional and translational lacZ reporter gene fusions to study regulation of promoters; insertion of promoter cassettes to drive transcription into a locus of interest in the genome, for example, an H-NS-bound locus; and construction of isogenic hns and stpA mutants and precautions in doing so.

Indexed as

DNA-Binding ProteinsEscherichia coliEscherichia coli ProteinsTranscription, GeneticDNA, BacterialGene Expression Regulation, BacterialGenes, ReporterPlasmidsPromoter Regions, GeneticDNA, BacterialDNA-Binding ProteinsEscherichia coli Proteinshns protein, E coliAttachment siteChromosomal integrationNucleoid-associated proteinsRecombineeringTranscription regulationTransduction

Identifiers

PMID39028509

DOI10.1074/jbc.M702753200

What OpenQuestion holds

Textmetadata

Read underepoch 390

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.